tecan ls series, LS300 Operating Manual

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Page 1

TECAN

Operating Manual for the

LS Series Scanner

Document Part No.: 30001798

2004-11

Document Revision No.: 1.5

Page 2

Tecan Affiliates and Service Centers

Austria

Tecan Austria GmbH

Untersbergstrasse 1a

A-5082 Grödig / Salzburg

Austria

Tel.: +43 62 46 89 33

Fax: +43 62 46 72 770

Belgium

Tecan Benelux B.V.B.A.

Vaartdijk 55

B-2800 Mechelen

Belgium

Tel.: +32 15 42 13 19

Fax. +32 15 42 16 12

Italy

Tecan Italia S.r.l.

Via F.lli Cervi

Palazzo Bernini

Centro Direzionale Milano2

20090 Segrate (Mi)

Italy

Tel.: +39 02 215 21 28

Fax: +39 02 215 97 441

Spain

Tecan Spain

Sabino de Arana, 32

E-08028 Barcelona

Spain

Tel.: +34 93 490 01 74

Fax: +34 94 411 24 07

United Kingdom

Tecan UK

Theale Court

11-13 High Street

Theale

UK-Reading RG7 5AH

United Kingdom

Tel.: +44 11 89 300 300

Fax: +44 11 89 305 671

Austria

Tecan Sales International GmbH

Untersbergstrasse 1a

A-5082 Grödig / Salzburg

Austria

Tel.: +43 62 46 89 33

Fax: +43 62 46 72 770

France

Tecan France26 Avenue Tony Garnier

69007 LYON

France

Tel.: +33 47 27 60 480

Fax: + 33 47 27 60 499

Japan

Tecan Japan Co. Ltd

Meiji Seimei Fuchu Building 10F

1-40 Miyamachi

Fuchu City, Tokyo

Japan

Tel.: +81 42 334 88 55

Fax: +81 42 334 04 01

Sweden

Tecan Nordic AB

Box 208, SE-431 23

Mölndal

Sweden

Tel: +46 31 75 44 000

Fax: +46 31 75 44 010

USA

Tecan US

P.O. Box 13953

Research Triangle Park,

NC 27709

USA

Tel.: +1 919 361 5200

Fax: +1 919 361 5201

Asia

Tecan Asia (Pte) Ltd.

80, Marine Parade #13-04

Singapore 449269

Singapore

Tel.: +65 44 41 886

Fax: +65 44 41 836

Germany

Tecan Deutschland GmbH

Theodor-Strom-Straße 17

D-74564 Crailsheim

Germany

Tel.: +49 79 51 94 170

Fax: +49 79 51 50 38

Netherlands

Tecan Benelux B.V.B.A.

Industrieweg 30

NL-4283 Giessen

Netherlands

Tel.: +31 018 34 48 17 4

Fax: +31 018 34 48 06 7

Switzerland

Tecan Sales Switzerland AG

Seestrasse 103

CH-8708 Männedorf

Switzerland

Tel: +41 922 8 922

Fax: +41 922 8 923

2 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11

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WARNING

CAREFULLY READ AND FOLLOW THE INSTRUCTIONS PROVIDED IN

Notice

Every effort has been made to avoid errors in text and diagrams, however, Tecan Austria GmbH assumes no responsibility for any errors which may appear in this publication.

It is the policy of Tecan Austria GmbH to improve products as new techniques and components become available. Tecan Austria GmbH therefore reserves the right to change specifications at any time.

We would appreciate any comments on this publication.

Tecan Austria GmbH

Untersbergstraße 1A

A-5082 Grödig/Salzburg

AUSTRIA / EUROPE

Telephone: 0043 (0) 6246 8933

FAX: 0043 (0) 6246 72770

E-mail: office.austria@tecan.com

THIS DOCUMENT BEFORE OPERATING THE INSTRUMENT.

The contents of this document are the property of Tecan Austria GmbH and are not to be copied, reproduced, or transferred to another person or persons without prior written permission.

Declaration for EU Certificate

See the back of this document.

About the Instructions for Use

This publication is intended as Instructions for Use for the LS Series Scanner

instruments, which are designed to detect highly quantitative fluorescence images that have been read from microarray slides or other compatible sample formats.

This document provides information about:

• Installing the instrument

• Operating the instrument

• Cleaning and maintenance routines

2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 3

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Warnings, Cautions and Notes

There are four types of notices used in this publication. These notices highlight important information or warn the user of a potentially dangerous situation. The notices appear below:

Note

Gives helpful information.

Caution

Indicates a possibility of instrument damage or data loss if instructions

are not followed.

WARNING

INDICATES THE POSSIBILITY OF SEVERE PERSONAL INJURY, LOSS

OF LIFE OR EQUIPMENT DAMAGE IF THE INSTRUCTIONS ARE NOT

FOLLOWED.

WARNING

INDICATES LASER. DO NOT STARE INTO THE BEAM!

WARNING

INDICATES THE POSSIBLE PRESENCE OF BIOLOGICALLY HAZARDOUS MATERIAL. PROPER LABORATORY SAFETY

PRECAUTIONS MUST BE OBSERVED.

4 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11

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Table of Contents

1 Safety

1.1 Instrument Safety .......................................................................... 1-1

2 General

2.1 Instrument Features ...................................................................... 2-1

2.1.1 Samples........................................................................................... 2-2

2.1.2 Modes of operation.......................................................................... 2-3

2.1.3 Automation friendliness................................................................... 2-4

2.1.4 Integrated Image Analysis Software Array Pro................................ 2-4

3 Installation

3.1 Unpacking & Inspection................................................................ 3-1

3.2 Remove Transport Lock ............................................................... 3-7

3.3 Filter Installation............................................................................ 3-8

3.4 Power Requirements..................................................................... 3-9

4 Technical Description

4.1 Optical System............................................................................... 4-1

4.2 Autofocus....................................................................................... 4-3

4.3 Data Processing ............................................................................ 4-3

5 Operation

5.1 General Operating Features ......................................................... 5-2

5.1.1 Instrument Start Up ......................................................................... 5-2

5.1.2 Instrument Power On....................................................................... 5-2

5.1.3 Connect to Instrument..................................................................... 5-3

5.1.4 Finish a Measurement Session....................................................... 5-3

5.2 Insert Slide(s) into Slide Adapter ................................................. 5-4

6 LSServer, Scanner Shell and Download

6.1 Introduction.................................................................................... 6-1

6.1.1 Overview.......................................................................................... 6-1

6.1.2 Hardware Requirements.................................................................. 6-1

6.1.3 Software Requirements...................................................................6-2

6.1.4 Software Installation Procedure....................................................... 6-2

6.2 Tecan LS Scanner Interface ......................................................... 6-4

6.2.1 Overview.......................................................................................... 6-4

6.2.2 Starting LS Scanner Interface ......................................................... 6-4

6.3 LSServer......................................................................................... 6-6

6.3.1 Starting the First Time..................................................................... 6-6

6.3.2 Measurement Control......................................................................6-6

6.3.3 File Types used in LSServer ........................................................... 6-9

6.3.4 Measurement................................................................................. 6-11

6.3.5 Instrument...................................................................................... 6-26

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6.3.6 Measurement Parameter................................................................ 6-28

6.3.7 Excitation Angle Tab ......................................................................6-49

6.3.8 Settings .......................................................................................... 6-54

6.3.9 Slide Adapter Format .....................................................................6-62

6.3.10 Slides to Process............................................................................6-62

6.4 LS Scanner Shell..........................................................................6-64

6.4.1 General ..........................................................................................6-64

6.4.2 Starting Scanner Shell....................................................................6-64

6.4.3 Window Elements...........................................................................6-64

6.4.4 File types used in Scanner Shell....................................................6-66

6.4.5 Scanner Shell Menus.....................................................................6-68

6.4.6 Service Menu .................................................................................6-75

6.4.7 Stacker Setup - Twister..................................................................6-89

6.4.8 Scanner Shell Wizards...................................................................6-91

6.4.9 The Transport Lock Wizard............................................................6-92

6.4.10 The Transport Unlock Wizard.........................................................6-95

6.5 LSDownload................................................................................6-101

6.5.1 Starting LSDownload....................................................................6-101

6.5.2 LSDownload Menus.....................................................................6-102

7 Instrument Features

7.1 Specifications.................................................................................7-1

7.1.1 Lasers ..............................................................................................7-4

7.1.2 Optional Barcode Scanner...............................................................7-4

7.1.3 Reproduction of labels placed on the instrument.............................7-5

8 Cleaning & Maintenance

8.1 Introduction ....................................................................................8-1

8.2 Liquid Spills....................................................................................8-1

8.3 Replacing the Fuse ........................................................................8-2

8.4 Remote Control and Data Exchange ............................................8-3

8.4.1 FTP up / download...........................................................................8-3

8.4.2 Working with pcAnywhere:...............................................................8-3

8.4.3 Working with CITRIX web conferencing manager:...........................8-5

8.5 Instrument Disinfection .................................................................8-6

8.5.1 Disinfection Solutions.......................................................................8-6

8.6 Disinfection Procedure..................................................................8-7

8.7 Disinfection Certificate ..................................................................8-7

8.8 Disposal of Instrument ..................................................................8-8

8.8.1 Disposal of Packing Material............................................................8-8

8.8.2 Disposal of Operating Material.........................................................8-8

Index

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1. Safety

1.1 Instrument Safety

1. Always follow basic safety precautions when using this product to reduce the risk of injury, fire, or electrical shock.

