Princeton Instruments Activity Tracker, MICROMAX SYSTEM User Manual

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4411-0039-CE

Version 6.B

January 24, 2005

*4411-0039-CE*

Printed in the United States of America.

IPLab is a trademark of Scanalytics, Inc.

Macintosh is a registered trademark of Apple Computer, Inc.

Microsoft, Windows, and Windows NT are registered trademarks of Microsoft Corporation.

Pentium is a registered trademark of Intel Corporation.

PVCAM is a registered trademark of Photometrics, Ltd.

Radio Shack is a registered trademark of TRS Quality, Inc.

TAXI is a registered trademark of AMD Corporation

The information in this publication is believed to be accurate as of the publication release date. However, Princeton Instruments does not assume any responsibility for any consequences including any damages resulting from the use thereof. The information contained herein is subject to change without notice. Revision of this publication may be issued to incorporate such change.

Chapter 1 Introduction.........................................................................................9

Introduction......................................................................................................................... 9

MicroMAX System Components ....................................................................................... 9

About this Manual ............................................................................................................ 12

Environmental Conditions................................................................................................ 13

Grounding and Safety....................................................................................................... 13

Precautions........................................................................................................................ 14

Repairs .............................................................................................................................. 14

Cleaning............................................................................................................................14

Princeton Instruments Customer Service.......................................................................... 15

Chapter 2 Installation Overview........................................................................17

Chapter 3 System Setup ....................................................................................19

Unpacking the System ...................................................................................................... 19

Checking the Equipment and Parts Inventory ..................................................................19

System Requirements .......................................................................................................20

Verifying Controller Voltage Setting............................................................................... 21

Installing the Application Software.................................................................................. 22

Setting up a PCI Interface................................................................................................. 22

Setting up a USB 2.0 Interface ......................................................................................... 24

Mounting the Camera ....................................................................................................... 27

Selecting the Shutter Setting............................................................................................. 32

Connecting the Interface (Controller-Computer) Cable................................................... 33

Connecting the Detector-Controller Cable.......................................................................34

Chapter 4 Operation...........................................................................................35

Introduction....................................................................................................................... 35

EMF and Xenon or Hg Arc Lamps................................................................................... 35

Vacuum............................................................................................................................. 35

Cooling ............................................................................................................................. 35

Baseline Signal .................................................................................................................36

Analog Gain Control......................................................................................................... 37

Imaging Field of View...................................................................................................... 38

RS-170 or CCIR Video..................................................................................................... 38

USB 2.0 and System On/Off Sequences........................................................................... 40

First Light (Imaging) ........................................................................................................ 40

First Light (Spectroscopy)................................................................................................ 45

Chapter 5 Timing Modes....................................................................................51

Fast and Safe Speed Modes .............................................................................................. 51

Standard Timing Modes ................................................................................................... 52

Frame Transfer Operation ................................................................................................ 57

Interline Operation............................................................................................................ 59

iii

iv MicroMAX System User Manual Version 6.B

Chapter 6 Exposure and Readout.....................................................................63

Exposure ........................................................................................................................... 63

Array Readout...................................................................................................................67

Digitization ....................................................................................................................... 76

Chapter 7 MicroMAX DIF Camera (Double Image Feature) ............................77

Introduction....................................................................................................................... 77

Timing Modes................................................................................................................... 78

Tips and Tricks .................................................................................................................84

Chapter 8 TTL Control........................................................................................87

Introduction....................................................................................................................... 87

TTL In............................................................................................................................... 87

Buffered vs. Latched Inputs.............................................................................................. 88

TTL Out ............................................................................................................................ 88

TTL Diagnostics Screen ................................................................................................... 89

Hardware Interface ........................................................................................................... 89

Chapter 9 System Component Descriptions ...................................................91

MicroMAX Camera.......................................................................................................... 91

ST-133 Controller ............................................................................................................. 94

Cables ............................................................................................................................... 99

Interface Card ................................................................................................................... 99

Application Software........................................................................................................ 99

User Manuals.................................................................................................................. 100

Chapter 10 Troubleshooting............................................................................101

Introduction..................................................................................................................... 101

Baseline Signal Suddenly Changes ................................................................................102

Changing the ST-133's Line Voltage and Fuses............................................................. 102

Controller Is Not Responding......................................................................................... 103

Cooling Troubleshooting................................................................................................ 103

Data Loss or Serial Violation .........................................................................................104

Data Overrun message.................................................................................................... 104

Demo is only Choice on Hardware Wizard:Interface dialog.......................................... 105

Demo, High Speed PCI, and PCI(Timer) are Choices on Hardware

Wizard:Interface dialog............................................................................................ 106

Detector Stops Working .................................................................................................108

Detector Temperature, Acquire, and Focus are Grayed Out .......................................... 108

Error Creating Controller message................................................................................. 109

Error occurs at Computer Powerup ................................................................................ 110

No CCD Named in the Hardware Wizard:CCD dialog.................................................. 112

Removing/Installing a Plug-In Module........................................................................... 113

Shutter Malfunctions ......................................................................................................114

Appendix A Specifications ..............................................................................115

CCD Arrays .................................................................................................................... 115

Temperature Control....................................................................................................... 116

Cooling ........................................................................................................................... 116

Mounting......................................................................................................................... 116

Shutters ........................................................................................................................... 117

Table of Contents v

Inputs ..............................................................................................................................117

Outputs............................................................................................................................ 117

Programmable Interface.................................................................................................. 118

A/D Converter ................................................................................................................ 118

Computer Requirements ................................................................................................. 118

Miscellaneous ................................................................................................................. 118

Appendix B Outline Drawings.........................................................................119

Detectors......................................................................................................................... 119

ST-133B Controller ........................................................................................................ 125

ST-133A Controller........................................................................................................ 125

Appendix C Kinetics Mode ..............................................................................127

Introduction..................................................................................................................... 127

Kinetic Timing Modes.................................................................................................... 128

Appendix D Virtual Chip Mode........................................................................131

Introduction..................................................................................................................... 131

Virtual Chip Setup.......................................................................................................... 132

Experimental Timing...................................................................................................... 136

Virtual Chip dialog box .................................................................................................. 136

Tips ................................................................................................................................. 137

Appendix E Repumping the Vacuum..............................................................139

Introduction..................................................................................................................... 139

Requirements .................................................................................................................. 139

Vacuum Pumpdown Procedure ......................................................................................140

Appendix F Spectrometer Adapters ...............................................................143

Acton (NTE with or without shutter) ............................................................................. 144

Chromex 250 IS (NTE with or without shutter)............................................................. 145

ISA HR 320 (NTE with or without shutter) ................................................................... 146

ISA HR 640 (NTE with or without shutter) ................................................................... 147

JY TRIAX family (NTE without shutter)....................................................................... 148

SPEX 270M (NTE with or without shutter)................................................................... 149

SPEX 500M (NTE with or without shutter)................................................................... 150

SPEX TripleMate (NTE with or without shutter) ..........................................................151

Appendix G USB 2.0 Limitations.....................................................................153

Declarations of Conformity .............................................................................155

Warranty & Service...........................................................................................159

Limited Warranty............................................................................................................ 159

Contact Information........................................................................................................ 162

Index ..................................................................................................................163

vi MicroMAX System User Manual Version 6.B

Figures

Figure 1. MicroMAX Cameras and Controller ................................................................. 9

Figure 2. Standard System Diagram................................................................................ 18

Figure 3. Controller Power Input Module ....................................................................... 21

Figure 4. WinView Installation: Interface Card Driver Selection................................... 22

Figure 5. RSConfig dialog box........................................................................................ 26

Figure 6. Hardware Wizard: PVCAM dialog box........................................................... 27

Figure 7. Bottom Clamps................................................................................................. 31

Figure 8. Bottom Clamp secured to Relay Lens.............................................................. 31

Figure 9. Shutter Setting for 25mm Internal Shutter ....................................................... 33

Figure 10. WinSpec/32 Detector Temperature dialog box.............................................. 36

Figure 11. Imaging Field of View ................................................................................... 38

Figure 12. Monitor Display of CCD Image Center Area ................................................ 39

Figure 13. Standard System Connection Diagram...........................................................41

Figure 14. F-mount Focus Adjustment............................................................................ 45

Figure 15. Chart of Safe and Fast Mode Operation......................................................... 53

Figure 16. Free Run Timing Chart (part of the chart in Figure 15)................................. 54

Figure 17. Free Run Timing Diagram ............................................................................. 54

Figure 18. Showing Shutter "Preopen" & "Normal" Modes in External Sync Operation55

Figure 19. External Sync Timing Diagram (- edge trigger)............................................. 55

Figure 20. Continuous Cleans Flowchart ........................................................................ 56

Figure 21. Continuous Cleans Timing Diagram.............................................................. 57

Figure 22. Frame Transfer where t Figure 23. Frame Transfer where t

w1 w1

+ t

+ tc < tR................................................... 58

exp

+ t

+ tc > tR................................................... 59

exp

Figure 24. Frame Transfer where Pulse arrives after Readout........................................ 59

Figure 25. Overlapped Mode where t Figure 26. Overlapped Mode where t

+ t

+ tc < tR............................................... 61

exp

+ tc > tR.................................................... 61

+ t

exp

Figure 27. Overlapped Mode where Pulse arrives after Readout.................................... 61

Figure 28. Block Diagram of Light Path in System......................................................... 63

Figure 29. CCD Exposure with Shutter Compensation................................................... 64

Figure 30. Full Frame at Full Resolution ........................................................................67

Figure 31. Frame Transfer Readout................................................................................. 69

Figure 32. Overlapped Mode Exposure and Readout...................................................... 71

Figure 33. Non-Overlapped Mode Exposure and Readout.............................................. 72

Figure 34. 2 × 2 Binning for Full Frame CCD ................................................................ 74

Figure 35. 2 × 2 Binning for Interline CCD .................................................................... 75

Figure 36. Free Run Mode Timing Diagram................................................................... 79

Figure 37. Setup using

to Trigger an Event....................................................... 79

Figure 38. Timing for Experiment Setup shown in Figure 37......................................... 79

Figure 39. Timing Diagram for Typical IEC Measurement ............................................ 81

Figure 40. Setup for IEC Experiment with Two Lasers.................................................. 81

Figure 41. Timing Diagram for IEC Experiment with Two Lasers................................. 81

Figure 42. Another Hardware Setup for an IEC Measurement ....................................... 82

Figure 43. EEC Timing Example with Exposure Time in Software Set to t Figure 44. ESABI Timing Example: Image Exposure time = t

set in software......... 84

exp

............. 83

exp

Figure 45. TTL In/Out Connector ................................................................................... 89

Figure 46. Controller Front Panel.................................................................................... 94

Figure 47. ST-133 Rear Panel ......................................................................................... 95

Table of Contents vii

Figure 48. Shutter Compensation Times ......................................................................... 98

Figure 49. Power Input Module..................................................................................... 102

Figure 50. Fuse Holder .................................................................................................. 102

Figure 51. Hardware Wizard: Interface dialog box....................................................... 105

Figure 52. RSConfig dialog box.................................................................................... 106

Figure 53. Hardware Wizard: PVCAM dialog box....................................................... 106

Figure 54. Hardware Wizard: Interface dialog box....................................................... 106

Figure 55. RSConfig dialog box: Two Camera Styles .................................................. 107

Figure 56. Hardware Wizard: PVCAM dialog box....................................................... 108

Figure 57. RSConfig dialog box: Two Camera Styles .................................................. 109

Figure 58. Error Creating Controller dialog box........................................................... 109

Figure 59. Hardware Wizard: Detector/Camera/CCD dialog box................................. 112

Figure 60. Module Installation ...................................................................................... 113

Figure 61. Rectangular Camera Head: C-Mount........................................................... 119

Figure 62. Rectangular Camera Head: F-Mount ........................................................... 120

Figure 63. Rectangular Camera Head: Spectroscopy Mount with Shutter.................... 121

Figure 64. Rectangular Camera Head: Spectroscopy Mount without Shutter .............. 122

Figure 65. 1 MHz and 100kHz/1MHz Round Head Camera: C-Mount Adapter and

Shutter..................................................................................................................... 123

Figure 67. 1 MHz Round Head Camera: F-Mount Adapter.......................................... 124

Figure 68. ST-133B Controller Dimensions.................................................................. 125

Figure 69. ST-133A Controller Dimensions .................................................................125

Figure 70. Kinetics Readout .......................................................................................... 127

Figure 71. Hardware Setup dialog box.......................................................................... 128

Figure 72. Experiment Setup dialog box....................................................................... 128

Figure 73. Free Run Timing Diagram ........................................................................... 129

Figure 74. Single Trigger Timing Diagram................................................................... 129

Figure 75. Multiple Trigger Timing Diagram ............................................................... 130

Figure 76. Virtual Chip Functional Diagram................................................................. 131

Figure 77. System Diagram ........................................................................................... 133

Figure 78. Virtual Chip dialog box................................................................................ 136

Figure 79. Vacuum Connector Required for Pumping.................................................. 140

Figure 80. Removing the Back Panel ............................................................................ 140

Figure 81. Attaching the Vacuum Connector................................................................ 141

Figure 82. Opening the Camera to the Vacuum System................................................ 141

Tables

Table 1. PCI Driver Files and Locations ......................................................................... 23

Table 2. USB Driver Files and Locations........................................................................ 26

Table 3. Bottom Clamps for Different Microscopes....................................................... 30

Table 4. ST-133 Shutter Setting Selection ...................................................................... 32

Table 5. Camera Timing Modes ...................................................................................... 51

Table 6. Approximate Readout Time for the Full-Frame CCD Array ............................ 68

Table 7. Approximate Readout Time for the Frame-Transfer CCD Array..................... 69

Table 8. Approximate Readout Time for the Interline CCD Arrays............................... 73

Table 9. Readout Rates for PI 1300 × 1030 Array at 1 MHz.......................................... 73

Table 10. Well Capacity for some CCD Arrays.............................................................. 76

Table 11. Bit Values with Decimal Equivalents: 1 = High 0 = Low.............................. 88

viii MicroMAX System User Manual Version 6.B

Table 12. TTL In/Out Connector Pinout ......................................................................... 89

Table 13. ST-133 Shutter Drive Selection ...................................................................... 97

Table 14. I/O Address & Interrupt Assignments before Installing Serial Card............. 111

Table 15. I/O Address & Interrupt Assignments after Installing Serial Card ............... 111

Table 16. MicroMAX Model and CCD Types Cross Reference .................................. 115

Table 17. Shutter Compensation Times ........................................................................ 117

Table 18. MicroMAX:512BFT: Virtual Chip Size, Exposure Time, and Frames per

Second........................................................................................................... 132

Table 19. Features Not Supported under USB 2.0 ........................................................ 153

Chapter 1 Introduction

Introduction

The Princeton Instruments MicroMAX system is a high-speed, low-noise CCD camera system designed for demanding imaging applications and is an optimal system for use in fluorescence microscopy applications such as high-resolution immunofluorescence, FISH or GFP imaging. The MicroMAX system incorporates a compact camera head, cooled CCD, advanced exposure-control timing, video output, and sophisticated readout capabilities.

Among the advantages of the MicroMAX concept are the range of CCD arrays available and the built-in video output mode. The system can be configured with a variety of interline CCDs to provide true 12-bit images at a readout rate of up to 5 million pixels per second or with a variety of front or back-illuminated CCDs to provide true 16-bit images. The built-in video output mode simplifies setup and focusing on the microscope. The combination of the MicroMAX system with one of a variety of specialty software packages results in a powerful digital imaging system that can meet most experimental needs.

Note: "WinView/32" and "WinView" are used throughout this manual when referring to the application software. Unless otherwise indicated, the information associated with these terms also applies to Princeton Instruments' WinSpec/32 spectroscopy software.

MicroMAX System Components

Overview

The MicroMAX imaging system consists of a camera (either a round head or a rectangular head depending on application), controller, digital interface card, a computer, cables, manuals, and application software. Together, these components allow you to acquire quantitative digital data under very low light imaging conditions. Each component is optimized for its specific function. In operation, data acquired by the camera is routed to the controller and from there to the computer for processing and display. A composite video output allows immediate viewing of the acquired images on a separate monitor. The application software (for example, Princeton Instruments WinView/32) allows the computer to control both the system configuration and data acquisition.

Figure 1. MicroMAX Cameras and

Controller

10 MicroMAX System User Manual Version 6.B

Camera

Introduction: The function of the camera is to collect very low intensity light and

convert the energy into a quantitative, electronic signal (photo-electrons) over a two dimensional space. To do this, light from the subject is focused onto a CCD array, which accumulates photoelectrons for the exposure time. At the end of the exposure time, the image thus formed is read out. The accumulated charge on each cell of the array is transferred out of the CCD array, amplified, and sent to the controller as an analog signal, where it is digitized prior to transfer to the computer.

The camera is highly integrated, containing the shutter (if applicable) and thermoelectric cooler with optional forced-air supplemental cooling in a single, shielded housing. Surface mount electronic technology is used wherever possible, giving a compact package with uncompromising performance.

Depending on your application, the camera included in your MicroMAX system will be either a compact round camera head or a high performance, cooled, rectangular camera head. The round head features interline CCDs; its small size ensures that the camera can be mounted on virtually any microscope port, including those found on inverted microscopes. The rectangular head features back-illuminated CCDs with frame transfer readout.

At the heart of the camera is the CCD array centered on the optic axis. Available formats include the:

•

EEV CCD57-10, 512×512, 13×13µm pixels for the MicroMAX:512BFT

•

EEV CCD47-10, 1024×1024, 13×13µm pixels for the MicroMAX:1024B

•

Sony ICX075, 782×582, 8.3× 8.3µm pixels for the MicroMAX:782Yand the

MicroMAX:782YHS systems

•

Sony ICX061,1300×1030, 6.7× 6.7µm pixels for the MicroMAX:1300Y, the

MicroMAX:1300YHS, and MicroMAX:1300YHS-DIF systems

A special clocking mode to minimize background signal is supported. See the Princeton Instruments brochures and data sheets for detailed specifications.

Cooling System: MicroMAX cameras have a multi-stage Peltier type cooler that is thermally coupled to the CCD surface. Heat is sequentially transferred through the Peltier stages and from there to the outer shell of the camera via a heat transfer block. This cooling system allows the camera to maintain CCD temperature of typically -15°C for round cameras head and -45°C for rectangular camera heads. Cameras equipped with a fan assembly can reach lower CCD temperatures for reduced thermal noise and extended exposure times.

Low Noise Readout: In order to achieve a low-noise readout of the CCD, several design features have been implemented. These include cooling the preamplifier on the CCD, isolating circuits to prevent electronic crosstalk and minimizing the path lengths of critical electronic circuits. The net result of these design features is the lowest available readout noise at the highest speed possible for these CCDs.

Chapter 1 Introduction 11

Controller

Data Conversion: The controller accepts the analog data and converts it to digital data

using specially designed, low-noise electronics supporting scientific grade 12- or 16-bit Analog to Digital (A/D) converters.

The standard MicroMAX Controller enables both high-speed and high-precision readout capabilities. It can collect 16-bit images at a readout rate of up to 1 million pixels per second (1 MHz) in the high-speed mode or at 100 thousand pixels per second (100 kHz) in the optional precision mode (16-bit). Switching between the two modes is under software control for total experiment automation.

Modular Design: In addition to containing the power supplies, the controller contains the analog and digital electronics, scan control and exposure timing hardware, and system I/O connectors, all mounted on user-accessible plug-in modules. The design is highly modularized for flexibility and convenient servicing.

Flexible Readout: There is provision for extremely flexible readout of the CCD. Readout modes supported include full resolution, simultaneous multiple subimages, and nonuniform binning. Single or multiple software-defined regions of interest can also be tested without having to digitize all the pixels of the array

High Speed Data Transfer: Data is transferred directly to the host computer memory via a high-speed serial link. A proprietary Interface card places the data from the controller directly into the host computer RAM using Direct Memory Access (DMA). The DMA transfer process ensures that the data arrives at sufficiently high speed to prevent data loss from the controller. Since the data transfer rate is much higher than the output rate from the A/D, the latter becomes the data acquisition rate-limiting factor. Once the digital data is in RAM, the image acquisition program can transfer the image into its own working RAM for viewing and further processing.

Note: A frame buffer with standard composite video, either RS-170 (EIA) or CCIR, whichever was ordered, is also provided.

Applications

With its small size, fully integrated design, cooled CCD and temperature control, advanced exposure control timing, and sophisticated readout capabilities, the MicroMAX system is well suited to both general macro imaging and microscopy applications.

12 MicroMAX System User Manual Version 6.B

About this Manual

Manual Organization

This manual provides the user with all the information needed to install a MicroMAX camera and place it in operation. Topics covered include a detailed description of the camera, installation, cleaning, specifications and more.

Note: The general identifier "ST-133" is used for both the ST-133A Controller and the ST-133B Controller. Where there is a difference, the specific identifier is used.

Chapter 1, Introduction

details the structure of this manual; and documents environmental, storage, and cleaning requirements.

Chapter 2, Installation Overview

relevant manuals and/or manual pages. It also contains system layout diagrams.

Chapter 3, System Setup

system components.

Chapter 4, Operation

vacuum degradation, and sensitivity to damage from EMF spikes generated by Xenon or Hg arc lamps. Includes step-by-step directions for verifying system operation.

Chapter 5, Timing Modes

related topics, including Fast and Safe speed modes, Free Run, External Sync, Continuous, Frame Transfer, and Interline operation.

