Ocean Optics HR4000CG-UV-NIR User Manual

HR4000 and HR4000CG-UV-NIR Series
High-Resolution Fiber Optic Spectrometers

HR4000 / HR4000CG-UV-NIR

Installation and Operation Manual

Document Number 210-00000-000-02-0908

Offices: Ocean Optics, Inc. World Headquarters

830 Douglas Ave., Dunedin, FL, USA 34698

Phone [phone]
Fax [phone]

8 a.m.– 8 p.m. (Mon-Thu), 8 a.m.– 6 p.m. (Fri) EST

E-mail: [e-mail] (General sales inquiries)

[e-mail] (Questions about orders)
[e-mail] (Technical support)

Additional
Offices:

Ocean Optics Asia

666 Gubei Road, Kirin Tower, Suite 601B, Changning District,
Shanghai, PRC. 200336

Phone [phone]

Fax [phone]
E-Mail [e-mail]

Ocean Optics Europe

Sales and Support Center
Geograaf 24, 6921 EW DUIVEN, The Netherlands

Phone [phone]

Fax [phone]
E-Mail

[e-mail]

Regional Headquarters
Maybachstrasse 11
73760 Ostfildern

Phone [phone]
Fax [phone]
E-Mail [e-mail]

Copyright © 2001-2008 Ocean Optics, Inc.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, by any means, electronic,
mechanical, photocopying, recording, or otherwise, without written permission from Ocean Optics, Inc.
This manual is sold as part of an order and subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or
otherwise circulated without the prior consent of Ocean Optics, Inc. in any form of binding or cover other than that in which it is published.

Trademarks

All products and services herein are the trademarks, service marks, registered trademarks or registered service marks of their respective owners.

Limit of Liability

Every effort has been made to make this manual as complete and as accurate as possible, but no warranty or fitness is implied. The information
provided is on an “as is” basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity with respect to any loss or
damages arising from the information contained in this manual.

Table of Contents

About This Manual .......................................................................................................... iv

Document Purpose and Intended Audience.............................................................................. iv

What’s New in this Document ................................................................................................... iv

Document Summary..................................................................................................................iv

Product-Related Documentation ............................................................................................... iv

Upgrades......................................................................................................................... v

Service ............................................................................................................................ v

Chapter 1: Introduction ......................................................................1

Product Overview ............................................................................................................ 1

System Requirements ..................................................................................................... 2

EEPROM Utilization .................................................................................................................. 2

About Ocean Optics Software ................................................................................................... 2

Sampling System Overview....................................................................................................... 2

How Sampling Works............................................................................................................ 2

Modular Sampling Accessories............................................................................................. 3

Interface Options ............................................................................................................. 3

Breakout Box ............................................................................................................................. 3

Shipment Components.................................................................................................... 4

Other Accessories Available ........................................................................................... 5

Chapter 2: Installing the HR4000 .......................................................7

Overview ......................................................................................................................... 7

HR4000 Installation ......................................................................................................... 7

USB Mode ................................................................................................................................. 7

Serial Port Mode........................................................................................................................ 8

Configuring the HR4000.................................................................................................. 8

Configuring the HR4000 in SpectraSuite ..................................................................................8

Configuring the HR4000 in OOIBase32 .................................................................................... 8

Connect Spectroscopic Accessories ............................................................................... 8

External Triggering Options............................................................................................. 9

210-00000-000-02-0908 i

Table of Contents

Chapter 3: Troubleshooting ...............................................................10

Overview ......................................................................................................................... 10

HR4000 Connected to Computer Prior to Operating Software Installation ..................... 10

Windows Operating Systems ....................................................................................................10

Remove the Unknown Device from Windows Device Manager ........................................... 10

Remove Improperly Installed Files........................................................................................ 11

Mac Operating Systems ............................................................................................................ 11

Linux Operating Systems ..........................................................................................................12

Older Version of OOIBase32 Installed ............................................................................ 12

Appendix A: Calibrating the Wavelength of the HR4000.................13

Overview ......................................................................................................................... 13

About Wavelength Calibration......................................................................................... 13

Calibrating the Spectrometer........................................................................................... 14

Preparing for Calibration............................................................................................................ 14

Calibrating the Wavelength of the Spectrometer ...................................................................... 14

Saving the New Calibration Coefficients: USB Mode ...................................................... 16

Saving the New Calibration Coefficients: Serial Mode .................................................... 17

Appendix B: Specifications................................................................19

Overview ......................................................................................................................... 19

How the HR4000 Works.................................................................................................. 19

HR4000 Components Table...................................................................................................... 20

HR4000 Specifications .................................................................................................... 21

CCD Detector Specifications .....................................................................................................21

HR4000 Spectrometer............................................................................................................... 21

System Compatibility....................................................................................................... 22

Compatibility for Desktop or Notebook PCs .............................................................................. 22

Compatibility for Handheld PCs ................................................................................................ 23

30-Pin Accessory Connector Pinout................................................................................ 23

30-Pin Accessory Connector Pinout Diagram........................................................................... 23

30-Pin Accessory Connector – Pin Definitions and Descriptions.............................................. 24

30-Pin J2 Accessory Connector - Part Numbers ...................................................................... 25

HR4000 15-Pin Accessory Cable Pinout......................................................................... 26

ii 210-00000-000-02-0908

Table of Contents

Appendix C: HR4000CG-UV-NIR Spectrometer................................27

HR4000CG-UV-NIR Features ......................................................................................... 27

New HC-1 Landis Composite Grating ....................................................................................... 27

Variable Order-Sorting Filter...................................................................................................... 27

HR4000CG-UV-NIR Spectrometer Specifications........................................................... 27

Index.....................................................................................................29

210-00000-000-02-0908 iii

About This Manual

Document Purpose and Intended Audience

This document provides the user of HR4000 Series Spectrometers (both HR4000 and
HR4000CG-UV-NIR) with instructions for setting up, calibrating and performing experiments with their
spectrometer.