2. Read and understand all information in the Operating manual. Failure to read, understand, and follow the instructions in the manual may result in damage to the product, injury to operating personnel or poor instrument performance.

3. Observe all WARNING and CAUTION statements in the manual.

4. Never open the LS SERIES SCANNER while the instrument is plugged into a power

source. The instrument contains class 2, 3a and 3b lasers inside.

5. Never force a slide or another sample into the instrument.

6. LS SERIES SCANNERS are intended for laboratory research use only. Observe

proper laboratory safety precautions, such as wearing protective clothing and using approved laboratory safety procedures.

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2. General

2.1 Instrument Features

The LS SERIES SCANNERS are laser-scanning instruments designed to detect highly quantitative fluorescence images. The scanners are designed to read microarray slides as well as other customer specific sample formats. They have exceptional flexibility with respect to sample formats and measurement modes. They can read samples up to the size of microplates as well as thick samples like gels or, for instance, liquid cells. They can read both in confocal and in nonconfocal mode and a selection of up to 4 excitation wavelengths (lasers) and an almost unlimited number (28) of emission wavelengths or emission filters.

Automation friendliness is another key feature of the LS SERIES SCANNERS. The design allows the use of standard microplate equipment to load very high numbers of slides automatically. For instance, with a Connect, up to 200 slides or 50 microplates can be loaded and processed automatically within one run.

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2. General

2.1.1 Samples

Slide adapters

Its special microplate/slide adapters accommodate 4 slides at once and loading is easily automated with standard microplate equipment.

Other formats

Due to its flexible design, other sample formats can be measured as well. The software allows special formats to be defined and special scanning areas to be processed. Due to an exceptionally high working distance of 6.5 mm, ‘thick’ samples, well structures, samples within a liquid cell or even gels can be measured. An automatic autofocus system is able to bring all of these samples into the proper focal plane. If you are in doubt whether a special sample format can be measured with the LS SERIES SCANNERS, please contact a Tecan representative.

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2. General

2.1.2 Modes of operation

Confocal or non-confocal

The LS SERIES SCANNERS are equipped with 3 different user selectable pinholes for selection of the appropriate depth of focus. The smaller the pinhole the higher is the confocality of the optical system and the shorter the depth of field. A small pinhole typically gives a better signal to background ratio, because all background contributions from outside the focal plane, e.g. the glass material or the backside of the slide are rejected. However for bulkier samples or samples with an uneven or a slightly bent surface confocality can result in lower signals or in a poor reproducibility. Here a larger pinhole is more appropriate. That’s why the LS SERIES SCANNERS offer the choice. Just choose the degree of confocality that is best suited for the samples.

Excitation wavelengths

• The LS Scanner can be equipped with up to 4lasers.

• Every Scanner has a HeNe laser with 633nm.

• Lasers with the wavelengths 488nm, 532nm and 694 nm are optional.

Emission wavelengths

Filters are located in special filter slides. The standard configuration comes with one filter for each excitation wavelength or laser respectively.

Additional filters can be added into the filter slides. The filter slides can be exchanged by the user. The ‘identity’ of each filter slide is automatically detected by the instrument when it is inserted into the slot.

Dual scanning

In order to increase the overall scan speed, two colors can be measured simultaneously with a dual channel instrument. A calibration algorithm takes care

of the crosstalk between the two colors and corrects for it online. If you have

purchased a single channel instrument, or if the wavelengths are too close to each other, the instrument can measure the two colors sequentially as well.

Resolution

The standard resolution is 10 µm.

For larger sample features there is the option to scan with 20 µm or 40 µm thus both increasing scan speed and decreasing the amount of data.

Smaller structures can be better resolved with 6 µm or 4 µm pixel resolution.

Scan widths for a single path scan are 22 mm for 10 µm, 20 µm and 40 µm, 6 µm pixels and 15 mm for 4 µm pixels.

Optimize sensitivity

For smaller scanning areas, there is a user selectable option to increase sensitivity without changing the scan time.

Another way to increase sensitivity is to scan transparent slides upside down. The reason is because surface bound molecules emit the greater part of their fluorescence into the medium with higher refractive index (e.g. glass).

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2. General

2.1.3 Automation friendliness

Because the LS SERIES SCANNERS are designed to interface with microplate technology, they are very well prepared for automation using existing microplate equipment. Four slides can be loaded in an adapter with the outer dimensions of a microplate. The number of slides is limited only by the stacking capacity of the external microplate device.

2.1.4 Integrated Image Analysis Software Array Pro

The LS SERIES SCANNERS come with an integrated array analysis software package.

Caution

If the instructions given in this manual are not correctly carried out, the

instrument May either become damaged or May no Longer be Able to

perform Its Procedures correctly and the Accuracy of the instrument

can no longer be guaranteed.

Note

In order to obtain reliable results it is strongly recommended to place

reference spots onto your sample for quality control. These spots should

represent every dye of your experiment and it is recommended that they are distributed in a non symmetric pattern across your sample. It is also

recommended to place ‘blank’ spots onto your arrays in order to check

for the variation of the background in your experiment.

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3. Installation

3.1 Unpacking & Inspection

The delivered container includes the following:

• Instrument

• PC

• PC Monitor

• Manual

• Software: Driver LS Series Scanner (1 CD-ROM)

• Cables (RS232 cable and 1 interface cable)

• Slide Adapters

• Filter Slide

• Reference slides (histological section of mouse; spots)

• Array Pro Software

• Hardware Key Array Pro SW

• Installation CD Array Pro SW

• Array Pro User Manual

• Scattered light glass slide

• Filter Slide for Calibration

• 2 Filter Slides

Caution

Before the instrument is installed and switched on, it should be left to

stand for at least three hours, so there is no possibility of condensation

causing a short circuit.

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3. Installation

Visually inspect the container for damage before it is opened.

Report any damage immediately.

Select a location to place the instrument that is flat, level, vibration free, away from direct sunlight, and free from dust, solvents and acid vapors. Allow at least 10 cm between the instrument and the wall or any other equipment.

Remove transportation locks.

Caution

The LS Series Scanners are precision instruments

and are very heavy. At least two people

3-2 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11

must carefully lift the instrument from the box.

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3. Installation

Visually inspect the instrument for loose, bent or broken parts.

Report any damage immediately.

Compare the serial number on the rear panel of the instrument with the serial number on the packing slip.

Report any discrepancy immediately.

Check the instrument accessories against the packing list. Save packing materials and transport locks (see next section) for further

transportation purposes.

Caution

Do not try to open or close

the instrument flap manually.

Ensure that the flap cannot be accidentally hit when it is opened automatically. Ensure that the main switch and the main cable can be reached at all times and are in no way obstructed.

Caution

The maximum load for the top of the housing

of an LS Series Scanner is 3 kg.

Caution

Keep fingers away from the flap when it is closing

or when a scan has been started.

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3. Installation

Place the PC with monitor, keyboard and mouse next to the instrument.

Ensure the computer is switched OFF and the instrument's main power switch on the back panel of the instrument is in the OFF position.

Check the voltage specifications on the computer and ensure that the voltage supplied to the computer is correct according to the specification input range selector (red button) at the power supply.

Caution

Check voltage specification on the computer BEFORE switching ON. If

computer is switched ON with the incorrect voltage supply it will be

Connect the computer to the instrument with the delivered RS 232 interface cable.

Connect the computer to the instrument with the delivered special interface cable.

The pictures below show the connection of the interface cables to the rear of the instrument:

damaged.

Data cable to connector box

RS232 to computer

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RS232 to instrument

3. Installation

The pictures below show the connection of the interface cables to the back of the computer:

Connection for monitor cables

Digital monitor cables

Connector box

Data cable to instrument

Analog monitor

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3. Installation

Insert the power cable (with protective ground connection) into the main power socket in the back panel of the instrument.