Chapter 6, Exposure and Readout

with many peripheral topics, including: shuttered and unshuttered exposure; saturation; dark charge; full frame, interline, and frame-transfer readout; and binning.

Chapter 7, MicroMAX DIF Camera (Double Image Feature)

(Dual Image Feature) camera and its operation.

briefly describes the MicroMAX family of cameras;

cross-references system setup actions with

provides detailed directions for interconnecting the

discusses number of topics, including temperature control,

discusses the basic Controller timing modes and

discusses Exposure and Readout, together

describes DIF

Chapter 8, TTL Control

connector on the rear of the controller.

Chapter 9, System Component Descriptions

system component.

Chapter 10, Troubleshooting

have problems with your system.

Appendix A, Specifications

Appendix B, Outline Drawings

cameras and the ST-133A and ST-133B Controllers.

Appendix C, Kinetics Mode

Kinetics option, which allows frame transfer CCDs to take time-resolved images/spectra.

provides information about how to use the TTL

provides descriptions of each

provides courses of action to take if you should

includes controller and camera specifications.

includes outline drawings of the MicroMAX

describes how to set up and acquire data with the

Chapter 1 Introduction 13

Appendix D, Virtual Chip Mode

Chip option, a special fast-acquisition technique.

Appendix E, Repumping the Vacuum

100kHz/1MHz round head camera's vacuum if that vacuum has deteriorated over time.

Appendix F, Spectrometer Adapters

spectrometer adapters available for MicroMAX rectangular head (NTE) cameras.

Appendix G

associated with operating under the USB 2.0 interface.

USB 2.0 Limitations

Declarations of Conformity

(includes 100 kHz/1MHz) MicroMAX systems.

Warranty and Service

information.

provides warranty and customer support contact

describes how to set up and use the Virtual

explains how to restore the 1 MHz or

provides mounting instructions for the

covers the currently known limitations

contains the Declaration of Conformity for 1 MHz

Safety Related Symbols Used in This Manual

Caution! The use of this symbol on equipment indicates that one or more

nearby items should not be operated without first consulting the manual. The same symbol appears in the manual adjacent to the text that discusses the hardware item(s) in question.

Caution! Risk of electric shock! The use of this symbol on equipment indicates that one or more nearby items pose an electric shock hazard and should be regarded as potentially dangerous. This same symbol appears in the manual adjacent to the text that discusses the hardware item(s) in question.

Environmental Conditions

• Storage temperature: < 55°C

• Operating environment: 0°C to 30°C

• Relative humidity: ≤50%, non-condensing.

Grounding and Safety

The apparatus described in this manual is of the Class I category as defined in IEC Publication 348 (Safety Requirements for Electronic Measuring Apparatus). It is designed for indoor operation only. Before turning on the controller, the ground prong of the power cord plug must be properly connected to the ground connector of the wall outlet. The wall outlet must have a third prong, or must be properly connected to an adapter that complies with these safety requirements.

WARNING

If the equipment is damaged, the protective grounding could be disconnected. Do not use damaged equipment until its safety has been verified by authorized personnel. Disconnecting the protective earth terminal, inside or outside the apparatus, or any tampering with its operation is also prohibited.

14 MicroMAX System User Manual Version 6.B

Inspect the supplied power cord. If it is not compatible with the power socket, replace the cord with one that has suitable connectors on both ends.

WARNING

Replacement power cords or power plugs must have the same polarity as that of the original ones to avoid hazard due to electrical shock.

Precautions

To prevent permanently damaging the system, please observe the following precautions:

•

Always switch off and unplug the ST-133 Controller before changing your system

•

Never remove the camera’s front window, as it is necessary to maintain vacuum (or

•

The CCD array is very sensitive to static electricity. Touching the CCD can destroy

•

Never operate the camera cooled without proper evacuation or backfill. This could

•

Never connect or disconnect any cable while the MicroMAX system is powered on.

•

Never prevent the free flow of air through the equipment by blocking the air vents.

configuration in any way.

to maintain a dry nitrogen environment).

it. Operations requiring contact with the device can only be performed at the factory.

damage the CCD!

Reconnecting a charged cable may damage the CCD.

Repairs

Cleaning

WARNING!

Repairs must be done by Princeton Instruments. If your system hardware needs repair, contact Princeton Instruments Customer Service. Please save the original packing material so you can safely ship the system to another location or return it for repairs.

Turn off all power to the equipment and secure all covers before cleaning the units. Otherwise, damage to the equipment or personal injury could occur.

Camera and Controller

Although there is no periodic maintenance that must be performed on the camera or the ST-133 Controller, you may clean these components from time to time by wiping them down with a clean damp cloth. This operation should only be done on the external surfaces and with all covers secured. In dampening the cloth, use clean water only. No soap, solvents or abrasives should be used. Not only are they not required, but they could damage the finish of the surfaces on which they are used.

Optical Surfaces

Optical surfaces may need to be cleaned due to the accumulation of atmospheric dust. We advise that the drag-wipe technique be used. This involves dragging a clean cellulose

Chapter 1 Introduction 15

lens tissue dampened with clean anhydrous methanol over the optical surface to be cleaned. Do not allow any other material to touch the optical surfaces.

Princeton Instruments Customer Service

Refer to the contact information located on page 162 of this manual.

16 MicroMAX System User Manual Version 6.B

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Chapter 2 Installation Overview

The list and diagrams below briefly describe the sequence of actions required to hookup your system and prepare to gather data. Refer to the indicated references for more detailed information. This list assumes that the application software is Princeton Instruments WinView/32.

Action Reference

1. If the system components have not already been unpacked, unpack them and inspect their carton(s) and the system components for intransit damage. Store the packing materials.

2. Verify that all system components have been received. Chapter 3 System Setup,

3. If the components show no signs of damage, verify that the appropriate voltage settings have been selected for the Controller.

4. If WinView/32 software is not already installed in the host computer, install it. In addition to installing the WinView/32 software, this operation will load all of the interface card drivers.

5. If the appropriate interface card is not already installed in the host computer, shut down the computer and install the interface card.

6. Depending on the application, attach a lens to the camera, mount the camera to a microscope, or mount the camera to a spectrometer.

7. With the Controller and computer power turned OFF, connect the interface cable (TAXI or USB) to the Controller and the interface card in the host computer. Then tighten down the locking hardware.

8. With the Controller power turned OFF, make the camera-tocontroller connections to the back of the Controller. Secure the latch(es) to lock the cable connection(s).

Chapter 3 System Setup, page 19

page 19

Chapter 3 System Setup, page 21

WinView/32 manual

Chapter 3 System Setup, page 22 or page 24

Chapter 3 System Setup, page 28, 28, or 32

Chapter 3 System Setup, page 33

Chapter 3 System Setup, page 34

9. With the Controller power turned OFF, make the camera-tocontroller connections to the back of the Camera. Secure the latch(es) to lock the cable connection(s).

10. With the Controller power turned OFF, connect the Controller power cable to the rear of the controller and to the power source.

11. If using a microscope Xenon or an Hg arc lamp, turn it on before turning on the controller and host computer.

12. Turn the Controller ON.

Chapter 3 System Setup, page 34

Chapter 4 Operation, page 35

18 MicroMAX System User Manual Version 6.B

Action Reference

13. Turn on the computer and begin running WinView/32. WinView/32 manual

14. Enter the hardware setup information or load the defaults from the controller.

Chapter 4 Operation, page 42 or page 46

15. Set the target array temperature. Chapter 4 Operation,

page 36, 42, or 46

16. When the system reaches temperature lock, begin acquiring data in focus mode.

Chapter 4 Operation, page 43 or page 48

17. Adjust the focus for the image. Chapter 4 Operation,

page 43 or page 48

Detector-Controller

Camera

Microscope

Detector

Controller

Interface cable

(TAXI or USB 2.0)

110/220

Serial Com or USB 2.0

110/220

Computer

EXPERIMENT

Figure 2. Standard System Diagram

Chapter 3 System Setup

Unpacking the System

During the unpacking, check the system components for possible signs of shipping damage. If there are any, notify Princeton Instruments and file a claim with the carrier. If damage is not apparent but camera or controller specifications cannot be achieved, internal damage may have occurred in shipment. Please save the original packing materials so you can safely ship the camera system to another location or return it to Princeton Instruments for repairs if necessary.

Checking the Equipment and Parts Inventory

Confirm that you have all of the equipment and parts required to set up the system. A complete MicroMAX system consists of a camera, a controller, a computer and other components as follows.

• Camera to Controller cable: DB25 to DB25, 10 ft (6050-0321). Two versions of this cable are available, one having an external shield and the other not. The shielded version offers superior noise performance and is required by regulation in some countries.

• Computer Interface Dependent Components:

• Controller-Computer Interface cable:

• TAXI cable: 25 ft DB9 to DB9 cable (6050-0148-CE) is standard. Lengths

up to 165 ft (50 m) are available. Optional fiber-optic transducers can be used to extend this distance to as much as 1000 m.or

• USB cable: Five (5) meter cable (6050-0494) is standard.

• Interface Card:

• TAXI: High Speed PCI Interface board or

• USB 2.0: Native on motherboard or user-provided USB 2.0 Interface Card

(Orange Micro 70USB90011 USB2.0 PCI is recommended for desktop computers and the SIIG, Inc. USB 2.0 PC Card, Model US2246 is recommended for laptop computers).

• Vacuum Pumpdown connector (2550-0181): This item is required if it becomes necessary to refresh the vacuum for round camera heads. Contact the factory

Technical Support Dept. for information on refreshing the vacuum. See page 162 for contact information.

• WinView/32 CD-ROM

• User Manual

20 MicroMAX System User Manual Version 6.B

System Requirements

Power

Detector: The MicroMAX detector receives its power from the controller, which in

turn plugs into a source of AC power.

ST-133: The ST-133 Controller can operate from any one of four different nominal line

voltages: 100, 120, 220, or 240 V AC. Refer to the Fuse/Voltage label on the back of the ST-133 for fuse, voltage, and power consumption information.

Caution

The plug on the line cord supplied with the system should be compatible with the linevoltage outlets in common use in the region to which the system is shipped. If the line cord plug is incompatible, a compatible plug should be installed, taking care to maintain the proper polarity to protect the equipment and assure user safety.

Host Computer

Note: Computers and operating systems all undergo frequent revision. The following

information is only intended to give an approximate indication of the computer requirements. Please contact the factory to determine your specific needs.

Requirements for the host computer depend on the type of interface, TAXI or USB 2.0, that will be used for communication between the ST-133 and the host computer. Those requirements are a listed below according to protocol.

TAXI Protocol:

• AT-compatible computer with 200 MHz Pentium

• Windows

2000, or Windows

95, Windows® 98SE, Windows® ME, Windows NT®, Windows®

XP operating system.

II (or better).

• High speed PCI serial card (or an unused PCI card slot). Computers purchased

from Princeton Instruments are shipped with the PCI card installed if High speed PCI was ordered.

• Minimum of 32 Mbytes of RAM for CCDs up to 1.4 million pixels. Collecting

multiple spectra at full frame or high speed may require 128 Mbytes or more of RAM.

• CD-ROM drive.

• Hard disk with a minimum of 80 Mbytes available. A complete installation of

the program files takes about 17 Mbytes and the remainder is required for data storage, depending on the number and size of images or spectra collected. Disk level compression programs are not recommended.

• Super VGA monitor and graphics card supporting at least 256 colors with at least

1 Mbyte of memory. Memory requirement is dependent on desired display resolution.

• IEEE-488 GPIB port (required by DG535 Timing Generator, if present). May

also be required by Spectrograph.

• Two-button Microsoft compatible serial mouse or Logitech three-button

serial/bus mouse.

Chapter 3 System Setup 21

USB 2.0 Protocol:

• AT-compatible computer with Pentium 3 or better processor and runs at 1 GHz or

better.

• Windows 2000 (with Service Pack 4), Windows XP (with Service Pack 1) or

later operating system.

• Native USB 2.0 support on the mother board or USB Interface Card (Orange

Micro 70USB90011 USB2.0 PCI is recommended for desktop; SIIG, Inc. USB

2.0 PC Card, Model US2246 for laptop)

• Minimum of 256 Mb of RAM.

• CD-ROM drive.

• Hard disk with a minimum of 80 Mbytes available. A complete installation of

• Super VGA monitor and graphics card supporting at least 256 colors with at

least 1 Mbyte of memory. Memory requirement is dependent on desired display resolution.

• IEEE-488 GPIB port (required by DG535 Timing Generator, if present). May

also be required by Spectrograph.

• Two-button Microsoft compatible serial mouse or Logitech three-button

serial/bus mouse.

Verifying Controller Voltage Setting

The Power Module on the rear of the Controller contains the voltage selector drum, fuses and the powercord connector. The appropriate voltage setting is set at the factory and can be seen on the back of the power module.

Each setting actually defines a range and the setting that is closest to the actual line voltage should have been selected. The fuse and

power requirements are printed on the panel above the power module. be shipped are installed at the factory.

Note: On ST-133s, the voltage ranges and fuse ratings may be printed above (see Figure 3) or below the power module.

To Check the Controller's Voltage Setting:

1. Look at the lower righthand corner on the rear of the Controller. The current voltage

The correct fuses for the country where the ST-133 is to

setting (100, 120, 220, or 240 VAC) is displayed on the Power Module.

Figure 3. Controller

Power Input Module

2. If the setting is correct, continue with the installation. If it is not correct, follow the instructions on page 102 for changing the voltage setting and fuses.

22 MicroMAX System User Manual Version 6.B

Installing the Application Software

Installation is performed via the WinView/32 installation process. If you are installing WinView or WinSpec for the first time, you should run the installation before installing the Princeton Instruments (RSPI) PCI or USB2.0 card in the host computer. On the

Components

dialog box (see Figure 4), click on the button to install the interface card drivers (the Princeton Instruments (RSPI) PCI and the USB drivers) and the most commonly installed program files. Select the button if you would like to choose among the available program files.

Note: WinView/32 (versions 2.6.0 and higher) do not support the ISA interface.

Select

AUTO PCI

Custom

Figure 4. WinView Installation: Interface Card

Driver Selection

Setting up a PCI Interface

A Princeton Instruments (RSPI) high speed PCI card must be installed in the host computer if the communication between computer and controller uses the TAXI

Caution

protocol (i.e., the

SERIAL COM connector as shown in the figure at right). With TAXI protocol, the

standard cable provided with an ST-133 is 7.6 meters (25 feet) (cable lengths up to 50 meters are available) and the digitization rate may be as high as 5 MHz.

A computer purchased from Princeton Instruments will be shipped with the PCI card already installed. Otherwise, a PCI card will be shipped with the system and you will have to install it in the host computer at your location.

Note: The PCI card can be installed and operated in any Macintosh having a PCI bus, allowing the ST-133 to be controlled from the Macintosh via IPLab™ software and the PI Extension.

If you are using WinView/32 software, either the selected Interface type. This selection is accessed on the Hardware Setup|Interface tab page. High Speed PCI allows data transfer to be interrupt-driven and gives the highest performance in some situations. PCI(Timer) allows data transfer to be controlled by a polling timer. This selection is recommended when there are multiple devices sharing the same interrupt.

To Replace a USB 2.0 Interface Control Module with a TAXI Module: If you ordered a TAXI Interface Control module separately and are retrofitting an ST-133 that you already own, follow the module replacement instructions in "Removing/Installing a Plug-In Module" starting on page 113.

Interface Control Module installed in the ST-133 has a 9-pin

TTL IN/OUT

AUX

SERIAL COM

High Speed PCI or PCI(Timer) can be

Chapter 3 System Setup 23

To Install a PCI Serial Buffer Card in the Host Computer:

1. Review the documentation for your computer and PCI card before continuing with this installation.

2. To avoid risk of dangerous electrical shock and damage to the computer, verify that the computer power is OFF.

3. Remove the computer cover and verify that there is an available PCI slot.

Install the PCI card in the slot.

5. Make sure that the card is firmly seated and secure it.

6. Replace and secure the computer cover and turn on the computer only. If an error occurs at bootup, either the PCI card was not installed properly or there is an address or interrupt conflict. Refer to "Error occurs at Computer Powerup", starting on page 110.

Note: The PCI card has no user-changeable jumpers or switches.

Administrator privileges are required under Windows NT

, Windows® 2000, and

Windows® XP to install software and hardware.

To Install the PCI Card Driver

The following information assumes that you have already installed the WinView/32 software.

1. After you have secured the PCI card in the computer and replaced the cover, turn the computer on.

2. At bootup, Windows will try to install the new hardware. If it cannot locate the driver, you will be prompted to enter the directory path, either by keyboard entry or by using the browse function.

If you selected AUTO PCI during the application software installation, WinView automatically put the required INF file into the Windows/INF directory and put the PCI card driver file in the "Windows"/System32/ Drivers directory. Refer to Table 1 below for the appropriate file names and locations.

Windows Version PCI INF Filename

Located in "Windows"/INF

directory*

Windows® 2000 and XP

Windows NT® N/A pi_pci.sys

Windows® 95, 98, and Windows

rspi.inf (in WINNT/INF, for example)

pii.inf pivxdpci.vxd

Located in "Windows"/System32/Drivers

rspipci.sys (in WINNT/System32/Drivers, for example)

PCI Device Driver Name

Setting up a USB 2.0 Interface

Administrator privileges are required under Windows® 2000 and Windows® XP to install software and hardware.

Your system has been configured to use the USB communication protocol if the

Interface Control Module installed in the ST-133 has a USB 2.0 connector as shown

in the figure at right). The advantages to the USB 2.0 interface are that it uses a much higher data transfer rate than many common serial data formats (such as the TAXI protocol) and it simplifies the connection to external devices. USB supports "plug and play" -- you do not need to be heavily involved in the setup process.

USB 2.0 Limitations

• Maximum cable length is 5 meters (16.4 feet)

• 1 MHz is currently the upper digitization rate limit for the ST-133 Controller.

Large data sets and/or long acquisition times may be subject to data overrun because of host computer interrupts during data acquisition.

• USB 2.0 is not supported by the Princeton Instruments PC Interface Library (EZ- DLLS).

• Some WinX (WinView and WinSpec) 2.5.X features are not fully supported with USB 2.0. Refer to Appendix G, page 153, for more information.

Note: If you are installing the USB 2.0 interface on a laptop, you will need to perform all of the operations described in this section. In addition, if you are using the recommended USB Interface Card (SIIG, Inc. USB 2.0 PC Card, Model US2246), you must replace the OrangeUSB USB 2.0 Host Controller driver installed for that card with the appropriate Microsoft driver. Instructions for making the replacement are included in "To Update the OrangeUSB USB 2.0 Driver", below.

USB 2.0

IN/OUT

AUX

TTL

To Replace a TAXI Module Interface Control Module with a USB 2.0 Module: If you ordered a USB 2.0 Interface module separately and are retrofitting an

ST-133 that you already own, follow the module replacement instructions in "Removing/Installing a Plug-In Module" starting on page 113.

To Update the OrangeUSB USB 2.0 Driver:

This procedure is highly recommended when a laptop computer will be used to communicate with the ST-133. As stated before, we recommend the SIIG, Inc. USB 2.0 PC Card, Model US2246 if USB 2.0 is not native to the laptop's motherboard. To reduce the instances of data overruns and serial violations, the OrangeUSB USB 2.0 Host Controller installed for the SIIG card, should be replaced by the appropriate Microsoft driver (Windows 2000 or Windows XP, depending on the laptop's operating system.)

Note: This procedure may also be performed for desktop computers that use the Orange Micro 70USB90011 USB2.0 PCI.

1. Download and install Microsoft Service Pack 4 (for Windows 2000) or Service Pack 1 (for Windows XP) if the service pack has not been installed.

2. From the Windows Start menu, select Settings|Control Panel.

3. Select System and then System Properties.

Chapter 3 System Setup 25

4. Select the Hardware tab and click on Device Manager button.

5. Expand Universal Serial Bus Controllers.

6. Right-mouse click on OrangeUSB USB 2.0 Host Controller and select Properties.

7. On the Driver tab, click on the Update Driver… button. You may have to wait a minute or so before you will be allowed to click on the button.

8. When the Upgrade Device Driver Wizard appears, click on Next. Select the Search for a suitable driver … radio button.

9. On the next screen select the Specify a location checkbox.

10. Browse and select the location. Click on OK.

11. In the Driver Files Search Results window, check the Install one of the other drivers check box.

12. Select the NEC PCI to USB Enhanced Host Controller B1 driver. Click on

Next and the installation will take place. When the Completing the Upgrade Device Driver Wizard window appears, click on Finish. You will then be given

the choice of restarting the computer now or later. According to the window text, the hardware associated with the driver will not work until you restart the computer.

To Install the Princeton Instruments USB2 Interface:

The following information assumes that:

• You have verified that the host computer meets the required specifications for USB 2.0 communication with the MicroMAX system (see page 20).

• A USB 2.0 board and its driver are installed in the host computer.

• The ST-133 has an installed USB 2.0 Interface Control module.

• You have already installed the WinView/32 or WinSpec/32 software

(versions 2.5.15 and higher). Versions 2.5.15 and higher automatically install the driver and INF files required to support the USB 2.0 Interface Control module.

1. Before installing the Princeton Instruments USB2 Interface, we recommend that you defragment the host computer's hard disk. This operation reduces the time the computer spends locating files. Typically, the "defrag" utility "Disk Defragmenter" can be accessed from the Windows

Start menu and can

usually accessed from the Programs/Accessories/System Tools subdirectory.