What’s New in this Document

This version of the HR4000 and HR4000CG-UV-NIR Series High-Resolution Fiber Optic Spectrometers
HR4000 / HR4000CG-UV-NIR Installation and Operation Manual updates the integration time

specification and adds service information.

Document Summary

Chapter Description

Chapter 1: Introduction

Chapter 2: Installing the HR4000

Chapter 3: Troubleshooting

Appendix A: Calibrating the

Wavelength of the HR4000

Appendix B: Specifications

Appendix C: HR4000CG-UV-NIR

Spectrometer

Contains descriptive information about the HR4000
Spectrometer and how sampling works. It also provides a list
of system requirements, interface options, and shipment
components.

Provides installation and configuration instructions.

Contains recommended steps to isolate and correct common
problems.

Provides instructions for calibrating the HR4000 Series
Spectrometer.

Contains technical specifications and connector pinouts for the
HR4000 Series Spectrometer.

Contains features and specifications unique to the
HR4000CG-UV-NIR Spectrometer.

Product-Related Documentation

You can access documentation for Ocean Optics products by visiting our website at

http://www.oceanoptics.com. Select Technical → Operating Instructions, then choose the appropriate

document from the available drop-down lists. Or, use the Search by Model Number field at the bottom
of the web page.

210-00000-000-02-0908 iv

About This Manual

• Detailed instructions for SpectraSuite Spectrometer Operating Software are located at:

http://www.oceanoptics.com/technical/SpectraSuite.pdf.

• Detailed instructions for OOIBase32 Operating Software are located at:

http://www.oceanoptics.com/technical/ooibase32.pdf.

•

• Detailed instructions for the Breakout Box are located at:

http://www.oceanoptics.com/technical/HR4_breakout.pdf.

• Detailed instructions for external triggering are located at:

http://www.oceanoptics.com/technical/External-Triggering.pdf

Engineering-level documentation is located on our website at Technical → Engineering Docs.

You can also access operating instructions for Ocean Optics products from the Software and Technical
Resources CD that ships with the product.

.

Upgrades

Occasionally, you may find that you need Ocean Optics to make a change or an upgrade to your system.
To facilitate these changes, you must first contact Customer Support and obtain a Return Merchandise
Authorization (RMA) number. Please contact Ocean Optics for specific instructions when returning a
product.

Service

Our Total Technical Service protection plans protect your spectrometer for one year for any contingency -

- no matter what the circumstances, including total loss. Under these plans, Ocean Optics will repair or
replace your instrument with no deductible or any other out-of-pocket expense required from you. HR
service plans include the following:

• TTS-HR: Protects your Ocean Optics HR200/2000+/4000 spectrometer for any contingency for

1 year. Provides for full spectrometer replacement, if necessary. Limited to 1 full replacement per

year.

• TTS-HR-ES: This special plan for Ocean Optics HR2000/4000 spectrometers not previously

covered protects for any contingency for 1 year. Provides for full spectrometer replacement, if

necessary. Limited to 1 full replacement per year. This coverage starts 30 days after purchasing

the plan.

In addition, we also have the WAVECAL-USB spectrometer maintenance and calibration
service available to recalibrate, clean and perform any adjustments necessary on your
spectrometer.
Contact us to learn more about these great service plans.

210-00000-000-02-0908 v

About This Manual

vi 210-00000-000-02-0908

Chapter 1

Introduction

Product Overview

The HR4000 High-Resolution Miniature Fiber Optic Spectrometer provides optical resolution as good as

0.025 nm (FWHM). The HR4000 is responsive from 200-1100 nm, but the specific range and resolution
depends on your grating and entrance slit selections.

The HR4000 is perfect for applications where high resolution is necessary, such as absorbance of gases or
atomic emission lines (for solution chemistry or for color measurements, the USB4000 is more
appropriate).

Data programmed into a memory chip on each HR4000 includes wavelength calibration coefficients,
linearity coefficients, and the serial number unique to each spectrometer. Our spectrometer operating
software simply reads these values from the spectrometer — a feature that enables hot swapping of
spectrometers among computers.

The HR4000 Spectrometer connects to a notebook or desktop computer via USB port or serial port. When
connected to the USB port of a computer, the HR4000 draws power from the host computer, eliminating
the need for an external power supply.

Ocean Optics HR4000 High-Resolution Fiber Optic Spectrometer

210-00000-000-02-0908 1

1: Introduction

System Requirements

You can use the HR4000’s USB connectivity with any computer that meets the requirements for the
spectrometer operating software being used (Windows 98/Me/2000/XP, Mac OS X and Linux). See

About Ocean Optics Software.

Alternately, the HR4000 has a serial port for connecting to PCs, PLCs, and other devices with a Windows
32-bit operating system that support the RS-232 communication protocol. However, this connection
method requires an external power supply to power the HR4000, the Breakout Box, and a serial cable.

EEPROM Utilization

An EEPROM memory chip in each HR4000 contains wavelength calibration coefficients, linearity
coefficients, and a serial number unique to each individual spectrometer. The OOIBase32 software
application reads these values directly from the spectrometer, enabling the ability to “hot-swap”
spectrometers between PCs without entering the spectrometer coefficients manually on each PC.

About Ocean Optics Software

SpectraSuite is the latest generation of operating software for all Ocean Optics spectrometers. It is a
completely modular, Java-based spectroscopy software platform that operates on Windows, Macintosh
and Linux operating systems. The software can control any Ocean Optics USB spectrometer and device,
as well as any other manufacturer’s USB instrumentation using the appropriate drivers.

SpectraSuite is a user-customizable, advanced acquisition and display program that provides a real-time
interface to a variety of signal-processing functions. With SpectraSuite, you have the ability to perform
spectroscopic measurements (such as absorbance, reflectance, and emission), control all system
parameters, collect and display data in real time, and perform reference monitoring and time acquisition
experiments. Consult the SpectraSuite manual for hardware requirements when using SpectraSuite (see

Product-Related Documentation).

OOIBase32 software has been discontinued, but still functions with the HR4000 Spectrometer. Consult
the OOIBase32 manual for hardware requirements when using OOIBase32 (see

Documentation

).