All connected devices must be approved and listed with regulations EN 60950, UL 1950 or CSA C22.2 No. 950 for Data Processing Devices.

Switch the computer ON.

Switch the instrument ON using the switch on the back panel of the instrument.

Caution

Keep fingers away from the flap when it is closing

or when a scan has been started.

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3. Installation

3.2 Remove Transport Lock

Start LS Scanner Shell.

Select Instrument and click Connect.

A message appears that instrument is locked.

For more information on removing the transport lock see chapter 6.4.10 The Transport Unlock Wizard.

Do not try to open or close

Save packing materials and transport locks

for further transportation purposes. The LS series scanners must be

and the transport locks must be installed.

the instrument flap manually.

shipped with the original packing

Caution

Before Transportation

Place the instrument carefully in the indicated orientation before fixing the

transportation locks, otherwise the instrument will become damaged.

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3. Installation

3.3 Filter Installation

Insert the Filter Slides into Filter Channel 1(vertical orientation) and Filter Channel 2 (horizontal orientation) and make sure that the filters are oriented properly, (see pictures below).

Filter Channel 1 Filter Channel 2

Note

Both filter slides are only necessary in dual channel instruments.

• Close the filter compartment

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3. Installation

3.4 Power Requirements

The instrument is auto sensing and it is, therefore, unnecessary to make any changes to the voltage range.

Check the voltage specifications on the rear panel of the instrument to ensure that the voltage supplied to the instrument is correct according to the specification.

The voltage range is 100-120 / 220-240 V.

If the voltage is not correct, please contact your distributor.

Ensure that a fuse of the correct type and rating is fitted.

Fuse = T 2.0 A / 250 V (slow blow) UL recognized

WARNING

RISK OF FIRE!

REPLACE ONLY WITH FUSES

OF THE SAME TYPE AND RATING.

Caution

When installing or uninstalling the instrument ensure that the instrument

and the computer are both switched off and disconnected from the main power supply before the RS 232 interface cable or the special connector

cable is connected or removed.

Caution

If the instructions given in this manual are not correctly carried out, the

instrument May either become damaged or May no Longer be Able to

perform Its Procedures correctly and the Accuracy of the instrument

can no longer be guaranteed.

2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 3-9

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4. Technical Description

4.1 Optical System

Figure 4.1

For excitation of fluorescence signals up to 4 lasers are installed. The lasers for 633 nm, and 594 nm are Helium Neon lasers; the lasers for 488 nm and 532nm are solid state lasers. Both of these laser types have excellent beam quality and stability.

Laser beams are combined with dichroic elements to enter the scanner in a collinear alignment.

2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 4-1

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4. Technical Description

Scanning is done in a first direction with the excitation beam. This very fast scanning mechanism scans 40 lines per second. The overall scanning speed and scanning time in this direction is independent from both pixel resolution and scan width. The second scanning dimension is achieved by moving the sample in a perpendicular direction. This movement is exactly synchronized with the first scan axis to create a 2-dimensional fluorescence image. For example at 10 µm resolution 4 mm are scanned within 10 s ((4 mm / 40 lines / s) * (100 lines / mm

10 µm pixel size)

) = 10 s). For this second direction the scanning speed is reciprocal to the resolution and the overall scanning time depends linearly on the scan length.

Fluorescence light is collected with a high aperture lens with exceptional working distance (up to 6.5 mm). This long working distance is the key for the ability to measure flexible sample formats other than slides.

A second lens refocuses the collected light onto a pinhole, thus creating a confocal detection scheme.

Three pinholes of different sizes are mounted on an automatic slide carrier. The smaller the pinhole, the lower the focal depth of the detected volume. The larger pinholes typically create images with a slightly lower signal to background ratio but offer the choice to measure bulky samples or uneven surfaces as well.

Behind the pinhole the fluorescence light passes through a bandpass filter that rejects light of the excitation wavelength and all other spectral contributions that are not within the detection bandwidth of the selected filter. Filters are arranged in filter slides that can hold up to four different filters. Each filter slide has five positions, but one of them has to stay open for autofocus purposes.

Filter slides can easily be removed or exchanged; up to 8 different slides can be automatically identified by the instrument firmware when they are inserted in the filter slots.

In the dual channel instrument a dichroic beamsplitter separates the two emission wavelengths of the first and the second dye (e.g. Cy3 and Cy5) and lets them pass trough two different emission filters and to two different photomultiplier tubes (PMT’s). The two different filters are located on two different filter slides in that case.

A reference diode monitors laser power before each measurement.

Figure 4.2

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4. Technical Description

4.2 Autofocus

A key element for the flexibility of the instrument is the autofocus system. It allows every sample individually to be adjusted - exactly in the focal plane of the optics. Because this is done immediately before each scan, out of focus images due to long term drifts of the optical alignment are not an issue with the LS SERIES SCANNERS.

Before each scan two z-scans are done across user defined lines in the sample. This way two short ‘vertical’ images are recorded typically close to both ends of the slide or the sample. (z-axis is moved instead of x-axis). These z-scan images are taken to calculate the exact position and the orientation of the sample. Orientation of the sample is also calculated because slight amounts of tilt could give poor results with a confocal measurement scheme.

The sample is then brought into the exact focal plane both with regard to z as well as the two angles of tilt. This process is fully automated. Signals are recorded in reflection mode and with a dimmed beam (4 orders) to prevent bleaching.

To realize this functionality a high precision 5-axis transport system is implemented in the LS SERIES SCANNERS. The five axis are: X (scan axis), Y (moves sample tray between different slides or different areas on larger samples), Z (brings sample into focal position), ϑ and Φ (correct for angles of tilt of the sample or tolerances of the adapters). Precisions for the axis’ are in the range of 1-2µm.

4.3 Data Processing

Further data processing is done by an analog amplifier PCB and fast 16 bit data acquisition boards. The latter ones are plugged into the PC and connected to the instrument with a special interface cable.

An internal Main-CPU takes control of all the actuators and data acquisition steps during scan. It is interfaced with a RS232 cable with the PC.

On the PC the Array Pro software is an integrated package both for instrument control and for array processing.

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5. Operation

The LS SERIES SCANNER is operated using personal computer based software control. The Array Pro Software is used both for instrument control and data

analysis.

This chapter describes the instrument and the instrument control software. It is intended for a general understanding of instrument parameters and operation. For details of the data analysis see the corresponding Array Pro software manual. Suggestions are made on how to optimize the instrument parameters for your applications.

Every effort has been made to ensure that the instrument will work correctly even if the default parameters are not appropriate for a particular application

- with an important exception:

When placing a sample into the sample carrier,

always make sure that the correct slide and slide carrier definitions are

Wrong definitions, especially with special samples can lead to damage of

the instrument or the sample.

Caution

selected in the software.

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5. Operation

5.1 General Operating Features

The LS Series Scanner has some general behavior and options, which are independent from particularly selected measurement techniques.

5.1.1 Instrument Start Up

Before the instrument is powered ON, ensure that both of the interface cables are

connected.

Caution

When the serial interface cable

or the special interface cable

is being plugged in or unplugged,

the instrument and the PC should be powered off.

5.1.2 Instrument Power On

When switching the instrument ON, the following actions are induced:

• The filter slides move into the reference position

• The dichroic filter carrier moves into the reference position

• The pinhole carrier moves into the reference position

• The microplate transport moves into the reference position

• The cooling fans start to ventilate

At the beginning of each session the user is requested to choose the lasers to be used in this session. Only the selected lasers will be switched on. This is done to increase the lifetime of the lasers.

The lasers need a warm up time of 20 minutes. The instrument is already

functional before that time, but performance according to the

specifications is guaranteed only after the warm up time has elapsed.

Scans can be done before that time.

Note

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5. Operation

5.1.3 Connect to Instrument

When the software connects to the instrument, communication is established between the instrument and the user interface. The instrument is ready for operation.

5.1.4 Finish a Measurement Session

Disconnect from Instrument

When disconnecting, communication between the instrument and the PC is terminated.

Please remove the recently measured sample before disconnect.

Instrument Shut Down

Note

Upon shut down, the instrument activity is stopped immediately. Normally, you should disconnect before shut down. In the rare case of an unexpected hardware error, immediate instrument shut down will reduce the risk of possible damage.

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5. Operation

5.2 Insert Slide(s) into Slide Adapter

Insert slide(s) into slide adapter as shown below:

Figure 5.5 a

Caution

Ensure that the slide is placed tightly on its support And in the right

orientation in the adapter. If it is not placed correctly in the adapter the

Place slide adapter on the plate transport in the same orientation as shown below (Fig. 5.5 b): - moveable spring should be located in the front

autofocus algorithm might fail to find a focal plane.