2. After defragmenting the hard disk, turn off the computer and make the USB cable connections between the host computer and the ST-133. Then, turn the ST-133 on before turning on the host computer.

3. At bootup, Windows will detect the Princeton Instruments USB2 Interface hardware (i.e., the USB 2.0 Interface Control module). You may be prompted to enter the directory path(s) for the apausbprop.dll and/or the apausb.sys file(s), either by keyboard entry or by using the browse function.

If you selected AUTO PCI during the application software installation, WinView/32 automatically put the required INF, DLL, and USB driver file in

26 MicroMAX System User Manual Version 6.B

the "Windows" directories shown below. Refer to the Table 2 below for the file locations.

Windows

Version

Windows® 2000 and XP

* The INF directory may be hidden.

USB INF

Filename

Located in

"Windows"/INF

directory*

rsusb2k.inf (in WINNT/INF, for example)

Table 2. USB Driver Files and Locations

USB Properties DLL

Located in

"Windows"/System32

Mounting the Camera

WARNING

General

The MicroMAX camera can be mounted either horizontally or vertically (nose up or nose down). The camera can rest on any secure surface. For mounting flexibility, the round head camera is equipped with four standard ¼″ x 20 UNC threaded 3/8″ deep holes spaced at 90° intervals around the body; in some situations it may prove convenient to secure the camera with a suitable mounting bracket. An optional tripod mount is available for the rectangular head camera.

In the case of cameras equipped with F-mount, do not mount the camera in the nose-up operation where the lens mount would be required to hold the camera’s weight. The F-mount is not designed to sustain the weight of the camera in this orientation and the camera could pull free. Contact the factory for special mounting options that enable

operation in this orientation.

Should the camera be mounted in the nose-up position beneath a table, take care to protect the mounting components from lateral stresses, such as might occur should someone accidentally bump the camera with a knee while working at the table. Two possible approaches to this problem would be to install a securely mounted bracket to the camera or to install a barrier between the camera and operator so as to prevent any accidental contact.

There are no special constraints on nose-down operation. Again, however, good operating practice might make it advisable to use a securing bracket to prevent accidental contact from unduly stressing the mounting components.

If the camera is going to be mounted to a microscope, the lens mounting instructions that follow will not apply. Where this is the case, users are advised to skip the following discussion and instead review "Mounting to a Microscope", beginning on page 28.

28 MicroMAX System User Manual Version 6.B

Mounting the Lens

The MicroMAX camera is supplied with the lens mount specified when the system was ordered, normally either a screw-type C-mount lens or a bayonet type F-mount lens, allowing a lens of the corresponding type to be mounted quickly and easily.

C-mount lenses simply screw clockwise into the threaded lens mount at the front of the camera. In mounting a C-mount lens, tighten it securely by hand (no tools).

Note: C-mount cameras are shipped with a dust cover lens installed (identifiable by its red rim). Although this lens is capable of providing images, its throughput is low and the image quality is not as good as can be obtained with a high quality camera lens. You should replace the dust cover lens with your own high quality laboratory lens before making measurements.

To mount an F-mount lens on the camera, locate the large indicator dot on the side of the lens. There is a corresponding dot on the front side of the camera lens mount. Line up the dots and slide the lens into the mount. Then turn the lens counterclockwise until a click is heard. The click means that the lens is now locked in place.

Removing either type lens is equally simple. In the case of a C-mount lens, simply rotate the lens counterclockwise until it is free of the mount. In the case of an F-mount lens, press the locking lever on the mount while rotating the lens clockwise until it comes free and can be pulled straight out.

Both types of lenses typically have provision for focusing and aperture adjustment, with the details varying according the make and model of the lens. In addition, in the case of the F-mount, there is provision for adjusting the focus of the lens mount itself, if necessary, to bring the focus within range of the lens focus. See the discussion on page 44 for more detailed information.

Mounting procedures are more complex when mounting to a microscope and vary according to the make and model of the microscope as discussed in Mounting to a Microscope, which follows.

Mounting to a Microscope

This section discusses the setup and optimization of your digital imaging system as applied to microscopy. Since scientific grade cooled CCD imaging systems are usually employed for low light level microscopy, the major goal is to maximize the light throughput to the camera. In order to do this, the highest Numerical Aperture (NA) objectives of the desired magnification should be used. In addition, you should carefully consider the transmission efficiency of the objective for the excitation and emission wavelengths of the fluorescent probe employed. Another way to maximize the transmission of light is to choose the camera port that uses the fewest optical surfaces in the pathway, since each surface results in a small loss in light throughput. Often the trinocular mount on the upright microscope and the bottom port on the inverted microscope provide the highest light throughput. Check with the manufacturer of your microscope to determine the optimal path for your experiment type.

A rule of thumb employed in live cell fluorescence microscopy is “if you can see the fluorescence by eye, then the illumination intensity is too high”. While this may not be universally applicable, it is a reasonable goal to aim for. In doing this, the properties of the CCD in your camera should also be considered in the design of your experiments. For instance, if you have flexibility in choosing fluorescent probes, then you should take

Chapter 3 System Setup 29

advantage of the higher Quantum Efficiency (QE) of the CCD at longer wavelengths (contact factory for current CCD specifications). Another feature to exploit is the high resolution offered by cameras with exceptionally small pixel sizes (6.7 µ m for MicroMAX:1300Y, 1300YHS, and 1300YHS-DIF or 8.3µm for MicroMAX:782Y and 782YHS). Given that sufficient detail is preserved, you can use 2x2 binning (or higher) to increase the light collected at each “super-pixel” by a factor of 4 (or higher). This will allow the user to reduce exposure times, increasing temporal resolution and reducing photodamage to the living specimen.

Another method to minimize photodamage to biological preparations is to synchronize a shutter on the excitation pathway to the exposure period of the camera. This will limit exposure of the sample to the potentially damaging effects of the excitation light. Timing and synchronization are explained in Chapter 5.

The camera is connected to the microscope via a standard type mount coupled to a microscope specific adapter piece. There are two basic camera mounting designs, the C-mount and the F-mount. The C-mount employs a standard size thread to connect to the camera to the adapter while the F-mount uses a tongue and groove type mechanism to make the connection.

C-Mount

For a camera equipped with a C-mount thread, use the standard C-mount adapter supplied by the microscope manufacturer to attach the camera to the microscope. The adapter can be screwed into the camera and then the assembly can be secured to the microscope using the standard setscrews on the microscope. The camera can be mounted on the trinocular output port, the side port, or the bottom port of the inverted microscope. When mounting the larger cameras perpendicular to the microscope on the side port, it is ADVISED that you provide some additional support for your camera to reduce the possibility of vibrations or excessive stress on the C-mount nose. For the bottom port of the inverted microscope, the C-mount is designed to support the full weight of the camera, however, IT IS ADVISED that you provide some additional support for the larger cameras since the camera is in a position where it could be deflected by the operator’s knee or foot. This kind of lateral force could damage the alignment of the nose and result in sub-optimal imaging conditions.

Most output ports of the microscope do not require additional optical elements to collect an image, however please check with your microscope manual to determine if the chosen output port requires a relay lens. In addition, all optical surfaces should be free from dust and fingerprints, since these will appear as blurry regions or spots and hence degrade the image quality.

F-Mount

For a camera with the F-mount type design, you will need two elements to mount the camera on your microscope. The first element is a Diagnostic Instruments Relay Lens. This lens is usually a 1X relay lens that performs no magnification. Alternatively, you may use a 0.6X relay lens to partially demagnify the image and to increase the field of view. There is also a 2X relay lens available for additional magnification. The second element is a microscope specific Diagnostic Instruments Bottom Clamp. Table 3 shows which bottom clamps are routinely used with each of the microscope types. They are illustrated in Figure 7. If you feel that you have received the wrong type of clamp, of if you need a clamp for a microscope other than those listed, please contact the factory.

30 MicroMAX System User Manual Version 6.B

To assemble the pieces, first pick up the camera and look for the black dot on the front surface. Match this dot with the red dot on the side of the relay lens. Then engage the two surfaces and rotate them until the F-mount is secured as evidenced by a soft clicking sound. Next place the long tube of the relay lens into the bottom clamp for your microscope, securing it to the relay lens with the three setscrews at the top of the clamp as shown in Figure 8. This whole assembly can now be placed on the microscope, using the appropriate setscrews on the microscope to secure the bottom clamp to the output port of the microscope.

Microscope Type

Leica DMR L-clamp

Leitz All types NLW-clamp

Nikon Optiphot, Diaphot, Eclipse O-clamp

Olympus BH-2, B-MAX, IMT-2 V-clamp

Zeiss Axioscope, Axioplan, Axioplan 2, Axiophot Z-clamp

Zeiss Axiovert ZN-clamp

Table 3. Bottom Clamps for Different Microscopes

Diagnostic Instruments

Bottom Clamp Type

The F-mount is appropriate for any trinocular output port or any side port. When mounting the camera perpendicular to the microscope on the side port, it is ADVISED that you provide some additional support for your camera to reduce the possibility of vibrations or excessive stress on the F-mount nose. Princeton Instruments DOES NOT advise using an F-mount to secure the camera to a bottom port of an inverted microscope due to possible failure of the locking mechanism of the F-mount. Contact the factory for information about a special adapter for operating in this configuration.

Focusing information for a camera and a camera lens mount is included in the First Light section of Chapter 4 (page 44). Although it is unlikely that you would ever need to use the lens mount adjustment in operation with a microscope (the relay-lens focus adjustment would normally suffice), it could be used if necessary. The procedure for using the adjustment is provided in Chapter 4 and illustrated in Figure 14.

Chapter 3 System Setup 31

HRP 100-NIK

NLW

Figure 7. Bottom Clamps

HRP 100-NIK

"L" bottom clamp

Figure 8. Bottom Clamp secured to Relay Lens

32 MicroMAX System User Manual Version 6.B

Caution

Microscope optics have very high transmission efficiencies in the infrared region of the spectrum. Since typical microscope light sources are very good emitters in the infrared, some microscopes are equipped with IR blockers or heat filters to prevent heating of optical elements or the sample. For those microscopes that do not have the better IR blockers, the throughput of infrared light to the CCD can be fairly high. In addition, while the eye is unable to see the light, CCD cameras are particularly efficient in detecting infrared wavelengths. As a result, the contaminating infrared light will cause a degradation of the image quality due to a high background signal that will be invisible to the eye. Therefore, it is recommended that you add an IR blocker in the light path if you encounter this problem with the microscope.

Mounting to a Spectrometer

The camera must be properly mounted to the spectrometer to achieve maximum spectral resolution across the array. Depending on the spectrometer and camera type, special adapters may be required to mount the camera to the spectrometer. The appropriate adapters should have been included with your system if the spectrometer type was indicated when the system was ordered.

Because of the many possible camera and spectrometer combinations, all of the adapter mounting instructions are located in Appendix F. Refer to the table at the beginning of that appendix to find the instruction set appropriate to your system.

The distance to the focal plane from the front of the mechanical assembly depends on the specific configuration. Refer to the outline drawings in Appendix B for the focal plane distance information.

Selecting the Shutter Setting

Caution

The Shutter Setting push switch on the rear of the Controller sets the shutter hold voltage. Each shutter type, internal or external, requires a different setting. Consult the table below for the proper setting for your shutter. The Shutter Setting is correctly set at

the factory for the camera’s internal shutter if one is present.

Shutter Setting* Shutter Type

1 25 mm Princeton Instruments supplied External shutter

2 25 mm Princeton Instruments Internal shutter

4 35 mm Princeton Instruments Internal shutter (requires 70

5 40 mm Princeton Instruments Internal shutter (supplied

* Shutter settings 0, 3, and 6-9 are unused and are reserved for future use.

Table 4. ST-133 Shutter Setting Selection

(typically an Entrance slit shutter)

V Shutter option)

with LN camera having a 1340 × 1300 or larger CCD)

Chapter 3 System Setup 33

To Select the Shutter Setting:

SHUTTER CONTROL

1. Verify that the Controller power is OFF.

2. Refer to Table 4 when looking at the rear of the Controller.

3. If the setting is not correct, press the "-" or the "+" button until the correct setting is displayed in the window.

REMOTE

Figure 9. Shutter Setting for

25mm Internal Shutter

Connecting the Interface (Controller-Computer) Cable

TAXI® Cable (6050-0148-CE)

Turn the Controller power OFF (OFF = 0, ON = |) and the Computer power OFF before connecting or disconnecting the Controller-Computer (TAXI) cable.

To Connect the TAXI Cable:

1. Verify that the Controller power is OFF.

2. Verify that the Computer power is OFF.

3. Connect one end of the TAXI

host computer.

4. Tighten down the screws to lock the connector in place.

5. Connect the other end of the cable to the "Serial Com" port on the rear of the

Controller.

6. Tighten down the screws to lock the connector in place.

cable to the 9-pin port on the Interface card in the

SETTING

USB 2.0 Cable (6050-0494)

Turn the Controller power OFF (OFF = 0, ON = |) and the Computer power OFF before connecting or disconnecting the Controller-Computer (TAXI) cable.

To Connect the USB 2.0 Cable:

1. Verify that the Controller power is OFF.

2. Verify that the Computer power is OFF.

3. Connect one end of the USB cable to the USB port on the host computer.

4. Connect the other end of the cable to the USB 2.0 port on the rear of the

Controller.

34 MicroMAX System User Manual Version 6.B

Connecting the Detector-Controller Cable

Caution

Turn the Controller power OFF (OFF = 0, ON = |) before connecting or disconnecting the Detector-Controller cable.

To Connect the Detector-Controller Cable:

1. Verify that the Controller power is OFF.

2. Connect male end of the Detector-Controller cable to the “Detector” port on the back of the Controller.

3. Move the slide latch over to lock the connector in place.

4. Connect the female end of the cable to the Camera.

5. Move the slide latch over to lock the connector in place.

Chapter 4 Operation

Introduction

This chapter begins with sections regarding a number of operating considerations such as EMF, vacuum, cooling, baseline signal, and imaging field of view. The final section provides a step-by-step procedure for placing the system in operation the first time. At this point a lens should be mounted on the camera (or, if necessary, the camera mounted on a microscope) and you should be ready to operate the system and proceed to viewing your first MicroMAX images.

EMF and Xenon or Hg Arc Lamps

WARNING

Vacuum

Before You Start, if your imaging system includes a microscope Xenon or Hg arc lamp, it is CRITICAL to turn off all electronics adjacent to the arc lamp, especially your digital camera system and your computer hardware (monitors included) before turning on the lamp power.

Powering up a microscope Xenon or Hg arc lamp causes a large EMF spike to be produced that can cause damage to electronics that are running in the vicinity of the lamp. We advise that you place a clear warning sign on the power button of your arc lamp reminding all workers to follow this procedure. While Princeton Instruments has taken great care to isolate its sensitive circuitry from EMF sources, we cannot guarantee that this protection will be sufficient for all EMF bursts. Therefore, in order to fully

guarantee the performance of your system, you must follow this startup sequence.

The camera’s CCD chamber is pumped to a vacuum level of ~10 mTorr or better at the factory. This level of vacuum is necessary to be assured of achieving temperature lock and to prevent condensation from damaging the CCD array. Because outgassing continues for some time in new units, the vacuum could degrade, which would make it increasingly difficult to achieve temperature lock. Temperature lock can be restored by repumping the vacuum. Contact the factory Technical Support Dept. for information on refreshing the vacuum. See page 162 for contact information.

Cooling

Most MicroMAX cameras must be cooled during operation. A Peltier-effect thermoelectric cooler, driven by closed-loop proportional-control circuitry, cools the CCD. A thermal sensing diode attached to the cooling block of the camera monitors its temperature. Heat generated at the exhaust plate of the cooler is conducted to the

36 MicroMAX System User Manual Version 6.B

enclosure of the camera. Fins on the round head camera shell radiate the heat outward to the surrounding atmosphere. The fan inside the rectangular head camera draws air through the vents in the camera shell, blows it through the internal fins, and exhausts it back into the atmosphere through the vents.

MicroMAX CCDs typically have the following temperature ranges:

• Better than -15°C with passive cooling and under vacuum

• Better than -30°C with the optional forced air accessory and under vacuum

Setting the Temperature

The temperature of the CCD array is set through software. With WinView/32, you enter and set the target temperature after selecting

Temperature

Note: If you are using the USB 2.0 interface,

theDetector Temperature dialog box will not display temperature information while you are acquiring data.

from the Setup menu.

Detector

Figure 10. WinSpec/32 Detector

Temperature dialog box

Temperature Stabilization

After the system begins cooling, it takes from 10-20 minutes for the CCD to reach its preset temperature. Because the control loop is designed to achieve temperature lock as quickly as possible, overshoot may occur. If this happens, temperature lock will be briefly indicated and then discontinue during the overshoot. However, the lock indication will be quickly restored as stable control is re-established. This is normal behavior and should not be a cause for concern. Once temperature lock is established, the temperature is thermostated to within ±0.050°C. The controller is equipped with an LED that indicates temperature lock: this indicator may simply light or it may change color from orange to green to indicate lock.

Note: The time to reach temperature lock is affected by CCD array size and the ambient temperature. Typically, the larger the array or the warmer the ambient temperature, the longer the time to reach lock. Temperature regulation does not reach its ultimate stability for at least 30 minutes after lock is established.

Baseline Signal

With the camera completely blocked, the CCD will collect a dark charge pattern, dependent on the exposure time and camera temperature. The longer the exposure time and the warmer the camera, the larger and less uniform this background will appear. This background can be dealt with in a couple of ways: background subtraction, in which a background image is acquired and then subtracted from an illuminated image, or by offsetting the baseline so that much of the background is ignored during analog-to-digital conversion (ADC).

The baseline offset is a voltage that is added to the signal to bring the A/D output to a non-zero value, typically 50-100 counts. This offset value ensures that all the true variation in the signal can really be seen and not lost below the A/D “0” value. Since the

Chapter 4 Operation 37

offset is added to the signal, these counts only minimally reduce the range of the signal from 65535 (16-bit ADC) to a value in the range of 50-100 counts lower.

Notes:

1. Do not be concerned about either the DC level of this background or its shape unless it is very high (i.e., 400 counts). What you see is not noise. It is a fully subtractable readout pattern. Each CCD has its own dark charge pattern, unique to that particular device. Every device has been thoroughly tested to ensure its compliance with Princeton Instruments' demanding specifications.

2. The baseline can be adjusted by using the F and S Zero pots located on the rear panel of the controller. If these pots are not present, the baseline may be softwareadjustable.

3. Do not adjust the offset values to zero or some low-level data will be missed.

Caution

If you observe a sudden change in the baseline signal you may have excessive humidity in the vacuum enclosure of the camera. Turn off the controller and have the camera repumped before resuming normal operation. Contact the factory Technical Support

Dept. for information on how to refresh the vacuum. See page 162 for contact information.

Analog Gain Control

Analog gain control is used to change the number of electrons required to generate an Analog-to-Digital Unit (ADU, also known as a count). In WinView/32, the choice of analog gain settings varies depending on the CCD array and the number of output amplifiers. If your camera is not designed for analog gain selection, these settings will not be accessible in the software.

In WinView (version 2.X and higher), analog gain selection is made on the

Experiment Setup…|ADC

card, analog gain may not be selectable or it may be controlled by a gain switch on the camera. When software-selection of Analog Gain is available, the software selection will override any hardware setting that may be selected at the camera.

The analog gain of the camera should generally be set so that the overall noise is ~1 count RMS. In most instances this will occur with the switch set to Medium. In situations where the A/D range exceeds that of the array, it will generally be better to set the Analog Gain to High so that the signal can be spread over as much of the A/D range as possible. Users who consistently measure low-level signals may wish to select High, which reduces some sources of noise. Users who measure high-level signals may wish to select Low to allow digitization of larger signals. Customized values of gain can be provided. Contact the factory for additional information.

Acquisition|

tab card. If there is no Analog Gain parameter on that tab

Example: The following descriptions assume that the actual incoming light level is identical in all three instances. The numbers used illustrate the effect of changing

an analog gain setting and do not reflect actual performance: gain at the Low, Medium, and High settings depends on the CCD installed.

Low requires eight electrons to generate one ADU. Strong signals can be acquired without flooding the CCD array. If the gain is set to Low and the images or spectra appear weak, you may want to change the gain setting to Medium or High.

38 MicroMAX System User Manual Version 6.B

Medium requires four electrons to generate one ADU. If the gain is set to Medium and the images or spectra do not appear to take up the full dynamic range of the CCD array, you may want to change the gain setting to High. If the CCD array appears to be flooded with light, you may want to change the setting to Low.

High requires two electron to generate one ADU and some noise sources are reduced. Because fewer electrons are needed to generate an ADU, weaker signals can be more readily detected. Lower noise further enhances the ability to acquire weak signals. If the CCD array appears to be flooded with light, you may want to change the setting to Medium or Low.

Note: The baseline level may require adjustment if you change the analog gain. See the "Baseline Signal" section on page 36 for more information.

Imaging Field of View

When used for two-dimensional imaging applications, the MicroMAX camera closely imitates a standard 35 mm camera. Since the CCD is not the same size as the film plane of a 35 mm camera, the field of view at a given distance is somewhat different. The imaging field of view is indicated in Figure 11.