Product-Related

Sampling System Overview

How Sampling Works

Ocean Optics components function in a sampling system as follows:

1. The user stores reference and dark measurements to correct for instrument response variables.

2. The light from the light source transmits through an optical fiber to the sample.

3. The light interacts with the sample.

4. Another optical fiber collects and transmits the result of the interaction to the spectrometer.

5. The spectrometer measures the amount of light and transforms the data collected by the

spectrometer into digital information.

2 210-00000-000-02-0908

1: Introduction

6. The spectrometer passes the sample information to OOI software.

7. OOI software compares the sample to the reference measurement and displays processed spectral

information.

Modular Sampling Accessories

Ocean Optics offers a complete line of spectroscopic accessories for use with the HR4000. Most of our
spectroscopic accessories have SMA connectors for application flexibility. Accordingly, changing the
sampling system components is as easy as unscrewing a connector and replacing an accessory.

Interface Options

The HR4000 has both USB and serial port connectors (with the use of an adapter), enabling you to
connect the spectrometer to a desktop or notebook computer via a USB port or to a desktop, notebook, or
to handheld PC via a serial port. However, you must create custom software if using the serial port.
SpectraSuite software is available if you are connecting via the USB port.

Computer
Interface

Computer via
USB Port

Desktop or
Notebook PC
via Serial
Port

Handheld PC
via Serial Port

Operating System Requirements Part Needed Description of Part

SpectraSuite: Windows2000/XPfor PC,
OS X version 10.0 or later for Mac, or
Red Hat 9 or later, Fedora (any
version), Debian 3.1 (Sarge), and SUSE
(9.0 or later) for Linux

OOIBase32: Windows 98/Me/ 2000/XP

Any 32-bit Windows operating system

Windows CE 2.11 or higher

Breakout Box

USB-CBL-1
(included)

USB-ADP-PC
(not included)

USB-ADP-H
(not included)

Cable that connects from USB
port on HR4000 to USB port on
the computer

Adapter block that enables
connection from serial port on
HR4000 to serial port on desktop
or notebook PC; comes with 5
VDC power supply (required
when connecting to serial port)

Adapter block that enables
connection (with standard 9-pin serial
cable) from serial port on HR4000 to
serial port on handheld PC; comes
with 5 VDC power supply (required
when connecting to serial port)

Ocean Optics also offers the Breakout Box (HR4-BREAKOUT), a passive module that separates the
signals from their 30-pin port to an array of standard connectors and headers, enabling easy access to a
variety of features found in Ocean Optics’ HR4000 Spectrometer. In addition to the accessory connector,
the breakout box features a circuit board based on a neutral breadboard pattern that allows custom
circuitry to be prototyped on the board itself.

210-00000-000-02-0908 3

1: Introduction

Note

The HR4000 Breakout Box is compatible with HR4000 Spectrometers with Revision B

or greater. HR4000 Spectrometers with serial numbers beginning with HR4A are not

compatible with the HR4000 Breakout Box.

Shipment Components

The following information and documentation ships with the HR4000 Spectrometer:

 Packing List

The packing list is inside a plastic bag attached to the outside of the shipment box (the invoice

arrives separately). It lists all items in the order, including customized components in the

spectrometer (such as the grating, detector collection lens, and slit). The packing list also includes

the shipping and billing addresses, as well as any items on back order.

 Wavelength Calibration Data Sheet

Each spectrometer is shipped with a Wavelength Calibration Data Sheet that contains information

unique to your spectrometer. Your spectrometer operating software reads this calibration data

from your spectrometer when it interfaces to a computer via the USB port. Any other interface

requires that you manually enter the calibration data in OOIBase32 (select Spectrometer |

Configure | Wavelength Calibration tab). See the OOIBase32 documentation for more

information (refer to

documentation).

Product-Related Documentation for instructions on accessing OOIBase32

Note

Please save the Wavelength Calibration Data Sheet for future reference.

 Software and Technical Resources CD

Each order ships with the Ocean Optics Software and Resources CD. This disc contains software,

operating instructions, and product information for all Ocean Optics software, spectrometers, and

spectroscopic accessories. You need Adobe Acrobat Reader version 6.0 or higher to view these

files. Ocean Optics includes the Adobe Acrobat Reader on the Software and Technical Resources

CD.

With the exception of OOIBase32 Spectrometer Operating Software, all Ocean Optics software

requires a password during the installation process. You can locate passwords for the other

software applications on the back of the Software and Technical Resources CD package.

4 210-00000-000-02-0908

1: Introduction

Other Accessories Available

Visit us at www.OceanOptics.com for a complete list of products available for all of your spectroscopy
needs.

 Fibers
 Light Sources
 Integrated Sampling Systems
 Cuvettes
 Filter Holders
 Lithium Ion Battery Pack
 HR4-BREAKOUT Breakout Box

210-00000-000-02-0908 5

1: Introduction

6 210-00000-000-02-0908

Chapter 2

Installing the HR4000

Overview

You must install the operating software application prior to connecting the HR4000 Spectrometer to the
computer. The Ocean Optics spectrometer operating software installs the drivers required for the HR4000
spectrometer installation. If you do not install the software first, the system will not properly recognize
the HR4000.

If you have already connected the HR4000 to the computer prior to installing the operating software,
consult Chapter 3:

Troubleshooting for information on correcting a corrupt HR4000 installation.

HR4000 Installation

This section contains instructions for connecting the HR4000 via both USB and serial modes.

USB Mode

To connect the HR4000 to a computer via the USB port, the PC must be running a Windows
98/Me/2000/XP, Mac OS X or Linux operating system.

Note

The USB port on a computer can power up to five HR4000 spectrometer channels.

Systems with more than five channels require a powered USB hub.