Figure 5.5 b

Note

The adapter is semi-disposable. The clamps that secure the slide might

5-4 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11

wear and the slides might become too loose in the adapter. Please call

your Tecan sales representative to order new adapters.

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6. LSServer, Scanner Shell and Download

6.1 Introduction

6.1.1 Overview

LSServer and Scanner Shell are software applications designed to give the user an easy and flexible way to operate Tecan LS SERIES SCANNER instruments.

LSServer is called up in Array Pro 4.5, a special tool for analyzing microarrays, and Scanner Shell.

LSServer Functions:

• Connecting to LS Series Scanner

• Preparing measurement parameters in order to get the best results in

scanning

• Scanning in different modes

Scanner Shell Functions:

• Connecting to Tecan LS Series Scanner

• Preparing measurement parameters in order to get the best results in

scanning

• Calibrating LS Series Scanner instruments

• Creating special formats for scanning different plates and slides

• Filter Definition

• Stacker Setup

LSDownload is a software tool needed for downloading new firmware versions to LS SERIES SCANNER instruments.

For details on

• data analysis, see the corresponding Array Pro 4.5 operating manual.

• instrument features and technical description refer to the Tecan LS Series

Scanner operating manual.

6.1.2 Hardware Requirements

The following hardware requirements are needed for LSServer and Scanner Shell:

Hardware Minimum Recommend

Memory 512 Mbytes 1 Gbyte

CPU Pentium III 1 GHz Pentium IV 1.7 GHz

Resolution 1024 x768 1280 x 1024

Serial Ports 2 2

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6.1.3 Software Requirements

The following software requirements are needed for LSServer and Scanner Shell:

Operating system Minimum Recommend

Microsoft Windows Windows 2000 Windows 2000

Additional supported software:

Array Pro 4.5 for microarray image analysis.

Note

Microsoft®Excel and Microsoft®Word must be registered by the user !

6.1.4 Software Installation Procedure

Automatic Software Setup

LSServer / Scanner Shell and LSDownload are installed by an automatic

software setup program:

Note

Before installing LSServer components be sure that Array Pro 4.5

Software for Microarray Image Analysis is installed on your system.

Note

It is necessary that the person who installs the software has administrator

rights on a PC with a Win 2000 operating system.

Step Procedure

1. Place the LS Driver for Tecan LS V2.2 Setup CD in the CD-ROM drive.

2. Open the CD drive folder and start LSServer.exe. The installation

procedure begins.

3. A Welcome window informs the user about the beginning of the installation process. Click Next to continue.

4. A Read Me File window informs the user about the new features of the setup.

5. The installation of the required files is carried out and files are copied to the computer. At the end of a successful installation the user can quit the installation wizard by clicking the Finish button.

After successful installation, installed software components for LSServer can be started via the Window Start menu by selecting Start - Programs - Array-Pro Analyzer 4.5 - Array-Pro Analyzer and installed software components for Scanner Shell and LSDownload can be started via the Window Start menu by selecting Start - Programs - Tecan - ScannerShell or LSDownload.

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Automatic Software Removal

Scanner Shell / LSDownload can be removed using the Windows standard

uninstall routine:

Step Procedure

1. Make sure the ScannerShell / LSDownload application is closed.

2. Select Add / Remove software from Settings - Control Panel in the

3. Select the ScannerShell / LSDownload icon and click Remove.

4. The Uninstall wizard is started. Select the preferred uninstall method

5. In the next window press Finish to uninstall ScannerShell /

6. A message box pops up asking if shared components should be

Start menu.

(Automatic or Custom) and click Next to continue.

LSDownload.

removed. Select Yes to completely uninstall application. Leaving the components will not harm your system. If you are not sure what to do, it is suggested that the shared components not be removed.

The ScannerShell / LSDownload is now uninstalled.

Note

This chapter does not apply to LSServer application.

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6.2 Tecan LS Scanner Interface

6.2.1 Overview

The Tecan LS Scanner Interface is a dialog box in which the options for connecting to instruments such as the Tecan LS Series Scanner can be set.

The next chapters describe how to:

• Set Communication port

• Choose Instrument type

• Work in Demo mode

6.2.2 Starting LS Scanner Interface

Port Setup

The Port Setup dialog box serves to set up options for connecting instruments: The desired instrument and the communication port are chosen. The demo mode provides the possibility to simulate any Tecan instrument.

To open the Port Setup dialog box:

• In Tecan LSA Software, Acquire menu select Tecan Scanner... or

• In Scanner Shell Software, Setup menu select Setup Port… or

• In LSDownload, Instrument menu select Connect…

The Port Setup dialog box:

In the Port Setup dialog box the instrument type and the communication port are selected.

Alternatively, select Find any and the LSServer can automatically search for a connected instrument.

Click OK to save changes and close the dialog box.

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The Port Setup dialog box contains the following elements:

Instrument group box The Instrument group box contains the following

elements:

• Select option button:

A specific instrument can be selected (choose in instrument type combo box).

• Find any option button:

The LSServer searches for available instruments automatically.

Port group box The Port group box contains the following elements:

• Select option button:

A list in which the appropriate communication port can be selected is shown.

• Find any option button:

The LSServer searches for any available port.

• Demo mode option button:

Allows the simulation of any instrument, e.g. for test purposes. Refer to chapter 6.4.6 Service Menu - Demo Mode Allowed for enabling the demo mode.

Stacker Port group box The Stacker Port group box contains the following

elements:

• Select option button:

A list in which the appropriate communication port can be selected is shown.

• Find any option button:

The LSServer searches for any available port.

• Demo mode option button: Allows the simulation of an instrument. Refer to chapter 6.4.6 Service Menu - Demo Mode Allowed for enabling the demo mode.

• None: option button

No Stacker available for the instrument.

OK button Click OK to save data and close the dialog box.

Cancel button Click Cancel to close the dialog box. The selected

options are not saved.

Help button Click Help to display the online help for the dialog box.

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6.3 LSServer

The LSServer is an instrument control and data scanning software specially designed for connecting to Tecan instruments such as the Tecan LS SERIES SCANNER. This chapter describes the parameters and operations; giving a general understanding in preparing and scanning data and in getting the best results for attached data analysis.

For details of data analysis see the corresponding Tecan LSA Software manual.

6.3.1 Starting the First Time

When starting LSServer for the first time, the Tecan LS Scanner Interface dialog box is opened. After selecting instrument type and communication port and confirming with OK the Measurement Control dialog box is displayed.

For all future starts of the LSServer:

In Tecan LSA Software, Acquire Menu select Tecan Scanner... and the Measurement Control dialog box is displayed.

6.3.2 Measurement Control

In the Measurement control dialog box, several groups, each containing

individual buttons, are shown that offer special operations for preparing and scanning data. Measurement parameters and measurement options are defined and finally measurements are started here.

The Measurement Control dialog box is divided into individual groups:

• Measurement group

• Instrument group

• Measurement Parameter group

• Settings group

• Slides to Process group

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Measurement

6. LSServer, Scanner Shell and Download

The Measurement Control dialog box consists of the following elements:

• The Measurement group element with the Start and Prescan button

• The Instrument group element to move plate and filters and to switch on

lasers

• The Measurement Parameter group element to Edit parameters or to Save and Load certain predefined parameter files

• The Settings group element with the Settings button to enter the filename and to select the scan areas

• The Slide Adapter Format group element to load existing Slide Adapter Format (.saf) files

• The Slides to Process group element to display arrangement of the scan areas

• File size of chosen slides

The Measurement group contains the following elements:

Start button Click the Start button to start a measurement with the

Prescan button Click the Prescan button to select three different

Instrument

The Instrument group contains the following elements:

Plate / Filter button Click the Plate / Filter button to open the Movements

Laser Control button Click the Laser Control button to open the Laser

Measurement Parameter

The Measurement parameter group contains the following elements:

current measurement parameter. The Status dialog box is displayed.

prescan modes:

o Image prescan o Adapter prescan o Focus prescan

dialog box: Plate and filter can be moved.

Control dialog box: Laser type can be selected and power control can be set / changed.

Edit button Click the Edit button to open the Measurement

Parameter dialog box: Measurement parameters can

be edited.

Load button Click the Load button to open the Open dialog box:

Measurement parameters can be loaded from a file.

Save button Click the Save button to open the Save As dialog box:

Measurement parameters can be saved to a file.

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Settings

The Settings group contains the following elements:

Settings button Click the Settings button to open the Slide Settings

dialog box: Filename can be entered and scan areas can be selected.