Object

Lens

Figure 11. Imaging Field of View

D = distance between the object and the CCD B = 46.5 mm for F-mount; 17.5 mm for C-mount F = focal length of lens S = CCD horizontal or vertical dimension O = horizontal or vertical field of view covered at a distance D M = magnification The field of view is:

CCD

RS-170 or CCIR Video

One of the limitations of scientific non-video rate cameras has been their difficulty in focusing and locating fields of view. The MicroMAX solves this problem by its combination of high speed operation with the implementation of true video output. The high-speed image update on the video monitor (via the VIDEO BNC connector on the rear of the Controller) makes focusing and field location as simple as with a video

Chapter 4 Operation 39

camera. This video output also makes possible archiving an experiment on a VCR, producing hardcopy data on a video printer, or even implementing autofocusing stages.

Note: If more than one device is connected to the video output, the last device is the one that should to be terminated in 75Ω. For example, to connect the video output to a VCR as well as to a monitor, the cable from the controller video output should be connected to the video input connector of the VCR, and another 75 Ω cable should extend from the video output connector of the VCR to the 75Ω input of the monitor. Do not use a BNC TEE to connect the controller video output to multiple devices.

The video output is selected by the Application software. In the case of WinView/32, this is done by selecting Video from the Acquisition menu. There is also provision in WinView/32 for intensity-scaling the video output, that is, selecting the specific gray levels to be displayed on the 8-bit video output.

In addition to intensity-scaling, you also need to be concerned about how the array pixels map to the video display. The 756×486 resolution of a typical video monitor corresponds well with the array size of a MicroMAX:782Y, MicroMAX:782YHS or MicroMAX:512BFT

In the case of a MicroMAX:1300YHS or a MicroMAX:1300YHS-DIF, the number of array pixels far exceeds the number of monitor pixels and mapping must be considered more carefully. WinView/32 software’s Video Focus mode (accessed from the Acquisition Menu) provides a Pan function that allows any one of nine different subsets of the array image to be selected for viewing on the video monitor with only a singleframe delay. An associated zoom function provides 1x, 2x, or 4x viewing. At 1x, the entire array image is displayed, but at reduced resolution (pixels are discarded and fine detail could be lost). At 2x, the mapping is 1:1 and the image portion selected by the Pan function is provided. The regions overlap, allowing the entire array image to be examined with no loss of resolution. At 4x, array pixels are enlarged so that a smaller part of the array image is displayed as selected by the Pan function.

Once proper focus has been achieved, the user can transfer to normal data-acquisition operation. The video output remains operative, but with a more limited and fixed view because of the resolution limitation of RS-170 video. Although this view is sufficient to cover the image from a small CCD array in its entirety, it will not cover all the pixels from a large array. Instead, a subset from the center of the image will be shown. For example, in the case of the MicroMAX:1300YHS, the monitor would display the 756×486 area from the center of the CCD image as shown in Figure 12.

1300 × 1030

756 × 486 RS-170

(EIA) monitor

image from center

of CCD image

Figure 12. Monitor Display of CCD Image Center Area

40 MicroMAX System User Manual Version 6.B

Note: With a 16-bit A/D converter (not a standard option), the composite video output is disabled during data acquisition.

In post-acquisition processing the WinView/32 ROI (Region of Interest) capability allows any portion of an acquired image to be displayed on the computer monitor.

Again, note that the described video output behavior applies specifically for the WinView/32 software only. Other application software may provide different video output capabilities.

USB 2.0 and System On/Off Sequences

The following on/off sequences are specific to the USB 2.0 interface:

1. The ST-133 must be turned on before WinView/32 is opened to ensure communication between the controller and the computer. If WinView is opened and the ST-133 is off, many of the functions will be disabled and you will only be able to retrieve and examine previously acquired and stored data. You must close WinView, turn on the ST-133, and reopen WinView before you can set up experiments and acquire new data.

2. WinView/32 must be closed before turning off the ST-133. If you turn off the ST-133 before closing WinView, the communication link with the controller will be broken. You can operate the program in a playback mode (i.e., examine previously acquired data) but will be unable to acquire new data until you have closed WinView, turned on the ST-133, and then re-opened WinView.

First Light (Imaging)

The following paragraphs provide step-by-step instructions for placing your MicroMAX system in operation the first time. The intent of this simple procedure is to help you gain basic familiarity with the operation of your system and to show that it is functioning properly. Once basic familiarity has been established, then operation with other operating configurations, ones with more complex timing modes, can be performed. An underlying assumption for the procedure is that the camera is to be operated with a microscope on which it has been properly installed (see "Mounting to a Microscope", page 28, for mounting instructions) and that a video monitor is available. Although it is possible to dispense with the monitor and simply view the images on the computer monitor’s screen, operations such as focusing may be easier with a video monitor because the displayed data is updated much more quickly and will be as close to current as possible.

Once the MicroMAX camera has been installed and its optics adjusted, operation of the camera is basically straightforward. In most applications you simply establish optimum performance using the Focus mode (WinView/32), set the target camera temperature, wait until the temperature has stabilized, and then do actual data acquisition in the Acquire mode. Additional considerations regarding experiment setup and equipment configuration are addressed in the software manual.

Chapter 4 Operation 41

Detector-Controller

Camera

Detector

Controller

Microscope

EXPERIMENT

Figure 13. Standard System Connection Diagram

Interface cable

(TAXI or USB 2.0)

110/220

Serial Com or USB 2.0

110/220

Computer

Assumptions

The following procedure assumes that

1. You have already set up your system in accordance with the instructions in Chapter 3.

2. You have read the previous sections of this chapter.

3. You are familiar with the application software.

4. The system is air-cooled.

5. The system is being operated in imaging mode.

Cabling

If the system cables haven’t as yet been installed, make sure that the ST-133 and the host computer are turned off and then make the cable connections as follows: See Figure 13.

1. Connect the 25-pin camera-to-controller cable from the DETECTOR connector on

the Analog/Control module panel to the mating connector at the back of the camera. Secure the cable at both ends with the slide-lock latch

2. Connect one end of the 9-pin serial cable to the SERIAL COM connector on the Interface Control module panel. Connect the other end to the computer interface as described in Chapter 3. Be sure to secure both ends of the cable with the cableconnector screws.

3. Connect a 75 Ω BNC cable from the VIDEO connector on the back of the camera to the video monitor’s 75 Ω input. This cable must be terminated in 75 Ω. Many monitors have a switch for selecting the 75 Ω termination.

4. Connect the line cord from the Power Input assembly on the back of the controller to a suitable source of AC power.

42 MicroMAX System User Manual Version 6.B

Getting Started

1. If you haven’t already done so, install a lens on the camera. The initial lens settings aren’t important but it may prove convenient to set the focus to approximately the anticipated distance and to begin with a small aperture setting. In the case of operation with a microscope, review "Mounting to a Microscope", beginning on page 28, and mount the camera on the microscope.

2. Turn on the system power. The Power On/Off switch is located on the front of the controller.

Note: The camera overload alarm may sound briefly and then stop. This is normal and is not a cause for concern. However, if the alarm sounds continuously, even with no light entering the camera, something is wrong. Turn off the power and contact the factory for guidance.

3. Turn on the power at the computer and start the application software (WinView/32, for example).

Setting the Parameters

Note: The following procedure is based on WinView/32: you will need to modify it if

you are using a different application. Basic familiarity with the WinView/32 software is assumed. If this is not the case, you may want to review the software manual or have it available while performing this procedure.

Set the software parameters as follows:

Controller|Camera tab page (Setup|Hardware)

• Use PVCAM: 100 kHz or 1 MHz systems only. If you are using the USB 2.0 interface, verify that the box is checked.

• Controller type: ST-133

• Controller version: 4 or higher

• Camera type: Select array installed in your camera.

MicroMAX:512FT = EEV 512×512 FT CCD57 MicroMAX:512BFT = EEV 512×512 FT CCD57 MicroMAX:782Y = PID 582×782 MicroMAX:782YHS = PID 582×782 MicroMAX:1024 = EEV 1024×1024 CCD47_10 MicroMAX:1024B = EEV 1024×1024 CCD47_10 MicroMAX:1024FT = EEV 1024×1024 CCD47_20 MicroMAX:1024BFT = EEV 1024×1024 CCD47_20 MicroMAX:1300Y = PID 1030×1300 MicroMAX:1300YHS = PID 1030×1300 MicroMAX:1300YHS-DIF = PID 1030×1300

• Shutter type: None or Remote.

• Readout mode: Full frame, Interline or DIF depending on array type.

Detector Temperature (Setup|Detector Temperature…): -15°C for

round camera heads or -45°C for rectangular camera heads. The temperature should drop steadily, reaching the set temperature in about ten minutes (typical). At that point the green Temp Lock LED on the rear of the ST-133

Chapter 4 Operation 43

will light and there will be a locked indication at the computer monitor, indicating that temperature lock has been established. Note that some overshoot may occur. This could cause temperature lock to be briefly lost and then quickly re-established. If you are reading the actual temperature reported by the application software, there may be a small difference between the set and reported temperature when lock is established. This is normal and does not indicate a system malfunction. Once lock is established, the temperature will be stable to within ±0.05°C.

Note: If you are using the USB 2.0 interface, the Detector Temperature dialog box will not display temperature information while you are acquiring data.

Interface tab page (Setup|Hardware): High Speed PCI (or PCI(Timer))

Note: This tab page is not available if you are using the USB 2.0 interface.

Cleans and Skips tab page (Setup|Hardware): Default

Experiment Setup Main tab page (Acquisition|Experiment Setup…):

• Exposure Time: 100 ms

• Accumulations & Number of Images: 1

Experiment Setup ROI tab page (Acquisition|Experiment Setup…):

Use this function to define the region of interest (ROI).

• Imaging Mode: Selected if you are using WinSpec/32.

• Clicking on Full loads the full size of the chip into the edit boxes.

• Clicking on Store will store the Pattern so it can be reused at another

time.

Experiment Setup Timing tab page (Acquisition|Experiment Setup…):

• Timing Mode: Free Run

• Shutter Control: Normal

• Safe Mode vs. Fast Mode: Safe

Acquisition Menu: Select

Video if you have connected an RS-170 (or a CCIR)

video monitor to the system and plan to use it for focusing or other operations. There will be a check next to “

Video” to indicate that it is selected

Focusing

1. If you are using WinView/32 (or WinSpec/32 in Imaging Mode) and the computer monitor for focusing, select present, will open and successive images will be sent to the monitor as quickly as they are acquired. Because the time to acquire and read out an image varies directly with the size of the CCD, the observed frame rate will vary greatly depending on the CCD installed. With a short exposure time, it is not uncommon for the frame readout time to be significantly longer than the exposure time.

Focus from the Acquisition menu. The shutter, if

44 MicroMAX System User Manual Version 6.B

Note: If you are using WinView/32 (or WinSpec/32 in Imaging Mode) and a video monitor for focusing, select the Video Focus… mode from the Acquisition menu. Then select a short exposure time (0.1 s), an Intensity Scaling setting of 4096, and 2x Zoom. With an MicroMAX:1300Y camera (1030×1300 pixels), set the Pan selector as required for the 756×486 subset of the array image you wish to use for focusing purposes. Select the center pan position if the camera is a MicroMAX:782Y (782×582 pixels) or a MicroMAX:512BFT (512×512 pixels). Begin data collection by selecting RUN on the Interactive Camera Operation dialog box. The shutter, if present, will open and successive images will be sent to the monitor as quickly as they are acquired, giving as close to continuous video as possible.

2. Adjust the lens aperture, intensity scaling, and focus for the best image as viewed on the monitor. Some imaging tips follow.

a. Begin with the lens blocked off. Set the lens at the smallest possible aperture

(largest f-stop number).

b. Place a suitable target in front of the lens. An object with text or graphics works

best. If working with a microscope, use any easily viewed specimen. It is generally not advisable to attempt fluorescence imaging during this Getting Started phase of operation.

c. Adjust the intensity scaling and lens aperture until a suitable setting is found.

The initial intensity scaling setting of 4096 assures that the image won’t be missed altogether but could be dim. Once you’ve determined that the image is present, select a lower setting for better contrast. Check the brightest regions of the image to determine if the A/D converter is at full-scale. The A/D converter is at full-scale when any part of the image is as bright as it can be. Adjust the aperture to where it is just slightly smaller (higher f stop) than the setting where maximum brightness on any part of the image occurs.

d. Set the focus adjustment of the lens for maximum sharpness in the viewed

image.

If the camera is mounted to a microscope, first be sure to have a clear, focused

image through the eyepiece. Then divert the light to the camera and lower the illuminating light intensity.

To adjust the parfocality on an F-mount system, begin collecting images

with a short exposure time and focus the light on the camera by rotating the ring on the Diagnostic Instruments relay lens without touching the main focusing knobs on the microscope.

o In the case of a camera with an F-mount lens adapter, focusing is normally

done by means a focus adjustment on the relay-lens adapter.

o On a C-mount system, the camera should be very close to parfocal, although

some C-mounts will be adjustable using setscrews on the microscope to secure the adapter slightly higher or lower in position.

f. In the case of a camera with an F-mount, the adapter itself also has a focus

adjustment. If necessary, this focus can be changed to bring the image into range of the lens focus adjustment. The lens-mount adjustment is secured by four

Chapter 4 Operation 45

setscrews as shown in Figure 14. To change the focus setting, proceed as follows.

o Loosen the setscrews with a 0.050" Allen wrench. Do not remove the

screws; loosen them just enough to allow the lens mount to be adjusted.

Rotate the lens mount as required to bring the focus within range of the lens

focus adjustment.

Tighten the setscrews loosened above.

Set screws to lock front part of adapter in place

Lens release lever

Front part of adapter

for adjusting focus

Figure 14. F-mount Focus Adjustment

Acquiring Data

Once optimum focus and aperture have been achieved, you can switch from Focus (or

Video Focus) mode to standard data-acquisition operation as determined via the

Experiment Setup dialog box. (In WinView/32, you might want to begin with Free Run (Safe Mode) operation while gaining basic system familiarity.)

This completes First Light for imaging applications. If the MicroMAX system functioned as described, you can be reasonably sure it has arrived in good working order. In addition, you should have a basic understanding of how the system hardware is used. Other topics, which could be quite important in certain situations, are discussed in the following chapters. See the appropriate application software manual for information on using the software to control the system.

First Light (Spectroscopy)

The following paragraphs provide step-by-step instructions for placing your spectroscopy system in operation the first time. The intent of this simple procedure is to help you gain basic familiarity with the operation of your system and to show that it is functioning properly. Once basic familiarity has been established, then operation with other operating configurations, ones with more complex timing modes, can be performed. An underlying assumption for the procedure is that the detector is to be operated with a spectrograph such as the Acton SpectraPro light source, such as a mercury pen-ray lamp, should be mounted in front of the entrance slit of the spectrograph. Any light source with line output can be used. Standard fluorescent overhead lamps have good calibration lines as well. If there are no “line” sources available,

™

300i (SP300i) on which it has been properly installed. A suitable

46 MicroMAX System User Manual Version 6.B

it is possible to use a broadband source such as tungsten for the alignment. If this is the case, use a wavelength setting of 0.0 nm for alignment purposes.

Assumptions

The following procedure assumes that

1. You have already set up your system in accordance with the instructions in Chapter 3.

2. You have read the previous sections of this chapter.

3. You are familiar with the application software.

4. The system is air-cooled.

5. The system is being operated in spectroscopy mode.

6. An entrance slit shutter is not being controlled by the ST-133.

Cabling

If the system cables haven’t as yet been installed, make sure that the ST-133 and the host computer are turned off and then follow the cabling instructions on page 41. Then, return to this page.

Getting Started

1. Set the spectrometer entrance slit width to minimum (10 µm if possible).

2. Turn on the controller power.

Note: A detector overload alarm may sound briefly and then stop. This is normal and is not a cause for concern. However, if the alarm sounds continuously, even with no light entering the detector, something is wrong. Turn off the power and contact the factory for guidance.

3. Turn on the computer power.

4. Start the application software.

Setting the Parameters

Note: The following procedure is based on WinSpec/32: you will need to modify it if

you are using a different application. Basic familiarity with the WinSpec/32 software is assumed. If this is not the case, you may want to review the software manual or have it available while performing this procedure.

Set the software parameters as follows:

Environment dialog (Setup|Environment): Verify that the DMA Buffer

size is 8 Mbytes (min.). Large arrays may require a larger buffer size. If you change the buffer size, you will have to reboot the computer for this memory allocation to be activated, and then restart WinSpec.

Controller|Camera tab page (Setup|Hardware): Controller and Detector

parameters should be set automatically to the proper values for your system. However, you can click on the this tab page to load the default settings.

Load Defaults From Controller button on

Chapter 4 Operation 47

• Use PVCAM: 100 kHz or 1 MHz systems only. If you are using the USB 2.0 interface, verify that the box is checked.

• Controller type: ST-133

• Controller version: 3 or higher

• Camera type: Select the array installed in your detector.

• Shutter type: None or Remote.

• Readout mode: Full frame.

Detector Temperature (Setup|Detector Temperature…): -15°C for

round camera heads or -45°C for rectangular camera heads. When the array temperature reaches the set temperature, the green Temp Lock LED on the rear of the ST-133 will light and there will be a locked indication at the computer monitor. Note that some overshoot may occur. This could cause temperature lock to be briefly lost and then quickly re-established. If you are reading the actual temperature reported by the application software, there may be a small difference between the set and reported temperature when lock is established. This is normal and does not indicate a system malfunction. Once lock is established, the temperature will be stable to within ±0.05°C.

Note: If you are using the USB 2.0 interface, the Detector Temperature dialog box will not display temperature information while you are acquiring data.

Interface tab page (Setup|Hardware): High Speed PCI (or PCI(Timer))

Note: This tab page is not available if you are using the USB 2.0 interface.

Cleans and Skips tab page (Setup|Hardware): Default

Experiment Setup Main tab page (Acquisition|Experiment Setup…):

• Exposure Time: 100 ms

• Accumulations & Number of Images: 1

Experiment Setup ROI tab page (Acquisition|Experiment Setup…):

Use this function to define the region of interest (ROI).

• Spectroscopy Mode: Selected

• Clicking on Full loads the full size of the chip into the edit boxes.

48 MicroMAX System User Manual Version 6.B

Experiment Setup Timing tab page (Acquisition|Experiment Setup…):

• Timing Mode: Free Run

• Shutter Control: Normal

• Safe Mode vs. Fast Mode: Safe

Focusing

The mounting hardware provides two degrees of freedom, focus and rotation. In this context, focus means to physically move the detector back and forth through the focal plane of the spectrograph. The approach taken is to slowly move the detector in and out of focus and adjust for optimum while watching a live display on the monitor, followed by rotating the detector and again adjusting for optimum. The following procedure, which describes the focusing operation with an Acton 300I spectrograph, can be easily adapted to other spectrographs.

1. Mount a light source such as a mercury pen-ray type in front of the entrance slit of the spectrograph. Any light source with line output can be used. Standard fluorescent overhead lamps have good calibration lines as well. If there are no “line” sources available, it is possible to use a broadband source such as tungsten for the alignment. If this is the case, use a wavelength setting of 0.0 nm for alignment purposes.

2. With the spectrograph properly connected to the controller, turn the power on, wait for the spectrograph to initialize. Then set it to 435.8 nm if using a mercury lamp or to 0.0 nm if using a broadband source.

Hint: Overhead fluorescent lights produce a mercury spectrum. Use a white card tilted at 45 degrees in front of the entrance slit to reflect overhead light into the spectrograph. Select 435.833 as the spectral line.

3. Set the slit to 25 µm. If necessary, adjust the Exposure Time to maintain optimum (near full-scale) signal intensity.

4. Slowly move the detector in and out of focus. You should see the spectral line go from broad to narrow and back to broad. Leave the detector set for the narrowest achievable line. You may want to use the Focus Helper function (Process|Focus Helper…) to determine the narrowest line width: it can automatically locate peaks and generate a report on peak characteristics during live data acquisition (see the WinSpec/32 on-line help for more information).

Note that the way focusing is accomplished depends on the spectrograph, as follows:

• Long focal-length spectrographs such as the Acton 300i: The mounting adapter includes a tube that slides inside another tube to move the detector in or out as required to achieve optimum focus.

• Short focal-length spectrographs: There is generally a focusing mechanism on the spectrograph itself which, when adjusted, will move the optics as required to achieve proper focus.

• No focusing adjustment: If there is no focusing adjustment, either provided by the spectrograph or by the mounting hardware, then the only recourse will be to adjust the spectrograph’s focusing mirror.

Chapter 4 Operation 49

5. Next adjust the rotation. You can do this by rotating the detector while watching a live display of the line. The line will go from broad to narrow and back to broad. Leave the detector rotation set for the narrowest achievable line.

Alternatively, take an image, display the horizontal and vertical cursor bars, and compare the vertical bar to the line shape on the screen. Rotate the detector until the line shape on the screen is parallel with the vertical bar.

Note: When aligning other accessories, such as fibers, lenses, optical fiber adapters, first align the spectrograph to the slit. Then align the accessory without disturbing the detector position. The procedure is identical to that used to focus the spectrograph (i.e., do the focus and alignment operations while watching a live image).

Acquiring Data

Once optimum focus and aperture have been achieved, you can switch from Focus (or

Video Focus) mode to standard data-acquisition operation as determined via the

Experiment Setup dialog box. (In WinSpec/32, you might want to begin with Free Run (Safe Mode) operation while gaining basic system familiarity.)