► Procedure

Follow the steps below to connect the HR4000 to a computer via the USB port:

1. Install the spectrometer operating software on the destination computer.

2. Locate the USB cable (USB-CBL-1) provided with the HR4000.

3. Insert the square end of the cable into the side of the HR4000.

4. Insert the rectangular end of the cable into the USB port of the PC.

If you installed the spectrometer operating software prior to connecting the HR4000, the software installs
the HR4000 drivers. If the drivers do not successfully install (or if you connected the HR4000 to the
computer before installing the software), consult Chapter 3:

210-00000-000-02-0908 7

Troubleshooting.

2: Installing the HR4000

Serial Port Mode

To use the serial port capacity of the HR4000 Spectrometer, the PC must be running a 32-bit version of
the Windows operating system (or Windows CE 2.11 or higher for handheld PCs).

►

Procedure

Follow the steps below to connect the HR4000 to the PC via serial port:

1. Connect the serial cable adapter block to the appropriate pins of the HR4000’s 30-Pin Accessory

Connector.

2. Connect one end of the 9-pin serial cable to the adapter block on the HR4000, and then connect

the other end to a serial port on the PC.

3. Note the number of the serial port (COM Port) to which you connected the HR4000 (some PCs

may not have numbered ports; handheld PCs typically have only one serial port).

4. Plug the 5 VDC external power supply into an outlet and connect it to the HR4000.

Configuring the HR4000

The HR4000 can be used with either SpectraSuite or OOIBase32 software when connected to the USB
port. The configuration process differs, depending on whether you are running SpectraSuite or
OOIBase32 software.

Configuring the HR4000 in SpectraSuite

If you have followed the previous steps and started SpectraSuite, the spectrometer is already acquiring
data. Even with no light in the spectrometer, there should be a dynamic trace displayed in the bottom of
the graph. If you allow light into the spectrometer, the graph trace should rise with increasing light
intensity. This means the software and hardware are correctly installed.

Note the spectrometer(s) that you have installed are listed in the Data Sources pane.

Configuring the HR4000 in OOIBase32

Once you install the HR4000, you must configure OOIBase32’s Configure Spectrometer options so that
OOIBase32 recognizes the HR4000 Spectrometer. Consult the OOIBase32 Spectrometer Operating
Software Operating Instructions for detailed instructions on configuring the spectrometer in OOIBase32
(see

Product-Related Documentation).

Connect Spectroscopic Accessories

To find operating instructions for HR4000-compatible products (such as light sources, sampling
chambers, and probes), consult the Software and Technical Resources CD or the Ocean Optics website at

http://www.oceanoptics.com/technical/operatinginstructions.asp.

8 210-00000-000-02-0908

2: Installing the HR4000

External Triggering Options

You can trigger the HR4000 using a variety of External Triggering options through the 30-pin Accessory
Connector on the spectrometer. See the External Triggering Options document located at

http://www.oceanoptics.com/technical/External-Triggering.pdf. This document contains instructions

for configuring External Triggering options for the HR4000.

Note

Only the external software triggering option is available when using a handheld PC.

210-00000-000-02-0908 9

Chapter 3

Troubleshooting

Overview

The following sections contain information on troubleshooting issues you may encounter when using the
HR4000 Spectrometer.

Note

For issues encountered when using a handheld PC, consult the OOIPS2000 manual.

HR4000 Connected to Computer Prior to
Operating Software Installation

Windows Operating Systems

If you connected your Ocean Optics HR4000 device to the computer prior to installing your spectrometer
operating software application (SpectraSuite or OOIBase32) on a Windows platform, you may encounter
installation issues that you must correct before your Ocean Optics device will operate properly.

Follow the applicable steps below to remove the incorrectly installed device, device driver, and
installation files.

Note

If these procedures do not correct your device driver problem, you must obtain the

Correcting Device Driver Issues document from the Ocean Optics website:

http://www.oceanoptics.com/technical/engineering/correctingdevicedriverissues.pdf.

Remove the Unknown Device from Windows Device Manager

► Procedure

1. Open Windows Device Manager. Consult the Windows operating instructions for your computer

for directions, if needed.

210-00000-000-02-0908 10

3: Troubleshooting

2. Locate the Other Devices option and expand the Other Devices selection by clicking on the "+"

sign to the immediate left.

Note

Improperly installed USB devices can also appear under the Universal Serial Bus

Controller option. Be sure to check this location if you cannot locate the unknown device.

3. Locate the unknown device (marked with a large question mark). Right-click on the Unknown

Device listing and select the Uninstall or Remove option.

4. Click the OK button to continue. A warning box appears confirming the removal of the Unknown

Device. Click the OK button to confirm the device removal.

5. Disconnect the HR4000 from your computer.

6. Locate the section in this chapter that is appropriate to your operating system and perform the

steps in the following

Remove Improperly Installed Files section.

Remove Improperly Installed Files

► Procedure

1. Open Windows Explorer.

2. Navigate to the Windows | INF directory.

Note

If the INF directory is not visible, you must disable the Hide System Files and Folders

and Hide File Extensions for Known File Types options in Windows Folder Options.

Access Windows Folder Options from Windows Explorer, under the Tools | Folder

Options menu selection.

3. Delete the OOI_USB.INF in the INF directory. If your computer is running either the Windows

2000 or XP operating system, you must also delete the OOI_USB.PNF file in the INF directory.

4. Navigate to the Windows | System32 | Drivers directory.

5. Delete the EZUSB.SYS file.

6. Reinstall your Ocean Optics application and reboot the system when prompted.

7. Plug in the USB device.

The system is now able to locate and install the correct drivers for the USB device.

Mac Operating Systems

Since there are no device files for the HR4000 Spectrometer in a Mac operating system, you should not
encounter any problems if you installed the spectrometer before the SpectraSuite software.

210-00000-000-02-0908 11

3: Troubleshooting

Linux Operating Systems

For Linux operating systems, all you need to do is install the SpectraSuite software, then unplug and
replug in the spectrometer. Technically, the driver files for Linux simply give nonprivileged users
permission to use newly connected hardware. There isn’t any long-term harm to plugging in the device
before installing the software.