Slide Adapter Format

The Slide Adapter Format group contains the following elements:

Load button Click the Load button to open the Open Slide Adapter

Format dialog box: SAF can be selected.

Slides to Process

The Slides to process group gives a general view of the slide / plate format used and the arrangement of available scan areas. Scan areas that will be scanned after pressing Start / Prescan button are green, those that will not be scanned are dark gray. Select / unselect slides with left mouse click. Also the calculated file size will be displayed right under the scan area window.

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6.3.3 File Types used in LSServer

The following file types are used with LSServer:

File Type File

Extension

Image

Measurement Parameter

Slide adapter

ormat

Gain calibration

Crosstalk calibration

Focus

.tif Scanned image files are saved in a 16bit TIF

.lsp Measurement data is saved as .lsp files.

.saf Slide adapter format data is saved as .saf files.

.dat

.cvs

.dat Crosstalk data is saved as CrosstalkCor.dat

.tif Focus image files are saved as

Description

format (Tagged Image File)

Gain calibration data is saved as GainCalibration.dat files.

Gain calibration data is stored as a comma separated list (.cvs files). For analysis these files can be loaded in Excel or another calculation program.

files.

• Focus1.tif for first autofocus scan

• Focus2.tif for second autofocus scan

• Focus3.tif for third autofocus scan (only

created during MTP-autofocus)

Log

Each time the LSServer is started, the LSServer.log file is overwritten;

.log

.log1 -.log5

old data is saved in LSServer.logn file.

Log file data is saved in the following file format:

• LSServer.log:

A record of current measurement data.

• LSServer.log1 - LSServer.log5:

A record of earlier measurement data.

Note

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Locating Files

LSServer Files

By default the files associated with LSServer are stored as subdirectories in the directory where LSServer.dll is found:

C:\Program Files\Common Files\Tecan\Reader\….

The subdirectories are displayed in the table below:

Temporary Files

Type of File File

Extension

Measurement parameter

Slide adapter format

Gain calibration

Crosstalk

Temporary files needed for diagnostic and controlling purposes are stored in the directory:

C :\Documents and Settings\user_logged_in\Local Settings\

The file types are displayed below:

Type of File File Extension Directory

Focus

Log

.lsp Parameter

.saf SAF

.dat

.csv

.dat CalData

.tif Temp

.log

.log1 to .logn

Start

In the Measurement Control dialog box, Click Start…to start a measurement using the current measurement parameters. The Status dialog box appears and

displays the current process of the scanner as static text.

In the Time group box, the Elapsed time of the measurement and the Estimated run time are shown.

In the Gain control group box, the gain of the PMT can be adjusted online during the measurement.

The display of the Status dialog box can be changed using the Shrink or the

Default view button.

Click Break to interrupt the measurement.

The Status dialog box contains the following elements:

Instrument is…

This static text gives information about the current

process, e.g.:

Instrument is performing autofocus Instrument is measuring dark Instrument is measuring image

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Prescan

Image Prescan

Time

group box

Gain control group box

Please wait… progress bar

Shrink button Click Shrink to minimize the display of the Status

Default button Click Default to maximize the display of the Status

Break button Click Break to abort the current measurement.

• Elapsed time static text box

• Estimated run time static text box

• Gain 1 slider / spin control:

Use the slider or spin control to online adjust the gain in Channel 1.

• Gain 2 slider / spin control

Use the slider or spin control to online adjust the gain in Channel 2. (only active during dual parallel measurements).

Please wait… under the static text a progress bar indicates the progress of the ongoing process.

dialog box.

In the Measurement Control dialog box, click Prescan and select Image

Prescan to start an overview measurement for the first selected scan area.

The Image Prescan serves to position the autofocus scan lines and to select the

scan area for the final measurement. The image prescan procedure scans the complete Slide Area as defined in the selected .saf file. It is performed using the following default measurement parameters:

• Single Scan mode

• 40 µm scan resolution

• Large pinhole

• Optimize integration time selected

• No autofocus

• Scan Settings from Channel 1 only

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On clicking the Image Prescan option the Status dialog box appears and an

overview measurement is started.

The Status dialog box contains the following elements:

Instrument is… static text

The static text gives information about the actual process, e.g.:

Instrument is performing prescan

Instrument is measuring dark

Time group box

Gain control group box

• Elapsed time static text box

• Estimated run time static text box

• Gain 1 slider / spin control

Use the slider or spin control to online adjust the gain in Channel 1

• Gain 2 slider / spin control

Channel 2 is disabled in Prescan mode.

Please wait… progress bar

Shrink

button

Default button

Break

Please wait… under the static text a progress bar indicates

the progress of the ongoing process.

Click the Shrink button to minimize the display of the Status dialog box.

Click the Default button to maximize the display of the Status dialog box.

Click the Break button to abort the current measurement.

button

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Image Prescan Dialog Box

When the image prescan of the first selected area is complete, the Image Prescan dialog box appears with the Area Selection group box and the image

appears with an AOI (Area of Interest). The user is asked to set the Scan Area, the Autofocus Area and the AGC Scan Area. In Tecan LS with integrated barcode reader, it is also possible to set the Barcode Area. Click Apply to confirm the newly defined areas. Click OK to save the settings and close the dialog box.

The Image Prescan dialog box contains the following elements:

Area Selection group box

Scan Area option button

Select the Scan Area option button to adjust the boundaries of the rectangular AOI. To adjust a boundary, place the cursor along the edge or corner of the AOI and drag it when the 2-way cursor appears. To move the AOI, place the cursor in the middle of the rectangle and drag it when the 4-way cursor appears. Confirm the AOI position by clicking the Apply button.

figure 6-1

Minimum scan area: 1mm x1mm.

AOI

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Autofocus Area option button

Select the Autofocus Area option button to enable the Autofocus Settings group box.

Set the Autofocus lines by adjusting the boundaries of the rectangular AOI. To adjust a boundary, place the cursor along the edge or corner of the AOI and drag it when the 2-way cursor appears. To move the AOI, place the cursor in the middle of the rectangle and drag it when the 4-way cursor appears. Click Apply to confirm the newly defined areas. If HS or Wellmode Autofocus has been chosen, a green check mark appears and the Autofocus area is centered automatically to the scan area.

Legend:

barcode line

autofocus lines

scan area

AGC area

figure 6-2

Minimum distance between Autofocus lines: 3mm x 3mm.

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Barcode Area option button

Select the Barcode Area option button to enable barcode area selection. The barcode is always read centered to the slide width and must be set within the useable barcode area. The Barcode Area button is enabled only if a barcode top reader is available to

the Tecan LS Series Scanner and Read barcode has been selected from the Measurement Parameter dialog box.

Figure 6-3

The total slide area must be at least 37.5 x 15.0 mm, otherwise there is no room for a barcode. The barcode area is from 37.5 mm to the total slide length.

If your instrument is equipped with a barcode bottom reader, the barcode area is fixed. The barcode label has to be placed at the upper end of the slide. The barcode must cover at least the area about 5mm away from the upper end.

AGC Scan Area option button

Select the AGC Scan Area option button to enable the AGC area selection. If the AGC feature is activated the selected area will be scanned and that image will be consulted for the automatic gain calculation.

Set the AGC Scan Area lines by adjusting the boundaries of the rectangular AOI. To adjust a boundary, place the cursor along the edge or corner of the AOI and drag it when the 2-way cursor appears. To move the AOI, place the cursor in the middle of the rectangle and drag it when the 4-way cursor appears. Click Apply

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to confirm the newly defined areas, (see figure 6-2, on page 6-15 for a picture of the AGC area). AGC is only available in:

• Single Scan Mode

• Dual Sequential Scan Mode

It is not possible in Dual Parallel Scan Mode because the Cross Talk phenomenon with special dye combinations (e.g. Cy3 and Cy5), where signal from one channel will be detected in the other channel and can therefore lead to incorrectly calculated gain values. To start a scan with the AGC feature first of all a special area for AGC must be selected. This can be done from either the

Geometry Parameters tab of the Measurement Parameter dialog box or during a prescan from the Prescan dialog box:

Figure 6-4 Geometry Parameters tab Figure 6-5 Prescan dialog box

(For more information, see AGC (Automatic Gain Control) on page 6-37).

When a scan with AGC is started, the instrument performs a scan of the selected AGC-area. After this scan, all pixels of that image will be calculated and will be virtually drawn in a histogram, where the amount of pixels against the signal values will be plotted.

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On the Scan Settings tab of the Measurement Parameter dialog box, the values for calculating the AGC can be set: Noise level and Signal level.