This completes First Light for spectroscopy applications. If the MicroMAX system functioned as described, you can be reasonably sure it has arrived in good working order. In addition, you should have a basic understanding of how the system hardware is used. Other topics, which could be quite important in certain situations, are discussed in the following chapters. See the appropriate application software manual for information on using the software to control the system.

50 MicroMAX System User Manual Version 6.B

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Chapter 5 Timing Modes

The Princeton Instruments MicroMAX system has been designed to allow the greatest possible flexibility when synchronizing data collection with an experiment.

The chart below lists the timing mode combinations. Use this chart in combination with the detailed descriptions in this chapter to determine the optimal timing configuration.

Fast and Safe Speed Modes

The WinSpec/32 Experiment Setup Timing tab page allows the user to choose Fast or Safe Mode. Figure 15 is a flowchart comparing the two modes. In Fast Mode operation,

the MicroMAX runs according to the timing of the experiment, with no interruptions from the computer. In Safe Mode operation, the computer processes each frame as it is received. The MicroMAX cannot collect the next frame until the previous frame has been completely processed.

Mode Shutter

Free Run Normal

External Sync Normal

External Sync PreOpen

Continuous Cleans Normal

Continuous Cleans PreOpen

Table 5. Camera Timing Modes

Fast Mode operation is primarily for collecting "real-time" sequences of experimental data, where timing is critical and events cannot be missed. Once the MicroMAX is sent the Start Acquisition command (STARTACQ) by the computer, all frames are collected without further intervention from the computer. The advantage of this timing mode is that timing is controlled completely through hardware. A drawback to this mode is that the computer will only display frames when it is not performing other tasks. Image display has a lower priority, so the image on the screen may lag several images behind.

A video monitor connected to the VIDEO output will always display the current image.

A second drawback is that a data overrun may occur if the number of images collected exceeds the amount of allocated RAM or if the computer cannot keep up with the data rate.

Safe Mode operation is primarily useful for experiment setup, including alignment and focusing, when it is necessary to have the most current image displayed on the screen. It is also useful when data collection must be coordinated with external devices such as external shutters and filter wheels. As seen in Figure 15, in Safe Mode operation, the

52 MicroMAX System User Manual Version 6.B

computer controls when each frame is taken. After each frame is received, the camera sends the Stop Acquisition command to the camera, instructing it to stop acquisition. Once that frame is completely processed and displayed, another Start Acquisition command is sent from the computer to the camera, allowing it to take the next frame. Display is therefore, at most, only one frame behind the actual data collection.

One disadvantage of the Safe mode is that events may be missed during the experiment, since the MicroMAX is disabled for a short time after each frame.

Standard Timing Modes

The basic timing modes are Free Run, External Sync, and External Sync with Continuous Cleans. These timing modes are combined with the Shutter options to provide the widest variety of timing modes for precision experiment synchronization.

The shutter options available include Normal, PreOpen, Disable Opened or Disable Closed. Disable simply means that the shutter will not operate during the experiment. Disable closed is useful for making dark charge measurements, or when no shutter is present in the system. PreOpen, available in the External Sync mode, opens the shutter as soon as the MicroMAX is ready to receive an External Sync pulse. This is required if the time between the External Sync pulse and the event is less than a few milliseconds, the time it takes the shutter to open.

The shutter timing is shown in the timing diagrams that follow. Except for Free Run, where the modes of shutter operation are identical, both Normal and PreOpen lines are shown in the timing diagrams and flowchart.

The timing diagrams are labeled indicating the exposure time (t compensation time (t

), and readout time (tR). See Chapter 6 for additional information.

), shutter

exp

Free Run

In the Free Run mode the controller does not synchronize with the experiment in any way. The shutter opens as soon as the previous readout is complete, and remains open for the exposure time, t experiments with a constant light source, such as a CW laser or a DC lamp. Other experiments that can utilize this mode are high repetition studies, where the number of shots that occur during a single shutter cycle is so large that it appears to be continuous illumination.

. Any External Sync signals are ignored. This mode is useful for

exp

Chapter 5 Timing Modes 53

Safe Mode

Start

Computer programs

camera with exposure

and binning parameters

STARTACQ issued from

computer to camera

Cleans performed

1 frame collected

as per timing mode

STOPACQ issued from

computer to camera

Fast Mode

Start

Computer programs

camera with exposure

and binning parameters

STARTACQ issued from

computer to camera

Cleans performed

1 frame collected

as per timing mode

Background or

flatfield on?

Background or

flatfield on?

Ye s

Background and/or

flatfield correction

performed

Frame displayed

Frames

complete?

Ye s

Stop

Figure 15. Chart of Safe and Fast Mode Operation

Background and/or

flatfield correction

performed

Ye s

frames are displayed as

Frames

complete?

During next acquisition

time permits

STOPACQ issued from

computer to camera

Stop

Ye s

54 MicroMAX System User Manual Version 6.B

Shutter opens

Shutter remains open

for preprogrammed

exposure time

System waits while

shutter closes

Figure 16. Free Run Timing Chart (part of the chart in Figure 15)

Other experimental equipment can be synchronized to the detector by using the output signal (software-selectable SHUTTER or NOTSCAN) from the

connector on the back of the ST-133. Shutter operation and the NOTSCAN output signal are shown in Figure 17.

Shutter Open Close Open Close Open Close

NOTSCAN

exp

First exposure

Read Read Read

ctR

Data

stored

Figure 17. Free Run Timing Diagram

Second

exposure

Data

stored

Third

exposure

Data

stored

External Sync

In this mode all exposures are synchronized to an external source. As shown in the flowchart, Figure 18, this mode can be used in combination with Normal or PreOpen Shutter operation. In Normal Shutter mode, the controller waits for an External Sync pulse, then opens the shutter for the programmed exposure period. As soon as the exposure is complete, the shutter closes and the CCD array is read out.

External synchronization depends on an edge trigger (negative- or positive-going) which must be supplied to the Ext Sync connector on the back of the camera. The type of edge must be identified in the application software to ensure that the shutter opening is initiated by the correct edge (in WinView/WinSpec, this is done on the

Setup|Timing

tab page). Depending on the shutter, it may require up to 28 msec to fully open. Therefore, the External Sync pulse provided by the experiment should precede the actual signal by at least that much time. If not, the shutter may not be open for the duration of the entire signal, or the signal may be missed completely.

Experiment

Also, since the amount of time from initialization of the experiment to the first External Sync pulse is not fixed, an accurate background subtraction may not be possible for the

Chapter 5 Timing Modes 55

first readout. In multiple-shot experiments this is easily overcome by simply discarding the first frame.

In the PreOpen Shutter mode, on the other hand, shutter operation is only partially synchronized to the experiment. As soon as the controller is ready to collect data, the shutter opens. Upon arrival of the first External Sync pulse at the ST-133, the shutter remains open for the specified exposure period, closes, and the CCD is read out. As soon as readout is complete, the shutter reopens and waits for the next frame.

(shutter preopen)

Shutter opens

Controller waits for

External Sync pulse

Shutter remains open

for preprogrammed

exposure time

System waits while

shutter closes

(shutter normal)

Controller waits for

External Sync pulse

Shutter opens

Figure 18. Showing Shutter "Preopen" & "Normal" Modes in External Sync Operation

Shutter (Normal)

Open Close Open Close Open Close

Shutter (Preopen)

NOTSCAN

External Sync

(negative polarity shown)

Open Close Open

Read Read Read

First wait

and exposure

exp

Data

stored

Second wait

and exposure

Data

stored

Open Close

Third wait

and exposure

Data

stored

Figure 19. External Sync Timing Diagram (- edge trigger)

The PreOpen mode is useful in cases where an External Sync pulse cannot be provided 5-28 msec before the actual signal occurs. Its main drawback is that the CCD is exposed to any ambient light while the shutter is open between frames. If this ambient light is constant, and the triggers occur at regular intervals, this background can also be

56 MicroMAX System User Manual Version 6.B

subtracted, providing that it does not saturate the CCD. As with the Normal Shutter mode, accurate background subtraction may not be possible for the first frame.

Also note that, in addition to signal from ambient light, dark charge accumulates during the “wait” time (t

). Any variation in the external sync frequency also affects the amount

of dark charge, even if light is not falling on the CCD during this time.

Note: If EXT SYNC is still active at the end of the readout, the hardware will interpret this as a second sync pulse, and so on.

External Sync with Continuous Cleans

The third timing mode available with the MicroMAX camera is called Continuous Cleans. In addition to the standard “cleaning” of the array, which occurs after the controller is enabled, Continuous Cleans will remove any charge from the array until the moment the External Sync pulse is received.

(shutter preopen)

Shutter opens

CCD is continuously

cleaned until External Sync

pulse is received

Shutter remains open

for preprogrammed

exposure time

System waits while

shutter closes

(shutter normal)

CCD is continuously

cleaned until External Sync

pulse is received

Shutter opens

Figure 20. Continuous Cleans Flowchart

Once the External Sync pulse is received, cleaning of the array stops as soon as the current row is shifted, and frame collection begins. With Normal Shutter operation the shutter is opened for the set exposure time. With PreOpen Shutter operation the shutter is open during the continuous cleaning, and once the External Sync pulse is received the shutter remains open for the set exposure time, then closes. If the vertical rows are shifted midway when the External Sync pulse arrives, the pulse is saved until the row shifting is completed, to prevent the CCD from getting “out of step.” As expected, the response latency is on the order of one vertical shift time, from 1-30 µsec depending on the array. This latency does not prevent the incoming signal from being detected, since photo generated electrons are still collected over the entire active area. However, if the signal arrival is coincident with the vertical shifting, image smearing of up to one pixel is

Chapter 5 Timing Modes 57

possible. The amount of smearing is a function of the signal duration compared to the single vertical shift time.

Note: If EXT SYNC is still active at the end of the readout, the hardware will interpret this as a second sync pulse, and so on.

Shutter (Normal)

Shutter (Preopen)

NOTSCAN

External Sync

Open Close Open Close Open Close

Figure 21. Continuous Cleans Timing Diagram

Frame Transfer Operation

In frame transfer operation, half the CCD is used for sensing light and the other half for storage and readout. Not all CCD arrays are capable of readout in this mode, as it requires that charge be shifted independently in the two halves of the array. See

Chapter 6 for a detailed discussion of readout in the frame-transfer mode operation; the primary focus of this section is frame-transfer timing.

There are two timing options available in frame transfer mode, Free Run and External Sync. Both are similar to their counterparts in full frame (standard) operation, except that in frame transfer operation a shutter is not generally used. Because there is no shutter (or the shutter is only closed after the camera has collected a series of frames), shutter Normal, PreOpen, or Disable have no physical meaning here. The exposure half of the array sees light continuously. The actual exposure time is the time between data transfers from the exposure half of the array to the storage half of the array, and may be longer than the programmed exposure, t the storage half occurs very quickly at the start of each read. During the read, the stored data is shifted to the array’s output port, the same as in standard operation.

Open Close Open Close Open Close

Read

. Data transfer from the exposure half of the array to

exp

Read Read

In Free Run frame-transfer mode operation, half of the array is exposed for the set exposure time (t

). Then the data transfer to the storage half of the array takes place,

exp

marking the start of the read and the beginning of a new exposure.

In External Sync frame-transfer mode operation, the camera reads out one frame for every External Sync pulse received, providing the frequency of the External Sync pulse doesn’t exceed the maximum rate possible with the system. Other than for the first readout, initiated by starting acquisition, a Sync Pulse must be detected before the subsequent readout can occur.

Note: If EXT SYNC is still active at the end of the readout, the hardware will interpret this as a second sync pulse, and so on.

58 MicroMAX System User Manual Version 6.B

If operating without a shutter, the actual exposure time is set by the period of the sync signal. There is one exception, if the programmed exposure time is less than the readout time, then the actual exposure time is simply equal to t NOTSCAN low). More specifically, if the readout time, t the time the controller waits for the first External Sync pulse, plus t exposure time, plus t equal t

. If an External Sync pulse is detected during each read, frames will follow one

the shutter compensation time, then the actual exposure time will

, the readout time (marked by

, is greater than the sum of tw1,

, the programmed

exp

another as rapidly as possible as shown in Figure 22. In these figures, Shutter indicates

the programmed exposure time. If a shutter were present and active, it would also be the actual exposure time.

Prior to the first readout, clean cycles are performed on the array. When the software issues a Start Acquisition command, the first readout is generated in hardware and the rapid data transfer from the exposure half of the array to the storage half of the array occurs (marking the beginning of the first exposure). The initial data read are discarded because they are not meaningful. The first exposure continues until the next data transfer, which occurs at the beginning of the next readout, 50 ns after the first readout ends. The data acquired during the first exposure is then read out. This pattern continues for the duration of the experiment so that, during each frame, the data acquired during the previous frame is read out.

exp

Shutter

NOTSCAN

External Sync

(negative polarity shown)

cleans

actual exposure time

acquisition

50ns min.pulse between frames

Figure 22. Frame Transfer where t

+ t

+ tc < tR

exp

Figure 23 shows the case where the programmed storage time is greater than the time required to read out the storage half of the array, that is, where t

+ t

+ tc > tR. In this

exp

case, the programmed exposure time will dominate in determining the actual exposure time. In the situation depicted in Figure 23, the External Sync pulse arrives during the readout. As always, the External Sync pulse must be detected before the next readout can occur. However, there is no requirement as to when it must be applied or even that it be periodic. The timing of the External Sync pulse is entirely at the user’s discretion. In Figure 24, the External Sync pulse is shown arriving after the read. Detection of the External Sync pulse enables a new readout to occur on completion t

+ tc.

exp

Chapter 5 Timing Modes 59

exp

Shutter

actual exposure time

NOTSCAN

External Sync

(negative polarity shown)

NOTSCAN

External Sync

(negative polarity shown)

Interline Operation

Shutter

cleans

acquisition

Figure 23. Frame Transfer where t

exp

actual exposure time

cleans

acquisition

+ t

+ tc > tR

exp

Figure 24. Frame Transfer where Pulse arrives after Readout

Operating Modes

It is important to note that an interline chip can operate in either of two operating modes, overlapped or non-overlapped. The operating mode is always overlapped unless the exposure time is shorter than the readout time, in which case non-overlapped operation is automatically selected by the controlling software. Because overlapped operation is faster, to achieve the fastest possible operation, it is generally preferable to operate overlapped if possible. Thus there may be situations where increasing the exposure time slightly will cause the camera to switch from non-overlapped to overlapped operation. When this happens, the video may blank for a moment as the unit is reprogrammed, and then reappear with approximately double the frame rate that was available when it was operating non-overlapped. Detailed discussions of how the interline camera works and the implications for operation follow.

As stated before, there are two basic operating modes, overlapped and non-overlapped:

•

Overlapped: When the camera is operated in the overlapped mode, readout

begins at the end of the exposure time and a new exposure is initiated immediately. This mode allows the fastest possible speed. And, because the charge only has to transfer to the adjacent row, there is no smearing.

•

Non-overlapped: This operation mode is automatically selected by the

controlling software when the exposure time is less than the readout time. In non-overlapped operation, the image is transferred to the storage cells at the end

60 MicroMAX System User Manual Version 6.B

of the exposure time and no further accumulation occurs (the imaging cells are switched off). The accumulated charge on each storage cell is transferred out of the CCD array, amplified, and sent to the controller as an analog signal, where it is digitized prior to transfer to the computer.

Timing Options in Overlapped Readout Mode

Interline CCD arrays have columns of imaging cells alternating with columns of storage cells. During readout, the charge stored in the photo-sensitive imaging cells move only one row to the adjacent storage cells. From there they move downwards to the readout register and from there to the output node. This scheme serves to allow high speeds, no smearing and shutterless operation, a distinct advantage over frame-transfer sensors where the cell contents can be contaminated by the charge in other cells as data is moved across the CCD and under the mask.

There are two timing options available in the overlapped mode, Free Run and External Sync. (None should be the Shutter Type selection if using WinView/32 software and operating without a shutter.) In both Free Run and External Sync operation, the array photosensors see light continuously. The actual exposure time is the time between data transfers from a photo-sensitive imaging cell to the adjacent storage cell, and may be longer than the programmed exposure, t

. Data transfer from the photo-sensitive

exp

imaging cells to the storage cells occurs very quickly at the start of each readout. During the read, the stored data is shifted to the array’s readout register and from there to the output node.

•

In Free Run overlapped mode operation, the imaging cells are exposed for the set

exposure time (t

). Then the data transfer to the storage cells takes place,

exp

marking the start of the read and the beginning of a new exposure.

•

In the External Sync mode, overlapped operation only is provided. The camera

reads out one frame for every External Sync pulse received, providing the frequency of the External Sync pulse does not exceed the maximum rate possible with the system. A sync pulse must be detected before the subsequent readout can occur. If operating without a shutter, the actual exposure time is set by the period of the sync signal. There is one exception.

If the programmed exposure time is less than the readout time in the External Sync mode, then the actual exposure time is simply equal to t (marked by NOTSCAN low). More specifically, if the readout time, t than the sum of t pulse, plus t

exp

, the time the controller waits for the first External Sync

, the programmed exposure time, plus t

the shutter compensation

, the readout time

, is greater

time (zero with None selected as the Shutter type), then the actual exposure time will equal t

. If an External Sync pulse is detected during each read, frames will

follow one another as rapidly as possible as shown in Figure 25. In these figures, Shutter indicates the programmed exposure time. If a shutter were present and active, it would also be the actual exposure time.

Before the first readout, clean cycles are performed on the array. When the software issues a Start Acquisition command, the first exposure begins. Time counting of the programmed Exposure Time begins when the sync pulse arrives at the Ext Sync connector. The exposure ends on completion of the programmed Exposure Time. Then the data acquired during the first exposure is read out while the next frame of data is being acquired. This pattern continues for the

Chapter 5 Timing Modes 61

duration of the experiment so that, during each frame, the data acquired during the previous frame is read out.

exp

Shutter

NOTSCAN

External Sync

(negative polarity shown)

Figure 26 shows the case where the programmed exposure time is greater than the time required to read out the storage half of the array, that is, where t t

+ tc > tR. In this case, the programmed exposure time will dominate in

exp

determining the actual exposure time. In the situation depicted in Figure 26, the External Sync pulse arrives during the readout. As always, the External Sync pulse must be detected before the next readout can occur. However, there is no requirement as to when it must be applied or even that it be periodic. The timing of the External Sync pulse is entirely at the user’s discretion. In Figure 27, the External Sync pulse is shown arriving after the read. Detection of the External Sync pulse enables a new readout to occur on completion t

cleans

actual exposure time

acquisition

50ns min.pulse between frames

Figure 25. Overlapped Mode where t

exp

+ t

+ tc < tR

exp

+ tc.

exp

Shutter

NOTSCAN

External Sync

(negative polarity shown)

Shutter

NOTSCAN

External Sync

(negative polarity shown)

Figure 27. Overlapped Mode where Pulse arrives after Readout

actual exposure time

cleans

acquisition

Figure 26. Overlapped Mode where t

exp

actual exposure time

cleans

acquisition

+ t

+ tc > tR

exp

62 MicroMAX System User Manual Version 6.B

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Chapter 6

Exposure and Readout

Before each image from the CCD array appears on the computer screen, it must first be read, digitized, and transferred to the computer. Figure 28 is a block diagram of the image-signal path.

Incoming photons

Camera

CCD

Preamp

Cable driver

Controller

Up/down integrator

Slow A/D

Digital processor

Interface module

TAXI or USB 2.0

Interface board

RS PCI or USB 2.0

Fast A/D

Video

display

Computer

Display Storage

Figure 28. Block Diagram of Light Path in System

The remainder of this chapter describes the exposure, readout, and digitization of the image. Included are descriptions of binning for imaging applications and the specialized MicroMAX timing modes.

Exposure

Charge coupled devices can be roughly thought of as a two-dimensional grid of individual photodiodes (called pixels), each connected to its own charge storage “well.” Each pixel senses the intensity of light falling on its collection area, and stores a proportional amount of charge in its associated “well”. Once charge accumulates for the specified exposure time, the charge in the image pixels are moved to a different location. Depending on the CCD array type, the pixels are read out to a serial register or shifted under a masked area or into storage cells and then read out to a serial register.

CCD arrays perform three essential functions: photons are transduced to electrons, integrated and stored, and finally read out. CCDs are very compact and rugged.

64 MicroMAX System User Manual Version 6.B

Unintensified, uncoated CCDs can withstand direct exposure to relatively high light levels, magnetic fields and RF radiation. They are easily cooled and can be precisely temperature controlled to within a few tens of millidegrees.

Because CCD arrays, like film and other media, are always sensitive to light, light must not be allowed to fall on the array during readout. Unintensified full-frame CCD cameras like the MicroMAX use a mechanical shutter to prevent light from reaching the CCD during readout. ICCD (intensified) cameras use an image intensifier to gate the light on and off.

The software allows the user to set the length of time the camera is allowed to integrate the incoming light. This is called the exposure time. During each scan, the shutter or intensifier is enabled for the duration of the exposure period, allowing the pixels to register light.

Exposure with an Interline Array

Interline transfer CCDs contain alternate columns of imaging and storage cells that work in pairs. Light impinging on the imaging cells cause a charge buildup. As previously explained, the operating mode is always overlapped unless the exposure time is shorter than the readout time, in which case non-overlapped operation is automatically selected.