Older Version of OOIBase32 Installed

If the PC to be used to interface to your HR4000 already has an older version of OOIBase32 software
installed, you must install the latest version of OOIBase32. You can download the latest version of
OOIBase32 from the Software and Technical Resources CD or from the Ocean Optics website at

http://www.oceanoptics.com/technical/softwaredownloads.asp.

You do not need to uninstall previous versions of OOIBase32 when upgrading to the latest version.

12 210-00000-000-02-0908

Appendix A

Calibrating the Wavelength of

the HR4000

Overview

This appendix describes how to calibrate the wavelength of your spectrometer. Though each spectrometer
is calibrated before it leaves Ocean Optics, the wavelength for all spectrometers will drift slightly as a
function of time and environmental conditions. Ocean Optics recommends periodically recalibrating the
HR4000.

About Wavelength Calibration

You are going to be solving the following equation, which shows that the relationship between pixel
number and wavelength is a third-order polynomial:

λ

= I + C1 p + C2 p2 + C3 p

p

Where:

λ

= the wavelength of pixel p

I = the wavelength of pixel 0

= the first coefficient (nm/pixel)

C

1

= the second coefficient (nm/pixel2)

C

2

= the third coefficient (nm/pixel3)

C

3

= the reference intensity at wavelength λ

R

λ

You will be calculating the value for I and the three Cs.

3

210-00000-000-02-0908 13

A: Calibrating the Wavelength of the HR4000

Calibrating the Spectrometer

Preparing for Calibration

To recalibrate the wavelength of your spectrometer, you need the following components:

• A light source capable of producing spectral lines

Note

Ocean Optics’ HG-1 Mercury-Argon lamp is ideal for recalibration. If you do not have an

HG-1, you need a light source that produces several (at least 4-6) spectral lines in the

wavelength region of your spectrometer.

• An HR4000 spectrometer

• An optical fiber (for spectrometers without a built-in slit, a 50-

• A spreadsheet program (Excel or Quattro Pro, for example) or a calculator that performs third-

order linear regressions

µm fiber works best)

Note

If you are using Microsoft Excel, choose Tools | Add-Ins and check AnalysisToolPak

and AnalysisTookPak-VBA.

Calibrating the Wavelength of the Spectrometer

► Procedure

Perform the steps below to calibrate the wavelength of the spectrometer:

1. Place the operating software into Scope mode and take a spectrum of your light source. Adjust
the integration time (or the A/D conversion frequency) until there are several peaks on the screen
that are not off-scale.

2. Move the cursor to one of the peaks and position the cursor so that it is at the point of maximum
intensity.

3. Record the pixel number that is displayed in the status bar or legend (located beneath the graph).
Repeat this step for all of the peaks in your spectrum.

4. Use the spreadsheet program or calculator to create a table like the one shown in the following
figure. In the first column, place the exact or true wavelength of the spectral lines that you used.

In the second column of this worksheet, place the observed pixel number. In the third column,
calculate the pixel number squared, and in the fourth column, calculate the pixel number cubed.

14 210-00000-000-02-0908

A: Calibrating the Wavelength of the HR4000

Independent

Variable

Dependent

Variables

Values Computed

from the Regression

Output

True Wavelength (nm) Pixel # Pixel #

253.65

296.73

302.15

313.16

334.15

365.02

404.66

407.78

435.84

546.07

576.96

579.07

696.54

706.72

727.29

738.40

751.47

175
296
312
342
402
490
604
613

694
1022
1116
1122
1491
1523
1590
1627
1669

30625
87616

97344
116964
161604
240100
364816
375769
481636

1044484
1245456
1258884
2223081
2319529
2528100
2647129
2785561

2

1067462648
1389928896
1412467848
3314613771
3532642667
4019679000
4306878883
4649101309

3

Pixel #

5359375
25934336
30371328
40001688
64964808

117649000
220348864
230346397
334255384

Predicted

Wavelength

253.56

296.72

302.40

313.02

334.19

365.05

404.67

407.78

435.65

546.13

577.05

579.01

696.70

706.62

727.24

738.53

751.27

Difference

0.09

0.01

-0.25

0.13

-0.05

-0.04

-0.01

0.00

0.19

-0.06

-0.09

0.06

-0.15

0.10

0.06

-0.13

0.19

5. Use the spreadsheet or calculator to calculate the wavelength calibration coefficients. In the
spreadsheet program, find the functions to perform linear regressions.

• If using Quattro Pro, look under Tools | Advanced Math

• If using Excel, look under Analysis ToolPak

6. Select the true wavelength as the dependent variable (Y). Select the pixel number, pixel number
squared, and the pixel number cubed as the independent variables (X). After executing the
regression, you will obtain an output similar to the one shown below. Numbers of importance are
noted.

Regression Statistics

Multiple R 0.999999831
R Square 0.999999663 R Squared
Adjusted R Square 0.999999607
Standard Error 0.125540214
Observations 22

Intercept

Coefficients Standard Error

Intercept 190.473993 0.369047536 First coefficient
X Variable 1 0.36263983 0.001684745
X Variable 2-1.174416E-05 8.35279E-07
X Variable 3-2.523787E-09 2.656608E-10 Second coefficient

Third coefficient

210-00000-000-02-0908 15

A: Calibrating the Wavelength of the HR4000

7. Record the Intercept, as well as the First, Second, and Third Coefficients. Additionally, look at
the value for R squared. It should be very close to 1. If not, you have most likely assigned one of
your wavelengths incorrectly.

Keep these values at hand.

Saving the New Calibration Coefficients: USB Mode

Ocean Optics programs wavelength calibration coefficients unique to each HR4000 onto an EEPROM
memory chip in the HR4000.

You can overwrite old calibration coefficients on the EEPROM if you are using the HR4000 via the USB
port. If you are using the HR4000 via the serial port, consult the

Serial Mode

►

To save wavelength calibration coefficients using the USB mode, perform the following steps:

1. Ensure that the HR4000 is connected to the PC and that you have closed all other applications.

section later in this appendix.