Figure 6-6 Noise level and signal level

For more information, see Scan Settings Tab on page 6-38.

Noise level: = amount of pixels in the percentage, which will be discarded

Range: 0,01% - 1%

Signal level: = mean value of all pixels in the selected signal level range

will be set to

50.000 Range: 0,01% - 1%

50.000

%Noise level %Signal level

Amount of pixels

Signal intensity

65.535

Figure 6-7 Histogram of AGC image

Noise level are pixels, which have a very high signal value and derive from dust or other particles, which gave a high fluorescent signal. These pixels will be excluded for the calculation. For the right gain settings only all pixels in the signal level area will be consulted. Please keep in mind that only percentage of all pixels can be selected and not different signal values.

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A good starting point to find the right settings for the AGC will be 0,1% Noise level and 0,1% Signal level. To increase the overall signal, the noise level and/or signal level must be extended.

65.535

50.000

65.535

Amount of pixels

Signal intensit

Amount of pixels

Signal intensity

Before AGC scan

Figure 6-8 AGC Scan Functionality; Gain setting will be adjusted to the

appropriate value. The result is an automatic increase of the gain value!

Autofocus Settings group box

Autofocus Amplitude [mm]

Enter the amplitude in mm into the Autofocus Amplitude text box.

Select the appropriate autofocus from the Autofocus Selection group box:

• No Autofocus

• HS Autofocus

• Wellmode

• MTP mode

Select MTP in the Measurement Parameter dialog box to enable the MTP option button.

(For further information see chapter Advanced Autofocus).

Image Prescan Buttons

After AGC scan

Apply

button

OK button

Cancel button

Help button

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Click Apply to confirm the defined areas of the AOI.

Click OK to save data and close the dialog box.

Click Cancel to close the dialog box. The selected options are not saved.

Click Help to display the online help for the dialog box.

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Adapter Prescan

In the Measurement Control dialog box, click Prescan and select Adapter

Prescan to scan the currently used MTP adapter.

The Adapter Prescan serves to define the current slide adapter format (.saf) file.

The adapter prescan procedure scans the complete traverse path of the Tecan LS. It is performed using the following default measurement parameters:

• Single Scan mode

• 40 µm scan resolution

• Large pinhole

• Optimize integration time selected

• No autofocus

• Scan Settings from Channel 1 only

On the displayed traverse path it is possible to define the slide areas.

Enter the correct adapter height and sample height.

The chosen sample height of this dialog is taken as default height for the following adapter scan. The total height is only taken into account to avoid damaging the optics.

Maximum Values for total height = 16.0 mm

Maximum Value for sample height = 16.0 mm

Minimum Value for sample height = total height – 5.00 mm

Differences greater than 5.00 mm must be aborted, because of possible damage to the optics. The software produces a warning message for differences in the interval of 5.0 mm.

Caution

If the heights inserted in this dialog are not correctly entered, the

instrument may either become damaged or may no longer be able to

perform Its procedures correctly and the accuracy of the instrument

can no longer be guaranteed.

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After clicking OK on the Insert Plate Heights dialog box the instrument starts the

prescan:

After the adapter prescan has finished, the scanned image is displayed. The currently active .saf file is displayed as an overlay on the adapter prescan image. The red rectangles represents the available scan areas. The big green rectangle represents the outer dimension of the active area of the adapter.

After the instrument has performed the prescan, the first page of the adapter format wizard appears.

5 mm

14 mm

5 mm

Table MTP adapter

Adapter Prescan = Non confocal scan of the complete transport-table-area.

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The first page of the Adapter Format Wizard has the following buttons:

Reset

Click Reset to return all the values to the default settings.

button

Next button

Cancel button

Help

Click Next to save data temporarily and perform the second part of the wizard.

Click Cancel to close the dialog box. The selected options are not saved.

Click Help to display the online help for the dialog box.

button

After all the settings have been correctly entered click Next to continue to the second page of the wizard.

Example of current SAF parameters

Slide Thickness

Total Height

Sample

Table

Shuttle Height

Clamp Height

Carrier Height

MTP Adapter

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The second page of the Adapter Format Wizard has the following buttons:

Reset

Click Reset to return all the values to the default settings.

button

Back button

Finish

Click Back to save data temporally and perform the first part of the wizard.

Click Finish to save data and close the wizard.

button

Cancel button

Help

Click Cancel to close the dialog box. The selected options are not saved.

Click Help to display the online help for the dialog box.

button

After all the settings have been correctly entered click Finish to save the settings.

The Save dialog box will then appear.

To save the Slide Adapter Format file, type in the desired filename of the newly created .saf file and click Save.

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Focus Prescan

In the Measurement Control dialog box, click Prescan and select Focus

Prescan to perform a focus scan of the first selected scan area of the currently

used MTP adapter.

The focus prescan enables the user to define the desired focal plane and the focus offset on a z-scan image. This can also be used for probes, where the auto focus fails. The focus offset can be adjusted directly on the image, so refraction considerations are not necessary.

If no focus was previously selected, the focus prescan will be aborted with following error message: ‘No focus mode selected. Please select focus mode in Advanced Autofocus dialog!’

Fluorescence focus scans will be performed with the laser / filter setting of channel 1. This focus scan mode can be relevant for gel applications. The default settings are reflection modus with the red ( 633nm ) laser.

Click OK, and Focus Prescan dialog box appears:

Example of HS and well mode auto focus.

The Focus Prescan dialog box has the following buttons:

Reset button

OK button Click OK to save the settings. The focus values are stored for the

Cancel

button

Help button

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Click Reset to return all values to the default settings.

currently scanned slide. A message appears, which asks if the focus offset should only be stored for this slide or for all slides of the adapter.

Click Cancel to close the dialog box. The selected options are not saved.

Click Help to display the online help for the dialog box.

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Depending on the selected focus mode, two (HS and well mode) or three (MTP mode) focus scans will be performed.

The focus images will be displayed together with an overlay of lines, representing the Baseline (blue), Identified/scanning plane (red) and Focus Offset (green).

Manual Focus radio button: Changes in the three combo boxes changes the

plane that will be scanned for the next image scan. This plane will be displayed as red line in the focus images.

Focus Offset radio button: The green line represents the focus offset.

Example of focus prescan for MTP autofocus

After clicking OK, the following dialog box appears:

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6.3.5 Instrument

Plate/ Filter

In the Measurement Control dialog box, click Plate/ Filter…to move the plate carrier and the filter slides of certain instrument. The Movements dialog box will appear.

In the Movements dialog box, the respective In and Out buttons can be used to move the plate carrier into or out of the LS Series Scanner. The respective Out buttons for the filter slides can be used to move the filter slides out of the LS Series Scanner.

Click OK to close the dialog box.

The Movements dialog box contains the following elements:

Plate group box

Filter Slide 1 group box

Filter Slide 2 group box

OK button Click OK to close the dialog box.

The Plate group box consists of the following elements:

• Plate In button:

Click the Plate In button to close the door and to move in the plate transport.

• Plate Out button

Click the Plate Out button to open the door and to move out the plate transport.

The Filter Slide 1 group box consists of the following elements:

• In button

The In button is disabled. Insert the filter slide (making sure that it is properly oriented), until a slight resistance is felt, the LS Scanner will automatically move the filter slide in from this point.

• Out button:

Click the Out button to move out Filter Slide 1.

The Filter Slide 2 group box consists of the following elements:

• In button

The In button is disabled. See the description for Filter slide 1.

• Out button

Click the Out button to move out Filter Slide 2.

Help button Click the Help button to display the online help for the dialog box.

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Laser Control

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In the Measurement Control dialog box, select Laser Control… and the Lamp / Laser Control dialog box appears.

All lasers installed in your instrument are shown in the dialog box:

Click OK to save the changes and close the dialog box.

In the Laser Control dialog box specific lasers (1-4) can be activated / deactivated and laser power can be set (Laser 4).

The Laser Control dialog box contains the following elements:

Laser 1 (633 nm) check box

Laser 2 (532 nm) check box

Laser 3

check box

Laser 4

check box

OK button Click OK to save the selected options and close the dialog

Cancel button Click the Cancel button to close the dialog box.

Help button Click the Help button to display the online help for the dialog

Select Laser 1 check box to activate the 633 nm laser. Red LED is switched on at the rear of the instrument.

Select Laser 2 check box to activate the 532 nm laser. Green LED is switched on at the rear of the instrument.

Select Laser 3 check box to activate the 594 nm laser and the orange LED is switched on at the rear of the instrument.

Select Laser 4 check box to activate the 488 nm laser and the blue LED is switched on at the rear of the instrument. (The blue laser can be power controlled).

box.

The selected options are not saved.

box.