Note: The storage cells of an interline array are quite light-insensitive (the ratio of the light sensitivity of the storage cells, which are masked, to the light sensitivity of the imaging cells is ~4000:1). However, even with a rejection ratio of ~4000:1, there may be situations where this may not be sufficient to prevent light leakage from significantly affecting the data. That this is so becomes apparent when the on/off time factors are considered. In an experiment with a very short exposure compared to the readout rate, the ratio of the readout time to the exposure time may easily be of the same order as the rejection ratio of the interline array storage cells. Where this is the case, the signal buildup in the storage cells during the readout time may equal the signal transferred from the imaging cells to the storage cells at the end of the exposure time. The effect of this signal will be to cause data smearing. The only solutions to this problem at this time are to increase the exposure time to where the effect is insignificant, use a shutter, or to use a gated light source.

Exposure with a Mechanical Shutter

For some CCD arrays, the MicroMAX uses a mechanical shutter to control exposure of the CCD. The diagram in Figure 29 shows how the exposure period is measured. The NOTSCAN signal at the

to monitor the exposure and readout cycle (t The value of t

is shutter type dependent, and will be configured automatically for

MicroMAX systems shipped with an internal shutter.

Mechanical Shutter

NOTSCAN

Figure 29. CCD Exposure with Shutter Compensation

BNC on the ST-133 Analog/Control panel can be used

). This signal is also shown in Figure 29.

ClosedOpen

Acquire Readout

exp

Exposure time

Shutter compensation

Chapter 6 Exposure and Readout 65

Note that NOTSCAN is low during readout, high during exposure, and high during shutter compensation time.

Since most shutters behave like an iris, the opening and closing of the shutter will cause the center of the CCD to be exposed slightly longer than the edges. It is important to realize this physical limitation, particularly when using short exposures.

Exposure with an Image Intensifier

Although the standard MicroMAX camera is not intensified, it is possible to connect it to a lens-coupled intensifier. Contact the factory if you are interested in more information about operating an intensified version of the MicroMAX system.

Continuous Exposure (no shuttering)

Unlike video rate CCD cameras, slow scan scientific cameras require a shutter to prevent “smearing” of features during readout or transfer to a masked area or storage cells. Smearing occurs during readout because charge is moved horizontally or vertically across the surface of the CCD while charge continues to accumulate on the array. As the result, the image will be blurred along one direction only.

The fraction of total signal due to smearing is the ratio of the amount of time spent shifting divided by the exposure time between frames. Faster shifting and/or longer exposure times will minimize this effect. Note that while 1% smear is insignificant in an 8-bit camera (256 gray levels), in a 12-bit camera (over 4,000 gray levels) 1% smearing is over 40 counts, enough to obscure faint features in a high dynamic range image.

Full-Frame

For full-frame CCDs, the MicroMAX camera is usually equipped with an integral shutter. If a full-frame MicroMAX is being operated without a shutter, smearing can be avoided by ensuring that no light falls on the CCD during readout. If the light source can be controlled electronically via the NOTSCAN or SHUTTER signal at the

the CCD can be read out in darkness.

BNC,

Frame Transfer

For frame transfer CCDs, image smearing may occur, depending on the exact nature of the experiment. Smearing occurs only if the CCD is illuminated during shifting. In the case of lens-coupled intensified cameras (ICCDs), this effect can be eliminated by using a fast phosphor and gating the intensifier at the same frame rate as the CCD.

Interline

For interline CCDs, image smearing may occur due to a small amount of light leaking through to the storage cells during the readout time. In the case of lens-coupled intensified cameras (ICCDs), this effect can be eliminated by using a fast phosphor and gating the intensifier at the same frame rate as the CCD.

Saturation

When signal levels in some part of the image are very high, charge generated in one pixel may exceed the “well capacity” of the pixel, spilling over into adjacent pixels in a process called “blooming.” In this case a more frequent readout is advisable, with signal averaging to enhance S/N (Signal-to-Noise ratio) accomplished through the software.

66 MicroMAX System User Manual Version 6.B

For signal levels low enough to be readout-noise limited, longer exposure times, and therefore longer signal accumulation in the CCD, will improve the S/N ratio approximately linearly with the length of exposure time. There is, however, a maximum time limit for on-chip averaging, determined by either the saturation of the CCD by the signal or the loss of dynamic range due to the buildup of dark charge in the pixels (see below).

Dark Charge

Dark charge (or dark current) is the thermally induced buildup of charge in the CCD over time. The statistical noise associated with this charge is known as dark noise. Dark charge values vary widely from one CCD array to another and are exponentially temperature dependent. At the typical operating temperature of a round head camera, for example, dark charge is reduced by a factor of ~2 for every 6º reduction in temperature.

With the light into the camera completely blocked, the CCD will collect a dark charge pattern, dependent on the exposure time and camera temperature. The longer the exposure time and the warmer the camera, the larger and less uniform this background will appear. Thus, to minimize dark-charge effects, you should operate with the lowest CCD temperature possible.

Note: Do not be concerned about either the DC level of this background or its shape unless it is very high, i.e., > 1000 counts. What you see is not noise. It is a fully subtractable readout pattern. Each CCD has its own dark charge pattern, unique to that particular device. Simply acquire and save a dark charge “background image” under conditions identical to those used to acquire the “actual” image. Subtracting the background image from the actual image will significantly reduce dark-charge effects.

Chapter 6 Exposure and Readout 67

Array Readout

In this section, a simple 6 × 4 pixel CCD is used to demonstrate how charge is shifted and digitized. As described below, two different types of readout are available. Full frame readout, for full frame CCDs, reads out the entire CCD surface at the same time. Frame transfer operation assumes half of the CCD is for data collection and half of the array is a temporary storage area.

Full Frame

The upper left drawing in Figure 30 represents a CCD after exposure but before the beginning of readout. The capital letters represent different amounts of charge, including both signal and dark charge. This section explains readout at full resolution, where every pixel is digitized separately.

Empty Readout Register Readout Register with charge

from first line.

A1 B1 C1 D1

B1C2C1D2D1

A2A1B2

A4A3B4B3C4C3D4

C5D6D5

A6A5B6

Charge from first cell shifted into Output Node.

A2A1B2B1C2C1D2

A4A3B4B3C4C3D4

A5 B5 C5 D5 A5 B5 C5 D5

A6 B6

Figure 30. Full Frame at Full Resolution

A2 B2 C2 D2

A4A3B4B3C4C3D4

A5 B5 C5 D5

A6 B6

After first line is read out,next line

can be shifted into empty Readout Register.

A2 B2 C2 D2

A4A3B4B3C4C3D4

A6 B6

Readout of the CCD begins with the simultaneous shifting of all pixels one row toward the "shift register", in this case the row at top. The shift register is a single line of pixels along one edge of the CCD, not sensitive to light and used for readout only. Typically the shift register pixels hold twice as much charge as the pixels in the imaging area of the CCD.

After the first row is moved into the shift register, the charge now in the shift register is shifted toward the output node, located at one end of the shift register. As each value is "emptied" into this node it is digitized. Only after all pixels in the first row are digitized

68 MicroMAX System User Manual Version 6.B

is the second row moved into the shift register. The order of shifting in our example is

therefore A1, B1, C1, D1, A2, B2, C2, D2, A3....

After charge is shifted out of each pixel the remaining charge is zero, meaning that the array is immediately ready for the next exposure.

Below are the equations that determine the rate at which the CCD is read out. Tables of values for CCDs supported at the time of the printing of this manual also appear below.

The time needed to take a full frame at full resolution is:

+ t

exp

+ t

(1)

where

is the CCD readout time,

is the exposure time, and

exp

is the shutter compensation time.

The readout time is approximately given by:

= [Nx · Ny · (tsr + tv)] + (Nx · ti) (2)

where

is the smaller dimension of the CCD

is the larger dimension of the CCD

is the time needed to shift one pixel out of the shift register

is the time needed to digitize a pixel

is the time needed to shift one line into the shift register

, the time needed to discard a pixel, appears below and in later equations)

The readout time for a 1024x1024 full-frame CCD array is provided in Table 6 below.

CCD Array 1 MHz Readout Time

MicroMAX:1024B

1.1 sec. for full frame

EEV CCD47-10 1024x1024

Table 6. Approximate Readout Time for the Full-Frame CCD Array

A subsection of the CCD can be read out at full resolution, sometimes dramatically increasing the readout rate while retaining the highest resolution in the region of interest (ROI). To approximate the readout rate of an ROI, in Equation 2 substitute the x and y dimensions of the ROI in place of the dimensions of the full CCD. Some overhead time, however, is required to read out and discard the unwanted pixels.

Chapter 6 Exposure and Readout 69

Frame Transfer

The MicroMAX fully supports frame transfer readout. Operation in this mode is very similar to the operation of video rate cameras. Half of the CCD is exposed continuously, raising the exposure duty cycle to nearly 100%. The other half of the CCD is masked to prevent exposure, and it is here that the image is “stored” until it can be read out. Figure 31 shows the readout of a masked version of our sample 4 × 6 CCD. The shading represents the masked area (masking is on the array).

Charge accumulates in unmasked cells during exposure.

Accumulated charge in exposed cells is quickly transferred under mask.

Charge from cells A1-D1 shifted to serial register. Exposed cells accumulate new charge.

B1C2C1D2D1

A2A1B2

A3 B3 C3 D3

A4 B4 C4 D4

A5 B5 C5 D5

A6 B6

A3 B3 C3 D3

A4 B4 C4 D4

A5 B5 C5 D5

A6 B6

B1C2C1D2D1

A2A1B2

A3 B3 C3 D3

Charges in serial register shift into Output Node, emptying the register so the next line can be transferred in.

B1 C1 D1

A2A1B2

A3 B3 C3 D3

A4 B4 C4 D4

A5 B5 C5 D5

A6 B6

C2 D2

B1C2C1D2D1

A2A1B2

A3 B3 C3 D3

Shifting continues until all masked

data has been shifted into serial register and from there to the Output Node.

C3 D3

A3 B3 C3 D3

A4 B4 C4 D4

A5 B5 C5 D5

A6 B6

All data from first exposure has been shifted out. Second exposure continues. Initial conditions are restored.

Figure 31. Frame Transfer Readout

Only the exposed region collects charge. At the end of the exposure, the charge is quickly shifted into the masked region. Since the shifting is accomplished in a short time, i.e., a few milliseconds, the incident light causes only minimal “smearing” of the signal. While the exposed region continues collecting data, the masked region is read out and digitized. The percentage of smearing can be determined by dividing the time needed to shift all rows from the imaging area by the exposure time. See the equation below.

CCD Array 1 MHz Readout Time

MicroMAX:512BFT

0.35 sec. for full frame

EEV CCD57-10 512 x 512

Table 7. Approximate Readout Time for the Frame-Transfer CCD Array

70 MicroMAX System User Manual Version 6.B

Interline

In this section, a simple 6 × 3 pixel interline CCD is used to demonstrate how charge is shifted and digitized. As described below, two different types of readout, overlapped and non-overlapped can occur. In overlapped operation, each exposure begins while the readout of the previous one is still in progress. In non-overlapped operation (selected automatically if the exposure time is shorter than the readout time) each readout goes to completion before the next exposure begins.

Overlapped Operation Exposure and Readout

Figure 32 illustrates exposure and readout when operating in the overlapped mode. Figure 32 contains four parts, each depicting a later stage in the exposure-readout cycle. Eight columns of cells are shown. Columns 1, 3, and 5 contain imaging cells while columns 2, 4, and 6 contain storage cells. The readout register is shown above the array.

Part 1 of the figure shows the array early in the exposure. The imaging cells contain charge proportional to the amount of light integrated on each of them. The storage cells are empty because no charge has been transferred to them. The arrows between adjacent imaging and storage cells indicate the direction the charge will be shifted when the transfer occurs.

Part 2 of Figure 32 shows the situation early in the readout. The charge in the imaging cells has been transferred to the adjacent storage cells and up-shifting to the readout register has started. Note that a new exposure begins immediately.

Part 3 of Figure 32 shows the transfer to the output node. The lowermost cell in each column is shown empty. Each row of charges is moved in turn into the readout register, and from there to the output node and off of the array for further processing. The process continues until all charges have been completely transferred out of the array. The imaging cells continue accumulating charge throughout the readout process. Integrating in this way while the readout takes place achieves the maximum possible time efficiency.

Part 4 of Figure 32 illustrates the situation at the end of the readout. The storage cells and readout register are empty, but the ongoing accumulation of charge in the imaging cells continues until the end of the programmed exposure.

Chapter 6 Exposure and Readout 71

Empty Readout Register. Exposure has ended and image is being transferred to storage cells.

Image has been shifted to storage cells, first line has been shifted to Readout Register, and second exposure begins.

A1 B1

Charge from first cell has been shifted to the Output Node.

A1 B1

A2 B2

Figure 32. Overlapped Mode Exposure and Readout

After first image is read out,storage cells are

empty. Second exposure continues.

A2 B2

Non-Overlapped Operation Exposure and Readout

Figure 33 illustrates exposure and readout when operating in the non-overlapped mode. Non-overlapped operation occurs automatically any time the exposure time is shorter than the readout time. Figure 33 contains four parts, each depicting a later stage in the exposure-readout cycle.

Part 2 of Figure 33 shows the situation early in the readout cycle. The charge in the imaging cells has been transferred to the adjacent storage cells and up-shifting to the readout register has started. Note that a second exposure doesn’t begin while the readout is in progress.

Part 3 of Figure 33 shows the transfer to the output node. The lowermost cell in each column is shown empty. Each row of charges is moved in turn into the readout register, and from there to the output node and off of the array for further processing. The process continues until all charges have been completely transferred out of the array. The imaging cells are electronically switched off and do not accumulate any charge as the readout takes place. Because this scheme is less time efficient than that used in the overlapped mode, the frame rate may be lower in non-overlapped operation than it is in overlapped operation with the some exposure time settings.

72 MicroMAX System User Manual Version 6.B

Part 4 of Figure 33 illustrates the situation at the end of the readout. Both the imaging and storage cells are empty. In Free Run operation, the imaging cells will be switched back on immediately, allowing charge accumulation to begin. In Ext Sync operation with no PreOpen, they are not switched back on until after the External Sync pulse is detected.

Empty Readout Register. Exposure has ended and image is being transferred to storage cells.

Image has been shifted to storage cells and first line has been shifted to Readout Register.

A1 B1

Charge from first cell has been shifted to the Output Node.

A1 B1

A2 B2

Figure 33. Non-Overlapped Mode Exposure and Readout

A2 B2

After first image are read out, storage cells are

empty. Second exposure begins if in Freerun mode. Otherwise, waits for Ext Sync.

A subsection of the CCD can be read out at full resolution, sometimes increasing the readout rate while retaining the highest resolution in the region of interest (ROI).

Readout Rate for Interline

Below are the equations that determine the rate at which the CCD is read out. Tables of values for CCDs supported at the time of the printing of this manual also appear below.

Assuming the shutter selection is None, the time needed to take a full frame at full resolution in non-overlapped timing mode is:

+ t

(1)

exp

where

is the CCD readout time,

is the exposure time.

exp

Chapter 6 Exposure and Readout 73

The readout time is approximately given by:

= [Nx · Ny · (tsr + tv)] + (Nx · ti) (2)

where

is the smaller dimension of the CCD

is the larger dimension of the CCD.

is the time needed to shift one pixel out of the shift register

is the time needed to digitize a pixel

is the time needed to shift one line into the shift register

CCD Array 1 MHz Readout

MicroMAX:782Y

0.5 sec. for full frame

Sony ICX075 782 x 582

MicroMAX:782YHS

N/A

Sony ICX075 782 x 582

MicroMAX:1300Y

1.43 sec. for full frame

Sony ICX061 1300x1030

MicroMAX:1300YHS

N/A

Sony ICX061 1300x1030

Table 8. Approximate Readout Time for the Interline CCD Arrays

The readout rate in frames per second for the PI 1300 × 1030 interline array running at 1 MHz is shown in Table 9.

Region of Interest Size

Binning

1 × 1

2 x 2

3 × 3

4 × 4

1300 × 1030 400 × 400 200 × 200 100 × 100

0.7 2.6 5.4 9

1.9 5.4 9 14

3.2 7.5 12 17

4.3 9 14 19

Table 9. Readout Rates for PI 1300 × 1030 Array at 1 MHz

A subsection of the CCD can be read out at full resolution, sometimes increasing the readout rate while retaining the highest resolution in the region of interest (ROI).

74 MicroMAX System User Manual Version 6.B

Binning

On-Chip Binning

Binning is the process of adding the data from adjacent pixels together to form a single pixel (sometimes called a super-pixel), and it can be accomplished in either hardware or software. Rectangular groups of pixels of any size may be binned together, subject to some hardware and software limitations.

Hardware binning is performed before the signal is read out by the preamplifier. For signal levels that are readout noise limited this method improves S/N ratio linearly with the number of pixels grouped together. For signals large enough to render the camera photon shot noise limited, the S/N ratio improvement is roughly proportional to the square-root of the number of pixels binned.

Figure 34 shows an example of 2 × 2 binning for a full frame CCD array. Each pixel of the image displayed by the software represents 4 pixels of the array. Rectangular bins of any size are possible

Empty Readout Register. Exposure has ended and image is about to be shifted into the Readout Register.

Charges from two lines in each column have been shifted to Readout Register and added.

A1 B1

++++

A2 B2 C2 D2

C1 D1

A2A1B2

A4A3B4

A6A5B6

Four charges have been shifted to the Output Node and added.

A1 B1

A2 B2

C1 D1

C2 D2

A4A3B4B3C4C3D4

A6A5B6

C2C1D2

C3D4D3

C5D6D5

Figure 34. 2 × 2 Binning for Full Frame CCD

A4A3B4B3C4C3D4

C5D6D5

A6A5B6

After sum of first four charges have been

transferred from Output Node, next four charges are shifted into Output Node and added.

C1 D1

C2 D2

A4A3B4B3C4C3D4

A6A5B6

C5D6D5

Binning also reduces readout time and the burden on computer memory, but at the expense of resolution. Since shift register pixels typically hold only twice as much charge as image pixels, the binning of large sections may result in saturation and “blooming”, or spilling of charge back into the image area.

Chapter 6 Exposure and Readout 75

The readout rate for n × n binning is approximated using a more general version of the full resolution equation. The modified equation is:

(3)

On-Chip Binning for Interline

Binning is the process of adding the data from adjacent cells together, and it can be accomplished in either hardware or software. Rectangular groups of cells of any size may be binned together, subject to some hardware and software limitations.

Hardware binning is performed before the signal is read out by the preamplifier. For signal levels that are readout noise limited this method improves S/N ratio linearly with the number of cells grouped together. For signals large enough to render the camera photon shot noise limited, the S/N ratio improvement is roughly proportional to the square-root of the number of pixels binned.

Figure 35 shows an example of 2 × 2 binning. Each cell of the image displayed by the software represents 4 cells of the CCD array. Rectangular bins of any size are possible.

Empty Readout Register. Exposure has ended and image has been shifted to storage cells.

Charges from two storage cells in each column has been shifted to Readout Register. and added.

A1 B1 C1

A2 B2

Four charges have been shifted to the Output Node and added.

After sum of first four charges have been transferred

from Output Node, next four charges are shifted into Output Node and added.

Figure 35. 2 × 2 Binning for Interline CCD

76 MicroMAX System User Manual Version 6.B

Software Binning

One limitation of hardware binning is that the shift register pixels and the output node are typically only 2-3 times the size of imaging pixels as shown in Table 10. Consequently, if the total charge binned together exceeds the capacity of the shift register or output node, the data will be corrupted.

This restriction strongly limits the number of pixels that may be binned in cases where there is a small signal superimposed on a large background, such as signals with a large fluorescence. Ideally, one would like to bin many pixels to increase the S/N ratio of the weak peaks but this cannot be done because the fluorescence would quickly saturate the CCD.

CCD Array Imaging/Storage

Cells Well Capacity

EEV CCD-37 512 x 512

PID 582 x 782 18 x 103 electrons 40 x 103 electrons 40 x 103 electrons

PID 1030 x 1300 34 x 103 electrons 34 x 103 electrons 65 x 103 electrons

100 x 103 electrons 200 x 103 electrons 400 x 103 electrons

Table 10. Well Capacity for some CCD Arrays

Readout Register

Well Capacity

Output Node

Well Capacity

The solution is to perform the binning in software. Limited hardware binning may be used when reading out the CCD. Software binning allows you to perform additional binning during the data acquisition process, producing a result that represents many more photons than was possible using hardware binning.

Software averaging can improve the S/N ratio by as much as the square root of the number of scans. Unfortunately, with a high number of scans, i.e., above 100, camera 1/f noise may reduce the actual S/N ratio to slightly below this theoretical value. Also, if the light source used is photon-flicker limited rather than photon shot-noise limited, this theoretical signal improvement cannot be fully realized. Again, background subtraction from the raw data is necessary.

This technique is also useful in high light level experiments, where the camera is again photon shot-noise limited. Summing multiple pixels in software corresponds to collecting more photons, and results in a better S/N ratio in the measurement.

Digitization

During readout, an analog signal representing the charge of each pixel (or binned group of pixels) is digitized. The number of bits per pixel is based on both the hardware and the settings programmed into the camera through the software. Depending on the MicroMAX system, single, dual (100 kHz/1 MHz), or multiple digitization rates may be available.

Dual and multiple digitization provide optimum signal-to-noise ratios at all readout speeds. Because the readout noise of CCD arrays increases with the readout rate, it is sometimes necessary to trade off readout speed for high dynamic range. In the most common ST-133 configurations, there will be a 1 MHz conversion speed for the fastest possible data collection and a 100 kHz conversion speed for use where noise performance is the paramount concern. Switching between the conversion speeds is completely under software control for total experiment automation.