Procedure

Saving the New Calibration Coefficients:

2. Point your browser to
scroll down to Microcode. Select USB EEPROM Programmer.

3. Save the setup file to your computer.

4. Run the Setup.exe file to install the software. The Welcome screen appears.

5. Click the Next button. The Destination Location screen appears.

6. Accept the default installation location, or click the Browse button to specify a directory. Then,
click the Next button. The Program Manager Group screen appears.

7. Click the Next button. The Start Installation screen appears.

8. Click the Next button to begin the installation. Once the installation finishes, the Installation
Complete screen appears.

9. Click the Finish button and reboot the computer when prompted.

10. Navigate to the USB EEPROM Programmer from the Start menu and run the software.

11. Click on the desired HR4000 device displayed in the left pane of the USB Programmer screen.

12. Double-click on each of the calibration coefficients displayed in the right pane of the USB
Programmer screen and enter the new values acquired in Steps 5 and 6 of the

Wavelength of the Spectrometer

13. Repeat Step 12 for all of the new values.

14. Click on the Save All Values button to save the information, and then Exit the USB Programmer
software.

http://www.oceanoptics.com/technical/softwaredownloads.asp and

Calibrating the

section in this appendix.

The new wavelength calibration coefficients are now loaded onto the EEPROM memory chip on the
HR4000.

16 210-00000-000-02-0908

A: Calibrating the Wavelength of the HR4000

Saving the New Calibration Coefficients: Serial Mode

If you are connecting the HR4000 Spectrometer to the serial port of the PC, you need to save the new
wavelength calibration coefficients to the .SPEC file that OOIBase32 accesses when opened.

Note

You cannot save the calibration coefficients to the EEPROM memory chip on the
HR4000 when using the serial mode.

► Procedure

To save Wavelength Calibration Coefficients using the Serial mode, perform the following steps:

1. Open the OOIBase32 application.

2. Select Spectrometer | Configure from the OOIBase32 menu bar. The Configure Spectrometer
screen appears.

3. Select the Wavelength Calibration tab to update the wavelength coefficients within OOIBase32.

4. Enter in the new values acquired from Steps 5 and 6 of the

Spectrometer

5. Click the OK button to save the information in OOIBase32.

section in this appendix.

Calibrating the Wavelength of the

210-00000-000-02-0908 17

A: Calibrating the Wavelength of the HR4000

18 210-00000-000-02-0908

Appendix B

Specifications

Overview

This appendix contains information on spectrometer operation, specifications, and system compatibility.
It also includes accessory connector pinout diagrams and pin-specific information.

How the HR4000 Works

Below is a diagram of how light moves through the optical bench of an HR4000 Spectrometer. The
optical bench has no moving parts that can wear or break; all the components are fixed in place at the time
of manufacture. Items with an asterisk (*) are user-specified.

HR4000 Spectrometer with Components

See

HR4000 Components Table on the following page for an explanation of the function of each

numbered component in the HR4000 Spectrometer in this diagram.

210-00000-000-02-0908 19

B: HR4000 Specifications

HR4000 Components Table

Ocean Optics permanently secures all components in the HR4000 at the time of manufacture. Only Ocean
Optics technicians can replace interchangeable components, where noted.

Item Name Description

1

2 Slit

3 Filter

4

5 Grating

SMA
Connector

Collimating
Mirror

Secures the input fiber to the spectrometer. Light from the input fiber enters the
optical bench through this connector.

A dark piece of material containing a rectangular aperture, which is mounted directly
behind the SMA Connector. The size of the aperture regulates the amount of light
that enters the optical bench and controls spectral resolution.

You can also use the HR4000 without a Slit. In this configuration, the diameter of
the fiber connected to the HR4000 determines the size of the entrance aperture.

Only Ocean Optics technicians can change the Slit.

Restricts optical radiation to pre-determined wavelength regions. Light passes
through the Filter before entering the optical bench. Both bandpass and longpass
filters are available to restrict radiation to certain wavelength regions.

Only Ocean Optics technicians can change the Filter.

Focuses light entering the optical bench towards the Grating of the spectrometer.

Light enters the spectrometer, passes through the SMA Connector, Slit, and Filter,
and then reflects off the Collimating Mirror onto the Grating.

Diffracts light from the Collimating Mirror and directs the diffracted light onto the
Focusing Mirror. Gratings are available in different groove densities, allowing you to
specify wavelength coverage and resolution in the spectrometer.

Only Ocean Optics technicians can change the Grating.

6

7

8

20 210-00000-000-02-0908

Focusing
Mirror

L2 Detector
Collection
Lens

CCD
Detector
(UV or VIS)

Receives light reflected from the Grating and focuses the light onto the CCD
Detector or L2 Detector Collection Lens (depending on the spectrometer
configuration).

An optional component that attaches to the CCD Detector. It focuses light from a tall
slit onto the shorter CCD Detector elements.

The L2 Detector Collection Lens should be used with large diameter slits or in
applications with low light levels. It also improves efficiency by reducing the effects
of stray light.

Only Ocean Optics technicians can add or remove the L2 Detection Collection Lens.

Collects the light received from the Focusing Mirror or L2 Detector Collection Lens
and converts the optical signal to a digital signal.

Each pixel on the CCD Detector responds to the wavelength of light that strikes it,
creating a digital response. The spectrometer then transmits the digital signal to the
OOIBase32 application.

B: HR4000 Specifications

HR4000 Specifications

The following sections provide specification information for the CCD detector in the HR4000, as well as
the HR4000 Spectrometer itself. HR4000CG-UV-NIR specifications are listed in Appendix C:

HR4000CG-UV-NIR Spectrometer.