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6.3.6 Measurement Parameter

Edit…

In the Measurement Control dialog box, click Edit… to edit general options like Scan Mode, Stacker and/or Barcode as well as define Geometry Parameters,

Scan Settings and Autofocus Settings. The Measurement Parameter dialog box

appears:

The Measurement Parameter dialog box contains the following elements:

• General Tab

• Geometry Parameter Tab

• Scan Settings Tab

Depending on the installed hardware features, a fourth element can also appear:

• Excitation Angle

(See 6.3.7 Excitation Angle).

Cancel

Help

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Click OK to save the selected options and close the dialog box.

Click Cancel to close the dialog box without saving the options.

Click Help to display the online help associated with the dialog box.

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General Tab

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In the General tab the type of Scan mode can be selected, as well as the Barcode reader and the Stacker options for automation purposes. The user can

also select the option of having the plate move out of the instrument after scanning.

The General tab:

The General tab contains the following elements:

• Scan Mode group box

• Stacker group box

• Plate group box

• Barcode group box

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Scan Mode

group box

In the Scan Mode group box, several scan modes can be selected.

• Single option button:

Selects the Single Scan Mode. One excitation (= laser) and one emission (= filter) wavelength can be selected. The detection will be performed in channel 1. This is appropriate for single label experiments.

• Dual Sequential option button:

Selects the Dual Sequential Scan Mode. Two excitation and emission wavelengths can be selected. This is appropriate for dual label experiments in single channel instruments. The second label is measured immediately after the first and the two emissions are detected sequentially in channel 1.

• Dual Parallel option button:

Selects Dual Parallel Scan Mode. Two excitation and emission wavelengths can be selected and are measured simultaneously. This requires dual channel instruments as detection is performed in both channels at once and scanning is done in half the time. The Dual Parallel Scan Mode needs a Crosstalk correction (see Scan Settings tab) and a valid set of K-factors in order to compensate for spectral crosstalk.

For further information, refer to the chapter 6.4.6 Service Menu Crosstalk… description in this manual.

Stacker

Plate

Stacker group box

Plate group box

• Use Stacker check box:

The Use Stacker check box will be available, if a stacker is connected to the instrument and the instrument is turned on.

Selecting Use Stacker operates the instrument in an automatic mode. Autosave will be enabled automatically.

For further information about Stacker and Stacker Setup refer to the chapter 6.4.6 Service Menu -

Stacker Setup… description in this manual.

Tecan Connect Configuration

In the Measurement Control dialog box, select the General tab. Click

Configuration… and the Connect Configuration dialog box appears, in which

the plate settings and the number of plates used for the Demo Mode can

selected.

Click OK to close the dialog box and save the selected options.

Plates group box

Laser Handling

Demo Mode combo box

button

• Read plate barcode

Enabled if Tecan Connect is installed with barcode reader. If the checkbox is checked, a plate barcode will be read.

• Don’t read top most plate

If this box is checked the topmost plate will be ignored for stacking ( e.g. topmost plate can be used as light shield )

• Restack after last plate If this box is checked, Tecan Connect will automatically restack all plates from output stack to input stack.

Two check boxes are available:

• Start batch run only after all lasers have reached warm-up time

• Switch off laser after batch run has finished

• Number of plates

Enter the number of slides to be processed in Demo Mode. Maximum is 50. These setting will be ignored if the Tecan Connect instrument is connected.

Click the OK button to save the selected options and to close the dialog box

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Cancel button Click the Cancel button to close the dialog box. The selected

options are not saved.

Help

button

Advanced Autofocus

To edit the Autofocus parameters, select the Geometry Parameter tab in the

Measurement Control dialog box, and select Autofocus option button to make

Advanced Autofocus… available.

Click the Advanced Autofocus button and the Advanced Autofocus dialog box

appears.

Window Elements

The Advanced Autofocus dialog box:

Click the Help button to display the online help for the dialog box.

The Advanced Autofocus dialog box contains following elements:

• Z-Scan Height group box

• Focus Offset controls

• Focus Gain controls

• Focal Plane group box

• Autofocus Selection group box

The Advanced Autofocus dialog box contains following buttons:

button

Cancel button

Help

button

Click the OK button to save the selected options and to close the dialog box.

Click the Cancel button to close the dialog box. The selected options are not saved.

Click the Help button to display the online help for the dialog box.

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Z-Scan Height

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Z-Scan Height

group box

• Slide Thickness static edit box

The Slide Thickness static box gives information about the current slide thickness that has been defined in the Geometry Parameters tab.

The Slide Thickness is considered in displaying the slide scheme and needs to be defined for searching the focal plane within an appropriate range.

• Z-Scan End controls

Use the Z-Scan End controls (µm) to enter the End value of the

autofocus z-scan (= scan in vertical direction). Use the arrows or type in the value manually.

• Z-Scan Start controls

Use the Z-Scan Start controls (µm) to enter the Start value of the

autofocus z-scan (= scan in vertical direction). Use the arrows or type in the value manually.

For a Standard.saf file, the default start and end values for the autofocus search area are +/- 800 µm. The range considers the tolerance of the slide thickness, the tolerances of positioning the slide adapter to the instrument as well as internal tolerances of the instrument itself. However, it might be necessary to increase the z-scan to guarantee that the algorithm finds the focal position reliably.

Higher autofocus search areas (increased z-scan distances) prolong the time for autofocus determination.

Focus Offset

controls

• Focus Offset controls

Use the Focus Offset controls (µm) to measure a certain value below or above a focal plane. Set the value by spinning the arrows or by typing in the offset manually.

In certain cases the autofocus plane and the scan plane might differ, for instance: - slides with cover glasses, slides with membranes or filters. A certain value can be set as focus offset to perform the scan below (-) or above (+) the focal plane.

E.g.: For a cover glass with a thickness of 170 µm, the correct focus offset would be 113 µm, - calculated according to following formula:

Formula for the offset: d-[(n-1)/n]*d n= refractive index of the cover glass (= 1,5) d= thickness of cover glass

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Focus Gain

controls

Focal Plane

group box

Focus Gain controls

Use the Focus Gain controls to set the PMT gain for autofocus measurement.

The default value for the focus gain is 140. The gain is controlled automatically and dependent on the focus intensity profiles, but can also be adjusted manually either by using the arrows or typing in a value.

The intensity profile from autofocus scanning in z-direction shows the different surfaces of slides (different planes). The first surface found is defined as default focal plane, but any of three can be selected.

Plane 1 Plane 2

Plane 3

• Plane 1 option button:

Select Plane 1 option button to select Plane 1 (signal intensity) as focal plane calculated in the order from top to bottom from the Focus.tif images. The measurement will be performed on the selected plane 1.

• Plane 2 option button:

Select Plane 2 option button to select Plane 2 (signal intensity) as focal plane calculated in the order from top to bottom from the Focus.tif images. The measurement is performed on the selected second plane from the signal intensity profile in z-direction.

• Plane 3 option button: Select Plane 3 option button to select Plane 3 (signal intensity) as focal

plane calculated in the order from top to bottom from the Focus.tif images. The measurement is performed on the selected third plane of the signal profile in z.

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Autofocus Selection

Autofocus Selection group box

• No Autofocus option button Select No Autofocus option button, if no autofocus measurement is

required. The autofocus scan prior to the measurement is skipped and the

measurement is performed at the plane that is calculated from the Adapter height, Slide Thickness and Focus Offsets.

The scan level is calculated by considering the default height of the Tecan MTP Slide Adapter (= 11,5 mm), the slide thickness, as well as the Focus Offset.

No Autofocus eliminates the green autofocus scan lines from the

Geometry Parameter tab.

The No Autofocus option is recommended to use in combination with a

medium or large pinhole.

• HS Autofocus option button:

Select HS Autofocus option button to perform the so-called five point autofocus.

To determine the right focal plane, the plate transport is moved in vertical direction (z-direction) creating a signal intensity profile from the laser reflection at the surface of the samples. From the 5 detection points a focal plane will be determined.

• Well Mode option button:

Select the Well Mode option button to perform a two point autofocus prior to measurement.

The autofocus in Well Mode is appropriate for microplates and all similar formats, where due to wells or other reasons a continuous focal plane is missing. The algorithm considers only the edge values in the focus.tif image.

• MTP Mode option button:

Select MTP Mode option button to perform a triangle autofocus prior to measurement.

The autofocus in MTP Mode performs three z-scans (Focus1, 2 and 3) on three positions in a triangle order onto a microplate. Between these three points the overall focal area is calculated.

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Note

MTP Autofocus is aligned to the adapter,

i.e. all dimensions are oriented to the table.