Chapter 7 MicroMAX DIF Camera (Double Image Feature)

Supported by WinView/WinSpec Version 2.5 when the communication protocol is TAXI (PCI), this feature is not supported when the protocol is USB 2.0.

Introduction

This chapter describes operation of the MicroMAX DIF system. Both the Controller and a MicroMAX Interline camera must have factory modifications installed for DIF operation. In addition to the internal changes, a camera modified for DIF operation would ordinarily include a mechanical shutter. Execution of the DIF functions is done via the WinView/32 software (v2.2 or higher), which, when controlling a DIF system, provides three timing modes unique to DIF systems.

Basically, a DIF system is one that has been factory modified to allow images to be taken in pairs with very short exposure times (as small as 1 µ s). This capability makes it ideal for use in experiments where the goal is to obtain two fast successive images for the purpose of characterizing a time-differentiated laser-strobed process. LIF and velocity measurements are specific measurements that can be easily performed using the DIF system.

The ability of the interline chip to quickly transfer an image under the masked columns and hold it there makes this method of acquiring images possible. As soon as the first image is acquired, it is shifted under the masked area and held. The second exposure begins and is continuously held in the photodiode region until the mechanical shutter closes. Light entering the camera while waiting for the shutter to close is small compared to that captured during the strobed event and has little effect on the acquired data.

In addition to the Free Run mode, which allows single image acquisitions, three DIF timing modes, IEC (Internal Exposure Control), EEC (External Exposure Control) and ESABI (Electronic Shutter Active Between Images) are provided. Each works basically as follows.

IEC: Allows two successive fast images of equal duration to be acquired, with the

second image acquisition taking place immediately after the first. Acquisition is initiated by applying a single externally derived trigger to the controller's Ext.

Sync connector.

EEC: Allows two successive fast images of differing duration to be acquired, with the

second image acquisition taking place immediately after the first. Acquisition is initiated by applying a single externally derived trigger to the controller's Ext. Sync connector, the same as in IEC operation.

78 MicroMAX System User Manual Version 6.B

ESABI: Allows two fast images of equal duration to be acquired. Unlike the IEC and

EEC modes, in the ESABI mode, two pulses are applied to the Ext. Sync. connector. Each initiates a separate acquisition, allowing the user to set the time between acquisitions by externally adjusting the time between the two applied pulses.

When the data is saved, both images are saved in a single *.spe file. The header is followed by frame 1 and then immediately afterwards by frame 2. This system makes it convenient to later load the images from the file for post-processing analysis.

Notes:

1. The Readout Mode set on the Controller/Camera tab page (Hardware on the

Setup menu) must be set to DIF for DIF operation.

2. In the IEC, EEC or ESABI timing mode, set the Number of Images to 2 and

Accumulations to 1.

3. On the Setup Hardware Cleans/Skips tab page, click the Load Factory Values

button. This step is necessary for proper operation of the interline camera.

4. For most of the MicroMAX DIF cameras, the ESABI timing mode is activated and

deactivated via the application software. If a MicroMAX DIF camera has a switch on its back panel, this switch must be set to the ACTIVE position for operation in the

ESABI timing mode. At all other times it must be set to INACTIVE.

Timing Modes

The timing mode selections provided on the Acquisition Experiment Setup Timing page are different from those in standard systems. The provided timing modes are:

FREERUN (single shot) IEC: Internal Exposure Control (two shot) EEC: External Exposure Control (two shot) ESABI: Electronic Shutter Active Between Images (two shot)

A discussion of each mode follows.

Free Run

The Free Run mode allows the user to capture single images. The exposure time is set on the Experiment Setup Main tab page, the same as in non-DIF systems, with the difference that the exposure time can be as short as one 1 µs (maximum exposure time is

14.3 minutes). It often proves convenient to simply disable the mechanical shutter open in Free Run operation. The shutter requires ~8 ms to open and 8 ms to close. The camera waits until the shutter is completely open before acquiring the image, and in a typical experiment, the second image acquisition will be over long before the shutter closes. Readout doesn’t occur until the shutter closes.

The

such as the laser. As soon as the shutter is completely opened and all of the cleans have been performed,

image. As soon as the first exposure actually begins,

Figure 36. Thus the positive going edge of the

signal output of the controller can be used to trigger external equipment,

goes low to indicate that the camera is ready to capture an

returns high, as shown in

output marks the start of the first

Chapter 7 MicroMAX DIF Camera 79

exposure. In Free Run operation, the time that

remains low will typically be in

the range of 400 to 600 ns.

READY

400 ns

EXPOSURE

Figure 36. Free Run Mode Timing Diagram

Example: Figure 37 shows an experiment where the rising edge of the

is used to trigger a DG-535 Delay Generator, which provides the required delay and triggers a laser source, Q switch, or other device.

Computer DG-535

Camera

Head

Figure 37. Setup using

Controller

READY

Q Switch

to Trigger an Event

signal

Figure 38 illustrates the timing for a typical experiment like that shown in Figure 37.

READY

400 ns

EXPOSURE

To Q Switch

1 µs

2 µs

Figure 38. Timing for Experiment Setup shown in Figure 37

80 MicroMAX System User Manual Version 6.B

Summary of Free Run Timing mode

•

Allows user to capture single images.

•

Requires that the switch, if present on the back of the camera, be set to INACTIVE.

•

Uses Exposure Time set via software Experiment Setup.

•

Exposure time range is 1 µs < Exp. Time < 14.3 minutes

•

Exposure does not occur until the mechanical shutter is completely open and readout

does not begin until the mechanical shutter is completely closed.

•

The mechanical shutter may, however, be disabled open.

•

The

external hardware.

signal on the back of the controller may be used as a trigger to other

goes low when the system is ready to capture an image, then is reset high once exposure begins. In the FREERUN timing mode, this will be a short (400 ns to 600 ns) TTL 0 pulse.

IEC (Internal Exposure Control)

In this mode, a single external trigger applied to Ext Sync initiates two successive image acquisitions of equal duration. The Exposure Time is set in software (Experiment Setup Main tab page and elsewhere) the same as in a standard system and can be as short as 1 µs. On initiating the acquisition (ACQ button or Acquire on the Acquisition menu), the initialization routine runs and the shutter opens. When the shutter is completely open,

applied to Ext Sync. Continuous cleaning takes place until the trigger is applied. When the trigger is sensed, the first exposure begins and the first image is captured (shifted under the masked columns and held there). The exposure for capture of the second image begins. This sequence is illustrated in Figure 39.

If an external trigger is applied before

trigger source could be running continuously at some repetition rate (as long as that rep rate is fairly slow), but capture wouldn’t occur until

comes in, it begins exposure of the first image. The exposure time is that set on the Experiment Setup Main tab page. For example, if the exposure time is set to 5 µs, the first image will be 5 µs. After an additional 5 µs (second exposure), the shutter will begin to close. Even though the shutter takes ~8 ms to close, the presumption is that the strobe will be timed to occur during the 5 µs second exposure time. It would also be possible to strobe and capture while the shutter is in the act of closing. However, that would generally not be advisable because it would introduce non-linearity effects from the closing shutter. It is better to have capture occur during the time allotted for it. Once the shutter is closed, the readout begins. The first image captured is the first one read out.

drops low and remains in that state until an external trigger is

goes low, it will be ignored. Thus the

goes low. Once that trigger

Example 1: An external trigger initiates the imaging process.

the system is ready. Once

is low, an external trigger applied to Ext

goes low when

Sync initiates the double image capture. Figure 39 illustrates the timing for a typical IEC experiment with an exposure time of 5 µ s.

Chapter 7 MicroMAX DIF Camera 81

READY

EXT. SYNC.

Images

200 ns

~200 ns

Image1 Image 2

5 µs

NOTSCAN

Mechanical

Shutter

8 ms

>200 ns

8 ms

Laser Output

Laser 1 Laser 2

Figure 39. Timing Diagram for Typical IEC Measurement

Figure 40 illustrates the interconnections that might be used for such an experiment with two lasers. Figure 41 shows the timing for the two-laser experiment.

Delay Generator

Computer

Controller

A DG535 can run at a fairly slow rep rate or use READY signal as a trigger.

EXT SYNC

Laser 1

(i.e.,DG535)

ABC

Laser 2

Camera

Head

Sample Volume

STOP

Figure 40. Setup for IEC Experiment with Two Lasers

READY

EXT. SYNC.

Images

200 ns

Image 1 Image 2

5 µs 5 µs

NOTSCAN

Mechanical

Shutter

8 ms

>200 ns

8 ms

Laser Output

Laser 1 Laser 2

Figure 41. Timing Diagram for IEC Experiment with Two Lasers

82 MicroMAX System User Manual Version 6.B

Example 2: As shown in Figure 42, the

signal from the controller can be used to trigger the controller by connecting it back into the EXT SYNC connector. At the same time, it can be used to trigger a DG-535.

Computer

EXT SYNC

READY

Camera

Head

Controller

Delay Generator

(i.e.,DG535)

Ext.

Laser 1

Laser 2

Figure 42. Another Hardware Setup for an IEC Measurement

Note: This setup will not work in the EEC mode or the ESABI mode.

Summary of IEC Timing mode

•

Gives the user the ability to capture two images before readout.

•

Requires that the switch, if present on the back of the camera, be set to INACTIVE.

•

The Exposure Time set in software on the Experiment Setup Main tab page becomes

the exposure time of the first image and also the wait before closing the mechanical shutter.

•

An external trigger is required to initiate the imaging process. The

when the system is ready. Once

is low, an external trigger applied to the

goes low

EXT SYNC connector initiates the double image capture.

EEC (External Exposure Control)

Gives the user the ability to capture two images before readout with a different exposure time for each. EEC uses the external trigger to control the exposure time of the first image and the exposure time set in software to control the exposure time of the second image. When the external trigger applied to Ext Sync is detected, the first exposure begins. The end of the trigger marks the end of the first image and the start of the second. After an interval equal to the exposure time set on the Experiment Setup Main page, the shutter closes. As in the IEC mode, the system is receptive to an applied trigger when

goes low. Note that the shutter can be disabled open. With the shutter disabled open, if reading out a full array, the second exposure time would actually last ~1.4 s. If reading out a single strip, the readout time (and hence the second exposure) would be much shorter, on the order of a few hundred microseconds. Generally though, the experiment timing would be set up so that the second strobed event would occur during the second image time as set by the Exposure Time parameter on the Experiment Setup

Main page.

Example: The exposure time for the first image is controlled with the signal applied to

the EXT. SYNC connector. The exposure time for the second image is the exposure time set in software under Experiment Setup. An external trigger supplied by the user is required to initiate the imaging process and control the

Chapter 7 MicroMAX DIF Camera 83

first image exposure time. The controller

signal goes low when the

camera is ready to begin imaging. Figure 43 illustrates an EEC timing example.

READY

200 ns

EXT. SYNC. (A)

Images

NOTSCAN

Mechanical

Shutter

8 ms

Image 1

sync

Figure 43. EEC Timing Example with Exposure Time in Software Set to t

Image 2

exp

8 ms

exp

Summary of EEC Timing mode

•

Enables double image capture under external control.

•

Requires that the switch, if present on the back of the camera, be set to INACTIVE.

•

The width of the pulse applied to Ext Sync sets the exposure time of the first image.

The Exposure Time set in software on the Experiment Setup Main tab page sets the second image time, at the end of which the shutter begins to close.

•

An external trigger is required to initiate the imaging process. The

when the system is ready. Once

is low, an external trigger applied to the

goes low

Ext Sync connector initiates the double image capture.

ESABI (Electronic Shutter Active Between Images)

The last timing mode, ESABI, allows separation time between the two images. This mode gives the user the ability to capture two images and use the interline chip’s electronic shutter feature between images so that no signal is integrated in the time between. The exposure time for both images is the same but they can be separated in time. Each time the camera is ready to receive a trigger,

goes low twice during each ESABI cycle and the controller can be triggered once by a sync pulse applied to Ext Sync each time. Thus two sync pulses are required, one for each image, during each double capture. The programmed Exposure Time as set on the Experiment Setup Main tab page sets the first image time and the time after the start of the second image time when the shutter begins to close. Figure 44 illustrates ESABI mode timing.

Note that charge produced by light impinging on the photosensors during the interval between the two images is discarded and does not affect the second image. The time between the first and second image can be as long as required according to the experimental requirements. This can be particularly useful in fluorescence measurements. By doing captures with different intervals between the two images, the fluorescence decay characteristics can be easily measured.

goes low. Thus

84 MicroMAX System User Manual Version 6.B

READY

EXT. SYNC. (A)

Images

NOTSCAN

Mechanical

Shutter

8 ms

Figure 44. ESABI Timing Example: Image Exposure time = t

Note: The input trigger pulse, t

200 ns

trig

Image 1

exp

, must be shorter than the exposure time t

trig

No Signal

Integration

200 ns

trig

Image 2

exp

set in software

exp

8 ms

Otherwise the second image will occur immediately after the first.

Summary of ESABI Timing mode

•

The exposure time selected in Experiment Setup sets the exposure time of both the

first and second image.

•

Requires that the switch, if present on the back of the camera, be set to INACTIVE.

•

An externally derived trigger edge applied to Ext Sync is required to begin each

image exposure period.

•

Tips and Tricks

Lab Illumination

In DIF measurements, it is necessary to remain mindful of the possibility of laboratory light affecting the images. Because the first image can be timed with precision, laboratory light that reaches the camera would generally not be a problem in the first image, particularly if the capture time is short (few microseconds). The second image, on the other hand, is much more susceptible to degradation from laboratory illumination because, even though the second image time may be set to just a few microseconds, the time to close the shutter, ~8 ms, must be added to that value. Light impinging on the photosensors during that time will be integrated with the second image. Unless the experiment is arranged so that background light can’t reach the camera, or unless the signal is quite bright, the possibility of the second image becoming degraded must be considered. Where this is source of degradation is a problem, the solution may be to sharply reduce the laboratory illumination. It should be noted though, that the signal from many strobed measurements will be sufficiently bright to allow normal laboratory illumination to be maintained.

Background Subtraction

In any of the double imaging modes, a good idea would be to block both of your light sources and go ahead and take two images in the same DIF mode and with the same settings as will be used for the real measurements. That result will be two background images that can later be subtracted from the experimental data images.

goes low when the system is ready to capture each image.

Chapter 7 MicroMAX DIF Camera 85

Background subtraction allows you to automatically subtract any constant background in your signal. This includes both constant offsets caused by the amplifier system in the controller as well as time-dependent (but constant for a fixed integration time) buildup of dark charge. The background subtract equation is:

(Raw image data – Background) = Corrected image data.

When background and flatfield operations are both performed, background subtraction is always performed first.

Flatfield Correction

Flatfield correction allows the user to divide out small nonuniformities in gain from pixel to pixel. Flatfield correction is done before the images are saved to RAM or disk. Directions for doing Flatfield correction are provided in the WinView/32 software manual.

Mask Bleed-Through Correction

As described previously, the first image is stored under the mask while the second image is being acquired. Although the mask is basically opaque (light attenuation is on the order of 4000:1), a small amount of illumination does get through and could influence some measurements. One solution would be to establish a correction file by taking the first image with the light source dark, and the second image with the light source on. Any bleed through the mask during the second image will appear in the first image. This data could then be stored and used later to correct “real” first images in a post-processing math operation.

86 MicroMAX System User Manual Version 6.B

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Chapter 8 TTL Control

Fully supported by WinView/WinSpec Version 2.5 when the communication protocol is TAXI (PCI), this feature is not supported when the protocol is USB 2.0.

Introduction

This connector provides 8 TTL lines in, 8 TTL lines out and an input control line. Figure 45 illustrates the connector and Table 12 lists the signal/pin assignments.

Princeton Instruments WinView/32 software packages incorporate WinX32 Automation, a programming language that can be used to automate performing a variety of data acquisition and data processing functions, including use of the TTL IN/OUT functions. WinX32 Automation can be implemented in programs written in Vision Basic or Visual C++. See the WinX32 documentation for more detailed information.

TTL In

The user controls the 8 TTL Input lines, setting them high (+5 V; TTL 1) or low (0 V; TTL 0). When the lines are read, the combination of highs and lows read defines a decimal number which the computer can use to make a decision and initiate actions as specified in the user’s program. If a TTL IN line is low, its numeric value is 0. If a TTL IN line is high, its numeric value is as follows.

TTL IN Value TTL IN Value

1 1 5 16 2 2 6 32 3 4 7 64 4 8 8 128

This coding allows any decimal value from 0 to 255 to be defined. Thus, as many as 256 different sets of conditions can be specified, at the user’s discretion, using the TTL IN lines. Any unused lines will default to TTL high (+5 V). For example, to define the number three, the user would simply set the lines TTL IN 1 and TTL IN 2 both high (+5 V). It would be necessary to apply TTL low to the remaining six lines because they would otherwise default to TTL high as well.

TTL IN Value TTL IN Value

1 High (1) 5 Low (0) 2 High (2) 6 Low (0) 3 Low (0) 7 Low (0) 4 Low (0) 8 Low (0)

88 MicroMAX System User Manual Version 6.B

Table 11 illustrates this coding for decimal values 0 through 7. Obviously this table could easily be extended to show the coding for values all the way to 255.

Decimal

Equiv.

0 0 0 0 0 0 0 0 0

1 0 0 0 0 0 0 0 1

2 0 0 0 0 0 0 1 0

3 0 0 0 0 0 0 1 1

4 0 0 0 0 0 1 0 0

5 0 0 0 0 0 1 0 1

6 0 0 0 0 0 1 1 0

7 0 0 0 0 0 1 1 1

TTL

IN/OUT 8

1= dec 128

TTL IN/OUT 7 1=dec 64

TTL IN/OUT 6 1=dec 32

TTL

IN/OUT 5

1=dec 16

TTL

IN/OUT 4

1=dec 8

IN/OUT 3

1=dec 4

Table 11. Bit Values with Decimal Equivalents:

1 = High

0 = Low

TTL

IN/OUT 2

1=dec 2

TTL

IN/OUT 1

1=dec 1

Buffered vs. Latched Inputs

In controlling the TTL IN lines, users also have the choice of two input-line states, buffered or latched. In the buffered state, the line levels must remain at the intended levels until they are read. With reference to the preceding example, the high level at TTL IN 1 and TTL IN 2 would have to be maintained until the lines are read. In the latched state, the applied levels continue to be available until read, even if they should change at the TTL In/Out connector.

This control is accomplished using the EN/CLK TTL input (pin 6). If EN/CLK is open or high, buffered operation is established and the levels reported to the macro will be those in effect when the READ is made. With reference to our example, if pin 6 were left unconnected or a TTL high applied, TTL IN 1 and TTL IN 2 would have to be held high until read. If, on the other hand, EN/CLK were made to go low while TTL IN 1 and TTL IN 2 were high, those values would be latched for as long as EN/CLK remained low. The levels actually present at TTL IN 1 and TTL IN 2 could then change without changing the value that would be read by software.

TTL Out

The state of the TTL OUT lines is set from WinView/32. Typically, a program monitoring the experiment sets one or more of the TTL Outputs. Apparatus external to the MicroMAX system interrogates the lines and, on detecting the specified logic levels, takes the action appropriate to the detected condition. The coding is the same as for the input lines. There are eight output lines, each of which can be set low (0) or high (1). The combination of states defines a decimal number as previously described for the TTL IN lines.

Chapter 8 TTL Control 89

Pin # Assignment Pin # Assignment

1 IN 1 14 IN 2

2 IN 3 15 IN 4

3 IN 5 16 IN 6

4 IN 7 17 IN 8

5 GND 18 GND

6 EN/CLK 19 Reserved

7 (future use) 20 GND

8 GND 21 OUT 2

9 OUT 1 22 OUT 4

10 OUT 3 23 OUT 6

11 OUT 5 24 OUT 8

12 OUT 7 25 GND

13 Reserved

Table 12. TTL In/Out Connector Pinout Figure 45. TTL In/Out

TTL Diagnostics Screen

WinView/32 provides a TTL Diagnostics screen (located in WinView/32 under Hardware

Setup|Diagnostics

) that can be used to test and analyze the TTL In/Out lines.

Note: In WinView software versions prior to 1.6, Output Lines 5, 6, 7, and 8 are shown checked in the default state, incorrectly indicating that their default state is logic 1 in the MicroMAX.

Hardware Interface

A cable will be needed to connect the TTL In/Out connector to the experiment. The design will vary widely according to each user’s needs, but a standard 25-pin female type D-subminiature connector will be needed to mate with the TTL In/Out connector at the ST-133. The hardware at the other end of the cable will depend entirely on the user’s requirements. If the individual connections are made using coaxial cable for maximum noise immunity (recommended), the center conductor of the coax should connect to the proper signal pin and the cable shield should connect to the nearest available ground (grounds are conveniently provided at pins 5, 8, 18 and 20). Connector hardware and cables of many different types are widely available and can often be obtained locally, such as at a nearby Radio Shack although the items listed may be appropriate in many situations, they might not meet your specific needs.

Connector

store. A list of possibly useful items follows. Note that,

• 25-pin female type D-subminiature solder type connector (Radio Shack part no 276- 1548B).

• RG/58U coaxial cable.

90 MicroMAX System User Manual Version 6.B

• Shielded Metalized hood (Radio Shack part no 276-1536A).

• BNC connector(s) type UG-88 Male BNC connector (Radio Shack part no 278-103).