CCD Detector Specifications

Specification Value

Detector Toshiba TCD1304AP linear CCD array

No. of elements 3648 pixels

Sensitivity 100 photons per count at 800 nm

Pixel size 8 µm x 200 µm

Pixel well depth -100,000 electrons

Signal-to-noise ratio 300:1 (at full signal)

A/D resolution 14 bit

Dark noise 8 RMS counts

Corrected linearity >99.8%

Maximum pixel rate Rate at which pixels are digitized is 1 MHz

HR4000 Spectrometer

Specification Value

Dimensions 148.6 mm x 104.8 mm x 45.1 mm

Weight 570 g

Power consumption 450 mA @ 5 VDC

Detector 3648-element linear silicon CCD array

Detector range 200-1100 nm

Gratings 14 gratings available

210-00000-000-02-0908 21

B: HR4000 Specifications

Specification Value

Entrance aperture 5, 10, 25, 50, 100 or 200 µm wide slits

Order-sorting filters Installed longpass and bandpass filters

Focal length f/4, 101 mm

Optical resolution Depends on grating and size of entrance aperture

Stray light <0.05% at 600 nm; <0.10% at 435 nm

Dynamic range 2 x 109 (system); 2000:1 for a single acquisition

Fiber optic connector SMA 905 to single-strand optical fiber (0.22 NA)

Data transfer rate

Integration time 3.8 ms to 10 seconds

Interfaces

Operating systems

Onboard GPIO 10 user-programmable digital I/Os

Analog channels One 13-bit analog input and one 9-bit analog output

Full scans into memory every 4 milliseconds with USB 2.0 port,
every 600 milliseconds with the serial port

USB 2.0, 480 Mbps (USB 1.1 compatible); RS-232 (2-wire); SPI
(3-wire); I

Windows 98/Me/2000/XP, Mac OS X, and Linux when using the
USB port Any 32-bit Windows operating system when using the
serial port

2C

Inter-Integrated Circuit 2-wire serial bus

System Compatibility

The following sections provide information on hardware and software requirements for the HR4000.

Compatibility for Desktop or Notebook PCs

To use the HR4000, you must have a PC that meets the following minimum requirements:

• IBM-compatible PC with Pentium (or higher) processor

• 32 MB RAM

• OOIBase32 Spectrometer Operating Software

• Windows 98/ME/2000/XP operating system (when connecting the HR4000 to a PC via USB

port)

OR

210-00000-000-02-0908

22

B: HR4000 Specifications

Any 32-bit version of Windows (when connecting the HR4000 to a PC via serial port)

Compatibility for Handheld PCs

To use the HR4000 with your handheld PC, the computer must meet the following minimum
requirements:

• Handheld PC running Windows CE 2.11 or later

• 32 MB RAM

• OOIPS2000 Spectrometer Operating Software

• Serial port connectivity

30-Pin Accessory Connector Pinout

The HR4000 features a 30-pin Accessory Connector, located on the side of the unit as shown:

30-Pin Connector

Location of HR4000 30-Pin Accessory Connector

30-Pin Accessory Connector Pinout Diagram

When facing the 30-pin Accessory Connector on the front of the vertical wall of the HR4000, pin
numbering is as follows:

USB

Port

2 4 6 8 10 12 14 16 18 20 22 24 26 28 30

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

30-Pin Accessory Connector Pinout Diagram

210-00000-000-02-0908 23

B: HR4000 Specifications

30-Pin Accessory Connector – Pin Definitions and
Descriptions

The following table contains information regarding the function of each pin in the HR4000’s 30-Pin
Accessory Connector:

Pin
#

Function Input/Output Description

1 RS232 Rx Input RS232 receive signal – Communicates with a PC over DB9 Pin 3

2 RS232 Tx Output RS232 transmit signal – Communicates with a PC over DB9 Pin 2

3 GPIO (2) Input/Output

General purpose software-programmable, digital input/output
(channel number)

4 V5_SW Output Regulated 5 Volt power pin – Supplies 50 mA (maximum)

5 Ground Input/Output Ground

6 I2C SCL Input/Output I2C clock signal for communication to other I2C peripherals

7 GPIO (0) Input/Output

General purpose software-programmable, digital input/output
(channel number)

8 I2C SDA Input/Output I2C data signal for communication to other I2C peripherals

9 GPIO (1) Input/Output

10

Ext.
Trigger In

Input

General purpose software-programmable, digital input/output
(channel number)

TTL input trigger signal – See External Triggering Options document
for info.

11 GPIO (3) Input/Output

V

, V

12

13

14

15

24 210-00000-000-02-0908

CC

or 5V

IN

SPI Data
Out

V

, V

CC

or 5V

IN

SPI Data
In

USB

USB

,

,

Input or
Output

Output

Input or
Output

Input

General purpose software-programmable, digital input/output
(channel number)

Input power pin for HR4000 – When operating via USB, this pin can
power other peripherals – Ensure that peripherals comply with USB
specifications

SPI Master Out Slave In (MOSI) signal for communication to other
SPI peripherals

Input power pin for HR4000 – When operating via USB, this pin can
power other peripherals – Ensure that peripherals comply with USB
specifications

SPI Master In Slave Out (MISO) signal for communication to other
SPI peripherals

B: HR4000 Specifications

Pin
#

16 GPIO (4) Input /Output

17

18 GPIO (5) Input/Output

19 SPI Clock Output SPI clock signal for communication to other SPI peripherals

20

21

22 GPIO (6) Input/Output

23

Function Input/Output Description

General purpose software-programmable, digital input/output
(channel number)

Single
Strobe

Continuou
s Strobe

SPI Chip
Select

Analog In
(0-5V)

Output

Output

Output

Input 13-bit analog-to-digital input with a 0-5V range

TTL output pulse used as a strobe signal – Has a programmable
delay relative to the beginning of the spectrometer integration period

General purpose software-programmable, digital input/output
(channel number)

TTL output signal used to pulse a strobe – Divided down from the
master clock signal

SPI Chip/Device Select signal for communication to other SPI
peripherals

General purpose software-programmable, digital input/output
(channel number)

24

25

26 GPIO (7) Input/Output

27 Ground Input/Output Ground

28 GPIO (8) Input/Output

29 Ground Input/Output Ground

30 GPIO (9) Input/Output

Analog
Out (0-5V)

Lamp
Enable

Output 9-bit programmable output voltage with a 0-5V range

Output

TTL signal driven Active HIGH when the Lamp Enable command is
sent to the spectrometer

General purpose software-programmable, digital input/output
(channel number)

General purpose software-programmable, digital input/output
(channel number)

General purpose software-programmable, digital input/output
(channel number)

30-Pin J2 Accessory Connector - Part Numbers

The part numbers for the 30-pin accessory connector on the HR4000 Spectrometer are as follows:

• The connector is Pak50™ model from 3M Corp. Headed Connector – Part Number
P50–030P1–RR1–TG.