Example

Suppose you needed to build a cable to monitor the line TTL OUT 1. One approach would be to build a cable assembly as described in the following paragraphs. This procedure could easily be adapted to other situations.

1. Begin with a 25-pin female type D-subminiature solder type connector (Radio Shack part no 276-1548B). This connector has 25 solder points open on the back.

2. Referring to Figure 45, note that pin 8 = GND and pin 9 = TTL OUT 1.

3. Using coaxial cable type RG/58U (6 feet length), strip out the end and solder the outer sheath to pin 8 (GND) and the inner line to pin 9 (TTL OUT 1). Then apply shielding to the lines to insulate them.

4. Mount the connector in a Shielded Metalized hood (Radio Shack part no 2761536A).

5. Build up the cable (you can use electrical tape) to where the strain relief clamp holds.

6. Connect a BNC connector (UG-88 Male BNC connector) to the free end of the cable following the instructions supplied by Radio Shack on the box (Radio Shack part no 278-103).

7. To use this cable, connect the DB-25 to the TTL In/Out connector on the back of the Controller.

8. To check the cable, start WinView/32 and open the TTL Diagnostics screen (located in WinView under Then click the Output Line 1 box. Next click the OK button to actually set TTL OUT 1 high. Once you set the voltage, it stays until you send a new command.

9. Measure the voltage at the BNC connector with a standard voltmeter (red on the central pin, black on the surrounding shielding). Before clicking OK at the TTL Diagnostics screen you should read 0 V. After clicking OK you should read +5 V.

Note that adding a second length of coaxial cable and another BNC connector would be straightforward. However, as you increase the number of lines to be monitored, it becomes more convenient to consider using a multiple conductor shielded cable rather than individual coaxial cables.

Hardware Setup|Diagnostics). Click the Write radio button.

Chapter 9 System Component Descriptions

MicroMAX Camera

CCD Array: MicroMAX offers a choice of CCD technologies to improve quantum

efficiency (QE) and blue/green sensitivity. Arrays are available in full-frame, interline, and frame-transfer formats. Thinned, back-illuminated devices have a higher QE across the entire visible spectrum and far superior sensitivity in the blue/ green region than front-illuminated CCDs. The MicroMAX combines back-illumination technology with frame-transfer readout to provide high sensitivity with nonshuttered operation. Interlinetransfer CCDs contain alternate columns of imaging and storage cells.

Because the charge on each image pixel never has to transfer more than one row, the transfer can be made very quickly without smearing. By attaching microlenses to an interline-transfer CCD, incident light is directed to the photosensitive areas of the sensor. As a result, lens-on-chip formats dramatically improve the QE in the blue/green region of the spectrum while still allowing fast imaging. Since no shutter is required, high-speed gating and faster focus are possible.

CCD Chamber: The vacuum-sealed CCD chamber protects the CCD from contamination as well as insulates it from the warmer air in the camera body. The inherent low humidity prevents condensation on the cooled surface of the array. The thermal barrier provided by the vacuum isolates the window from the cooled CCD, keeps the window from cooling below the dewpoint, and thereby prevents condensation on the outside of the window.

MicroMAX cameras are normally shipped with a vacuum level of ~10 mTorr or better. Because this vacuum may deteriorate over time due to outgassing of electrical components, round head MicroMAX cameras are designed with a built-in vacuum port that can be used to restore the vacuum to its original level. Instructions for repumping the vacuum are provided in Appendix E.

Window: The camera has one window in the optical path. The high-quality optical quartz window is integral to the vacuum chamber. By having only one window, the MicroMAX camera reduces the chance of image degradation due to multiple reflections, stray light, and interference patterns that may occur with a multiple-window design.

Thermoelectric Cooler: While the CCD accumulates charge, thermal activity releases electrons, generating dark current. Cooling the CCD enhances the low-light sensitivity by reducing thermally generated charge. With forced-air assistance the MicroMAX camera’s thermoelectric cooler is capable of cooling the CCD to -35°C with ±0.04°C stability at temperature lock.

Cooling is accomplished by mounting the CCD on a cold finger, which in turn is seated on a thermoelectric (Peltier-effect) cooler, and then transferring heat through the Peltier stages to the camera body where the heat is then radiated via a fins and removed by

92 MicroMAX System User Manual Version 6.B

forced air. CCD temperature is controlled and monitored by via the host computer and the ST-133 Controller.

Shutter: Rectangular head cameras are available with an internal 25 mm shutter.

A shutter drive signal is available at the Remote shutter connector on the rear of the ST-133 Controller or on the rear of the camera.

Electronics: The camera electronics enclosure contains the preamplifier and array driver board. This design keeps all signal leads to the preamplifier as short as possible and also provides complete RF shielding.

Speed of data acquisition and dynamic range is determined primarily by the A/D converter used (binning on the array is also a factor). MicroMAX cameras are available with 100 kHz (16-bit A/D), 100 kHz /1 MHz (16-bit A/D), 1 MHz (12-bit A/D), or 1 MHz (16-bit A/D). The dual 16-bit digitizers give you the choice of the 100 kHz A/D for the better signal-to-noise ratio or the 1 MHz, 16-bit A/D for increased data acquisition speed.

Connectors: Power, control signals, and data are transmitted between the ST-133 and the MicroMAX camera via the 25-pin D connector located on the rear of the 1 MHz or 100kHz/1 MHz camera. The cables and connectors are keyed so that they cannot be connected incorrectly.

Caution

Lens Mount Housing: At the front of the camera is the lens mount housing, either C-

mount or F-mount. The C-mount employs a standard size thread to make the connection while an F-mount uses a tongue and groove type mechanism to secure the lens or microscope adapter to the camera. The details of the housing will vary depending on the type of mount.

Note: C-mount cameras are shipped with a dust cover lens installed. Although this lens is capable of providing surprisingly good images, its throughput is low and the image quality is not as good as can be obtained with a high-quality camera lens. Users should replace the dust-cover lens with their own high-quality laboratory lens before making measurements.

If you have a camera with a UV scintillator coated CCD, protect it from excessive exposure to UV radiation. This radiation slowly bleaches the scintillator, reducing sensitivity.

Mounting Holes: The round head camera has four ¼″ x 20 UNC threaded holes on the camera body at 90° intervals. These holes are provided for flexibility in mounting the camera to your system optics. The rectangular head camera can be ordered with an optional tripod mount kit.

Fan: Depending on the camera, there may be an internal fan located inside or on the camera's back panel. Its purpose is:

• to remove heat from the Peltier device that cools the CCD array

• to cool the electronics.

An internal Peltier device directly cools the cold finger on which the CCD is mounted. The heat produced by the Peltier device is then removed by the air drawn into the camera by the internal fan and exhausted through the back panel.

Chapter 9 System Component Descriptions 93

The fan is always in operation and air cooling of both the Peltier and the internal electronics takes place continuously. The fan is designed for low-vibration and does not adversely affect the image. For the fan to function properly, free circulation must be maintained between the rear of the camera and the laboratory atmosphere.

Shutter: In imaging applications an adapter is mounted to the camera and then the lens, either C-mount or F-mount, is mounted to the adapter. An F-mount adapter and a C-mount adapter differ not only in their lens-mounting provisions, but also in depth because the focal plane of F-mount lenses is deeper than that of C-mount lenses. Nevertheless, rectangular head cameras can be ordered with an internal 25 mm shutter and the appropriate lens mount adapter already installed.

Shutter Life: Note that shutters are mechanical devices with a finite lifetime, typically on the order of a million cycles, although some individual shutters may last a good deal longer. How long a shutter lasts in terms of experimental time will, of course, be strongly dependent on the operating parameters. High repetition rates and short exposure times will rapidly increase the number of shutter cycles and decrease the time when the shutter will have to be replaced. Possible shutter problems include complete failure, in which the shutter no longer operates at all, or the shutter may stick open or closed causing overexposed or smeared images. It may even happen that one leaf of the shutter will break and no longer actuate.

WARNING

Shutter replacement is usually done at the factory. If you find that the shutter on your camera is malfunctioning, contact the factory to arrange for a shutter-replacement repair.

Disconnecting or connecting the shutter cable to the camera while the controller is on can destroy the shutter or the shutter drive circuitry. Always power off the controller before adjusting the shutter cable.

94 MicroMAX System User Manual Version 6.B

ST-133 Controller

Electronics: The Model ST-133 is a compact, high

performance CCD Camera Controller for operation with Princeton Instruments cameras. Designed for high speed and high performance image acquisition, the ST-133 offers data transfer at speeds up to 5 megapixel per second, standard video output for focusing and alignment. A variety of A/D converters are available to meet different speed and resolution requirements.

In addition to containing the power supply, the controller contains the analog and digital electronics, scan control and exposure timing hardware, and controller I/O connectors, all mounted on useraccessible plug-in modules. This highly modularized design gives flexibility and allows for convenient servicing.

POWER Switch and Indicator: The power

Figure 46. Controller Front Panel

switch location and characteristics depend on the version of ST-133 Controller that was shipped with your system. In some versions, the power switch (located on the front panel as shown in Figure 46) has an integral indicator LED that lights whenever the ST-133 is powered. In other versions, the power switch is located on the back of the ST-133 and does not include an indicator LED.

WARNING

Rear Panel Connectors: There are three controller board slots. Two are occupied by

the plug-in cards that provide various controller functions. The third, covered with a blank panel, is reserved for future development. The left-most plug-in card is the Analog/Control module. Adjacent to it is the Interface Control module. Both modules align with top and bottom tracks and mate with a passive back-plane via a 64-pin DIN connector. For proper operation, the location of the modules should not be changed. Each board is secured by two screws that also ground each module’s front panel. Removing and inserting boards is described in Chapter 10, pages 113-114.

To minimize the risk of equipment damage, a module should never be removed or installed when the system is powered.

The Analog/Control Module, which should always be located in the left-most slot,

provides the following functions.

• Pixel A/D conversion • Timing and synchronization of readouts

• CCD scan control • Temperature control

• Exposure control • Video output control

The Interface Control Module, which should always be located in the center slot,

provides the following functions.

• TTL In/Out Programmable Interface

• Communications Control (TAXI or USB 2.0 protocol)

Chapter 9 System Component Descriptions 95

Always turn the power off at the Controller before connecting or disconnecting any cable

WARNING

that interconnects the camera and controller or serious damage to the CCD may result. This damage is NOT covered by the manufacturer’s warranty.

TTL IN/OUT

USB 2.0

VIDEO

TEMP

LOCK

EXT SYNC

SCAN

SHUTTER CONTROL

AUX

TTL

IN/OUT

READY

DETECTOR

ZERO

AUX

SERIAL COM

REMOTE

50-60Hz FUSES: LEFT: RIGHT:

100 - 120V ~ 0.75A - T 2.50A - T 220 - 240 V ~ 0.30A - T 1.25 A - T

SETTING

120Vac

USB 2.0 TAXI

Interface Control Module

Figure 47. ST-133 Rear Panel

96 MicroMAX System User Manual Version 6.B

The descriptions of the rear panel connectors are keyed to the accompanying figure. Depending on your system, either the TAXI or the USB 2.0 Interface Control Module will be installed in the second from the left slot (as you face the rear of the ST-133). In Figure 47, the TAXI module is shown in that position.

# Feature

1. Temperature Lock LED: Indicates that the temperature control loop has locked and that the temperature of the CCD array will be stable to within ± 0.05°C.

2. Video/Aux Output: Composite video output is provided at this connector; if labeled Aux, this output is reserved for future use. The Video output amplitude is 1 V pk-pk and the source impedance is 75 Ω. Either RS-170 (EIA) or CCIR standard video can be provided and must be specified when the system is ordered. The video should be connected to the monitor via 75 Ω coaxial cable and it must be terminated into 75 Ω.

Note that video output is not currently supported under USB 2.0.

3. External Sync Input: TTL input that has a 10 kΩ pullup resistor. Allows data acquisition and readout to be synchronized with external events. Through software, positive or negative (default) triggering can be selected.

6. Zero Adjustment: (1 MHz and 100kHz/1 MHz systems) Control the offset values of the Fast

Output WinView/32 (ver. 2.4 and higher) software selectable NOTSCAN or SHUTTER signal. Default is SHUTTER. NOTSCAN reports when the controller is finished reading out the CCD array. NOTSCAN is high when the CCD array is not being scanned, then drops low when readout begins, returning to high when the process is finished. The second signal, SHUTTER, reports when the shutter is opened and can be used to synchronize external shutters. SHUTTER is low when the shutter is closed and goes high when the shutter is activated, dropping low again after the shutter closes. See Figure 48 for timing diagram.

Output: Initially HIGH. After a Start Acquisition command, this output changes state on completion of the array cleaning cycles that precede the first exposure. Initially high, it goes low to mark the beginning of the first exposure. In free run operation it remains low until the system is halted. If a specific number of frames have been programmed, it remains low until all have been taken, then returns high.

(F) and Slow (S) A/D converters; if potentiometers are not present, bias may be softwaresettable. Preadjusted at factory. The offset is a voltage that is added to the signal to bring the A/D output to a non-zero value, typically 50-100 counts. This offset value ensures that all the true variation in the signal can really be seen and not lost below the A/D “0” value. Since the offset is added to the signal, these counts only minimally reduce the range of the signal from 4095 to a value in the range of 50-100 counts lower. Adjusting a potentiometer clockwise increases the counts while rotating it counterclockwise decreases the counts. If potentiometers are not present, bias may be software-settable.

CAUTION: Do not adjust the offset values to zero, or some low-level data will be missed.

7. Detector Connector: (1MHz and 1 MHz/100kHz systems) Transmits control information to the camera and receives data back from the camera via the Detector-Controller cable.

8. TTL In/Out: User-programmable interface with eight input bits and eight output bits that

can be written to or polled for additional control or functionality. Output is not currently supported under USB 2.0. See Chapter 8.

9. AUX Output: Reserved for future use.

Chapter 9 System Component Descriptions 97

# Feature

10. Serial COM Connector: Provides two-way serial communication between the controller and the host computer. Uses TAXI protocol. Contact the factory if an application requires use of the optional fiber-optic data link to increase the maximum allowable distance between the camera and the computer.

11. Fan: Cools the controller electronics. Runs continuously when the controller is turned on. Do not block the side vents or the fan exhaust port.

12. Shutter Setting Selector: Sets the shutter hold voltage. Dial is correctly set at the factory for the camera’s internal shutter if one is present. Refer to Table 13 for setting selection.

13. Remote Shutter Connector: Provides shutter-hold pulses for a 25 mm Princeton Instruments-supplied external shutter (typically an entrance slit shutter).

WARNING:

To avoid shock hazard, the Controller power should be OFF when connecting or disconnecting a remote shutter.

WARNING: If the camera has an internal shutter, then the Shutter Power connector should not be used to drive a second external shutter. This configuration will result in underpowering both shutters and may cause damage to the system In a system which requires both

an internal and an external shutter, use the Shutter signal (provided at the

connector when selected by an internal jumper or by software parameter selection) to control the external shutter. Suitable driver electronics will additionally be required. Contact the factory Technical Support Dept. for information.

14. Fuse/Voltage Label: Displays the controller’s power and fuse requirements. This label may appear below the power module.

15. Power Input Module: Contains the powercord socket and two fuses. Depending on the ST-133 version, the power switch may be located directly above the power module.

16. USB 2.0 Connector: Provides two-way serial communication between the controller and the host computer. Uses USB 2.0 protocol. .

Dangerous live potentials are present at the Remote Shutter Power connector.

WARNING: Dangerous live potentials are present at the Remote Shutter Power

connector. To avoid shock hazard, the Controller power should be OFF when connecting or disconnecting a remote shutter.

Shutter Setting* Shutter Type

1 25 mm Princeton Instruments supplied External shutter

(typically an Entrance slit shutter)

2 25 mm Princeton Instruments Internal shutter

4 35 mm Princeton Instruments Internal shutter (requires 70

V Shutter option), supplied with rectangular head camera having 1300 × 1340 CCD

5 40 mm Princeton Instruments Internal shutter

* Shutter settings 0, 3, and 6-9 are unused and are reserved for future use.

Table 13. ST-133 Shutter Drive Selection

98 MicroMAX System User Manual Version 6.B

WARNING

Selecting the wrong shutter setting will result in improper functioning of the shutter and may cause premature shutter failure.

exp

Shutter

NOTSCAN

= Exposure Time

exp

= Readout Time

= Shutter Compensation Time

Shutter Type Compensation Time

NONE 200 nsec

Electronic 6.0 msec

Remote (Roper Scientific 23 mm, External, 8.0 msec typically a slit shutter)

Small (Roper Scientific 25 mm, Internal) 8.0 msec

Large (Roper Scientific 35/40 mm, External) 28.0 msec

Figure 48. Shutter Compensation Times

Chapter 9 System Component Descriptions 99

Cables

Detector-Controller: 1 MHz or 100kHz/1MHz systems. The standard 10' cable (6050-0321) has DB-25 Male connectors with slide-latch locking hardware. This cable interconnects the Detector connector on the rear of the ST-133 with the Detector connector on the back of the MicroMAX camera. The DetectorController cable is also available in 6', 15', 20', and 30' lengths.

Interface Cable:

cable will be shipped.

TAXI:

connectors with screw-down locking hardware. The TAXI (Serial communication) cable interconnects the "Serial Com" connector on the rear of the ST-133 with the PCI card installed in the host computer. In addition to the standard length, this cable is available in 10', 50', 100', and 165' lengths. Also available are fiber optic adapters with fiber optic cables in 100, 300, and 1000 meter lengths.

Depending on the system configuration, either a TAXI or a USB

The standard 25' (7.6 m) cable (6050-0148-CE) has DB-9 Male

Interface Card

PCI Card:

protocol rather than USB 2.0. The PCI card plugs-into the host computer's motherboard and provides the serial communication interface between the host computer and the ST-133. Through WinView/32, the card can be used in either

Speed PCI

interrupt-driven and can give higher performance in some situations. allows data transfer to be controlled by a polling timer.

USB 2.0 Card:

USB 2.0 protocol rather the TAXI protocol and the computer does not have native USB 2.0 support. The USB 2.0 card plugs-into the host computer's motherboard and provides the communication interface between the host computer and the ST-133. The USB 2.0 PCI card (70USB90011) by Orange Micro is recommended for desktop computers; the SIIG, Inc. USB 2.0 PC Card, Model US2246 is recommended for laptop computers. See www.orangemicro.com more information.

USB 2.0:

that interconnect the "USB 2.0" connector on the rear of the ST-133 with a USB card installed in the host computer.

or PCI(Timer) mode. High Speed PCI allows data transfer to be

The standard 16.4' (5 m) cable (6050-0494) has USB connectors

This interface card is required when the system interface uses the TAXI

High

PCI(Timer)

This interface card is required when the system interface uses the

or www.siig.com, respectively, for

Application Software

The Princeton Instruments WinView/32 software package provides comprehensive image acquisition, display, processing, and archiving functions so you can perform complete data acquisition and analysis without having to rely upon third-party software. WinView/32 provides reliable control over all Roper Scientific detectors, regardless of array format and architecture, via an exclusive universal programming interface (PVCAM record functions to permit easy user customization of any function or sequence.

). WinView/32 also features snap-ins and macro

100 MicroMAX System User Manual Version 6.B

PVCAM is the standard software interface for cooled CCD cameras from Roper Scientific. It is a library of functions that can be used to control and acquire data from the camera when a custom application is being written. For example, in the case of Windows, PVCAM is a dynamic link library (DLL). Also, it should be understood that PVCAM is solely for camera control and image acquisition, not for image processing. PVCAM places acquired images into a buffer, where they can then be manipulated using either custom written code or by extensions to other commercially available image processing packages.

User Manuals

MicroMAX System User Manual: This manual describes how to install and

use the MicroMAX system components.

WinView/32 User Manual: This manual describes how to install and use the WinView/32 application program. A PDF version of this manual is provided on the installation CD. Additional information is available in the program's on-line help.

Princeton Instruments Activity Tracker, MICROMAX SYSTEM User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Table of Contents

Chapter 1 Introduction

Introduction

MicroMAX System Components

About this Manual

Environmental Conditions

Grounding and Safety

Precautions

Repairs

Cleaning

Princeton Instruments Customer Service

Chapter 2 Installation Overview

Chapter 3 System Setup

Unpacking the System

Checking the Equipment and Parts Inventory

System Requirements

Verifying Controller Voltage Setting

Installing the Application Software

Setting up a PCI Interface

Setting up a USB 2.0 Interface

Mounting the Camera

Selecting the Shutter Setting

Connecting the Interface (Controller-Computer) Cable

Connecting the Detector-Controller Cable

Chapter 4 Operation

Introduction

EMF and Xenon or Hg Arc Lamps

Vacuum

Cooling

Baseline Signal

Analog Gain Control

Imaging Field of View

RS-170 or CCIR Video

USB 2.0 and System On/Off Sequences

First Light (Imaging)

First Light (Spectroscopy)

Chapter 5 Timing Modes

Fast and Safe Speed Modes

Standard Timing Modes

Frame Transfer Operation

Interline Operation

Exposure

Array Readout

Digitization

Introduction

Timing Modes

Tips and Tricks

Chapter 8 TTL Control

Introduction

TTL In

Buffered vs. Latched Inputs

TTL Out

TTL Diagnostics Screen

Hardware Interface

Chapter 9 System Component Descriptions

MicroMAX Camera

ST-133 Controller

Cables

Interface Card

Application Software

User Manuals