210-00000-000-02-0908 25

B: HR4000 Specifications

• The mating connector is Part Number P50–030S–TGF.

• Mating the two components requires two 1.27 mm (50 mil) flat ribbon cables (3M 3365 Series is

recommended).

If you are customizing your HR4000 Spectrometer system or configuring External Triggering, you may
need these part numbers to complete your setup.

HR4000 15-Pin Accessory Cable Pinout

Pin # Description Pin # Description

1 Single_strobe 9 GPIO-9

2 ContStrobe 10 GND_SIGNAL

3 V5_SW 11 SDA

4 ExtTrigIn 12 SCL

5 ExtTrigIn 13 LampEnable

6 GPIO-8 14 A_IN

7 A_OUT 15 GPIO-7

8 ExtTrigIn

26 210-00000-000-02-0908

Appendix C

HR4000CG-UV-NIR Spectrometer

The HR4000CG-UV-NIR Composite Grating Spectrometer has a new proprietary grating and order­sorting filter to provide a 200-1100 nm wavelength range with 0.5 nm optical resolution in one
spectrometer.

The HR4000-CG-UV-NIR is functionally similar to the standard HR4000 Spectrometer. Follow the
instructions in Chapter 2:

HR4000CG-UV-NIR Features

The HR4000CG-UV-NIR contains the following features that differ from the standard HR4000:

Installing the HR4000 to configure the HR4000CG-UV-NIR.

New HC-1 Landis Composite Grating

The HR4000CG-UV-NIR uses the new HC-1 Landis grating designed to provide a 200-1100 nm
wavelength range. The HC-1 is fixed in place at the time of manufacture.

Variable Order-Sorting Filter

The HR4000CG-UV-NIR contains a new OFLV-200-1000 variable order sorting filter to eliminate
second and third order effects.

HR4000CG-UV-NIR Spectrometer Specifications

Specification Value

Dimensions: 148.6 mm x 104.8 mm x 45.1 mm

Weight 570 g

Power consumption 450 mA @ 5 VDC

Detector 3648-element linear silicon CCD array

Wavelength range 200-1100 nm

Optical resolution 0.75 nm FWHM

210-00000-000-02-0908 27

C: HR4000-UV-NIR Spectrometer

Specification Value

Gratings HC-1, 300 lines per nm grating

Entrance aperture

5 µm-wide slit

Order-sorting filters OFLV-200-1100 installed

Focal length f/4, 101 mm

Dynamic range 2 X 109 (system); 2000:1 for a single acquisition

Stray light <0.05% at 600 nm; <0.10% at 435 nm

Fiber optic connector SMA 905 to single-strand optical fiber (0.22 NA)

Full scans into memory every 4 milliseconds with the USB 2.0,

Data transfer rate

every 18 ms with the USB 1.1, every 600 milliseconds with the
serial port

Continuous – 4 milliseconds to 20 seconds

Integration time

Shutter – 10 microseconds to 4 milliseconds

Windows 98/Me/2000/XP, MAC OS X, and Linux when using the

Operating systems

USB port

Any 32-bit Windows operating system when using the serial port

Onboard GPIO 10 user-programmable digital I/Os

Analog channels One 13-bit analog input and one 9-bit analog output

210-00000-000-02-0908

28

Index

1

15-pin accessory cable

pinouts, 26

3

30-pin accessory connector

diagram, 23
part numbers, 25
pin definitions, 24

A

accessories, 5, 8
Accessories, 3
accessory connector

pinout, 23

Adobe Acrobat Reader, 4

B

breakout box, 3

D

detector, 21
Detector Collection Lens, 20
document

audience, iv
purpose, iv
summary, iv

E

EEPROM, 2
External Triggering, 9

F

filter, 20, 27
focusing mirror, 20

G

grating, 20

H

C

HC-1 Landis Composite Grating, 27
Calibrating, iv, 13
calibration, 13

preparing for, 14
procedure, 14

calibration coefficients

saving in Serial mode, 17

saving in USB mode, 16
CCD, 21
CCD Detector, 20
collimating mirror, 20
compatibility, 22

Desktop or Notebook PCs, 22

handheld PCs, 23
Components Table, 20
configuring, 8

210-00000-000-02-0908 29

HR4000

specifications, 21

HR4000CG-UV-NIR, 27

features, 27

HR4000CG-UV-NIR Spectrometer

specifications, 27

I

Installation, 7

Serial Port mode, 8

USB mode, 7
installed filter, 20
Interface, 3

Index

slit, 20

L

L2 Detector Collection Lens, 20
Lens, 20

M

memory chip, 2
mirror, 20

SMA Connector, 20
Software and Resources Library CD, 4
specifications, 19

detector, 21

HR4000, 21

HR4000CG-UV-NIR Spectrometer, 27
spectroscopic accessories, 8
System Requirements, 2

T

O

OOIBase32, 8
Options

Interface, 3

P

packing list, 4
passwords, 4
power supply (external), 2
product-related documentation, iv

S

Sampling

Accessories, 3

System, 2
Serial Port mode, 8
service, v
setup, 7
shipment components, 4

Triggering, 9
troubleshooting

Linux systems, 12
Mac systems, 11
older version of OOIBase32, 12

Troubleshooting, 10

U

upgrades, v
USB mode, 7
USB-ADP-H, 3
USB-ADP-PC, 3
USB-CBL-1, 3

W

Wavelength Calibration

about, 13
Wavelength Calibration Data File, 4
Wavelength Calibration Data Sheet, 4
what's new, iv

30 210-00000-000-02-0908