In contrast, HS and Well Autofocus are slide oriented .

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6.3.7 Excitation Angle Tab

The excitation beam of the laser scanner usually strikes the sample with an angle

of approximately 25° (see Figure 6-10). This improves the confocality and

minimizes unwanted stray light effects due to back reflections. Therefore this configuration (=‘Default‘) gives the best performance for standard slides and other flat sample formats.

However there might be applications where the default angle of incidence is not optimal or the samples cannot be measured at all. A typical example is a microplate with printed arrays at the bottom of the wells. When measured from the top an inclined laser beam would usually be blocked by the walls and would not reach the bottom of the well. The variable beamshift feature of the laser scanner allows these samples to be measured as well. The angle of incidence for the fluorescence excitation can be varied between 0° and 25° in steps of 0.1° via the software.

The geometry of the sample determines the angle of incidence. The angle should be set to a value that allows the excitation beam to excite the full area of interest at the bottom of your sample without hitting the wall of the MTP before reaching the measurement surface.

If the angle for the scan is changed, the angle used for autofocus should also be adjusted. Because the autofocus does not work with normal incidence, the lowest angle accepted by the scanner is 10°. If your sample has high walls we recommend using the lowest possible value (=10°).

If ‘Wellmode‘ is selected (in the advanced autofocus settings menu), except for the image scan, it is not necessary that the full area covered with spots is hit by the laser beam for the autofocus. In that case some shadowing effect can be tolerated. A minimum of 2.0 mm at the center part of the bottom is required however.

Default

It is recommended to select Default for all ‘flat‘ samples (e.g. slides).

Angle is set to 25° for both the image scan and for autofocus.

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MTP Mode

Select MTP Mode for most MTP applications.

Angle is set to 0° (normal incidence) for image scan and 10° for autofocus.

Set Beamshift

Set Beamshift may be a useful optimization parameter if your sample has only

‘flat‘ walls with a relatively low aspect ratio.

The excitation angle for the image scan can be set to any value between 0° and 25° in 0.1° increments

The angle of incidence for the autofocus scan can be set to any value between 10° and 25° in 0.1° increments

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Increasing the angle of incidence might reduce the background in your images. However, if it is too high for your kind of sample only a part of your sample area could visible on the scanned image. If the autofocus angle is set too high autofocus might fail. Use simple geometry according to figure below to calculate the appropriate angles for your samples.

6.5

25°

Figure 6-9

Adjustable laser beam angle (0.1° increments)

High working distance (6.5 mm)

0°

6.5 mm max object depth

(absolut range of object height)

5-16 m m

(Set beam angle to 0° to avoid shadows in wells)

Figure 6-10

Note

If your microplates have a transparent bottom and your process allows

them to be measured upside down it is still a good idea to compare an

upside down measurement with default settings with an upright measurement with the angles set to MTP mode or another value

determined as optimum for your samples.

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Load…

In the Measurement Control dialog box, click Load… to open existing Measurement Parameter (.lsp) files. The standard Windows

appears.

In the

Open dialog box all existing Measurement Parameter files will be shown.

After selecting the requested file it will appear in the filename line. Click load the new measurement parameters and close the dialog box.

When a Measurement Parameter file is opened the defined measurement parameters of the file will be loaded, which include all of the settings in the Measurement Parameter dialog box on the General, Geometry Parameter, and Scan Settings tabs.

Note

The selection of the slides to be processed will use the default settings

The Open dialog box:

in which all slides are selected (see Slide Settings).

Open dialog box

OK to

Open dialog box is the standard Windows file open dialog box. It contains

The the following elements:

In the

Look in

combo box

Workspace

list box

File name edit

box

Files of type

combo box

Open as read

check

only

box

Open

button

Look in combo box, the folder from which the

measurement parameter file can be opened, is selected.

The

Workspace list box shows the files and folders selected in

the

Look in combo box.

In the File name edit box the measurement parameter file can be selected. Either type the name of the file or use the selection to obtain a list of file names from which the measurement parameter file can be selected.

All Tecan measurement parameter files have the file extension

Look in

*.lsp.

Select being changed.

Click the parameter file (*.lsp).

Open as read only to view the file and protect it from

Open button to load a selected measurement

Cancel button Click the Cancel button to close the dialog box without loading

a file.

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Save…

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In the Measurement Control dialog box, click Save… to save the current measurement parameters under the selected filename. The standard Windows

file

Save As dialog box appears. Click OK to save the new parameters as a

Measurement Parameter (.lsp) file and close the dialog box. When a Measurement Parameter file is saved the currently defined measurement

parameters will be saved, which include all of the settings in the Measurement Parameter dialog box on the General, Geometry Parameter, and Scan Settings tabs.

Note

The selection of the slides to be processed will not be saved.

If a measurement parameter file with the same name already exists it will be overwritten.

The

Save As dialog box:

The

Save As dialog box is the standard Windows file Save As dialog box. It

contains the following elements:

In the

Save in

combo box

Workspace

list box

File Name edit

box

Save as type

combo box

Save in combo box, select the drive and the folder in

which the measurement parameter file should be saved.

The

Workspace list box shows the files and folders selected in

the Save in combo box.

Enter the File Name for your measurement parameter file or select one from the list.

All Tecan measurement parameter files are saved with the file extension

*.lsp.

Save button Click the Save button to save the current measurement

parameters in a file with the extension *.lsp.

Cancel button Click the Cancel button to close the dialog box without saving.

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6.3.8 Settings

Slide Settings

In the Measurement Control dialog box, click Settings … to display the slide

setting options:

• The filename(s) of the scanned image(s)

• The slides to be processed

• If the scanned image(s) should be saved automatically or not

• If the images should be stitched or not

• If the stitched image should be flipped or not

Filename can be either a standard name or an individual Filename Format.

The

AutoSave, Stitching of resulting images or Flipping can be selected, if desired.

Under

The

Measure, select the slides to process.

Slide Settings dialog box:

The

Slide Settings tab contains the following elements:

• Filename group box

• Measure

• Filename Format

•

Date Format group box

•

Stitch resulting images check box

• Rotate image group box

• Files group box

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Filename

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The Slide Settings tab also contains the following buttons:

Click

button

Cancel

button

Help

button

OK to save the selected options and close the dialog box.

Click

Cancel to close the dialog box without saving the options.

Click

Help to display the online help for the dialog box.

Filename

group box

In the Filename group box a standard name for the scanned image can be selected. This name will be part of the image filename shown later as the title of the image window.

The

Filename group box contains the following elements:

• Select the

standard name edit box. The name gets part of the image filename.

Normally, the standard image filename is grouped as follows:

Standard name + Filename Format

The Filename Format cannot be changed. It is fixed to:

Use standard name check box to enter the name in the

▪ Barcode - excitation wavelength - slide position - current date - image

counter, - if a barcode reader is installed and if the barcode option is selected.

▪ Excitation wavelength - slide position - current date - image counter, -

if no barcode reader is installed.

• In the

standard name edit box the image name must be entered. The

following limits must be considered:

▪ Maximum name length: 50 characters ▪ Input data allowed:

Alphanumerical data A -Z, a-z, digits 0-9 and underline.

Clear the

Measure grid box / Filename grid column)

Use standard name box to enable the Filename grid column (see

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Measure

grid box

Before starting a scan, the slides to be processed and name(s) of the image(s) must be defined (all slides selected is the default setting). This is done in the

Measure grid box consisting of 3 columns and a variable number of rows:

• The

For example, using a slide adapter with slide positions arranged in 2 columns and 2 rows the Slide grid column shows:

• The Process grid column displays check boxes for each slide defined. All

Select the check boxes of the corresponding slides to be processed.

Select several rows and press slides

Click the heading of the Process column to select all of the rows in this column. Press

to be processed

• In the Filename grid column the image name must be entered. The

Slide grid column displays the slide position in alphanumerical order.

The first character represents the row, the second character the column position in the defined slide adapter.

= slide on position column 1 / row 1

= slide on position column 1 / row 2

= slide on position column 2 / row 1

= side on position column 2 / row 2

slides selected are processed during next measurement.

Insert Key / Delete Key to mark the selected

to be processed / not to be processed.

Insert Key / Delete Key to mark all of the slides to be processed / not

following limits should be noted:

▪ Maximum name length: 50 characters ▪ Input data allowed:

Alphanumerical data A -Z, a-z, digits 0-9 and underline.

The

Filename grid column is disabled if Use standard name check box is

selected. The name entered in filename.

The

Filename grid column is enabled if Use standard name check box is

cleared. The name entered in filename.

standard name edit box is used creating image

Filename grid column is used creating the image

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Filename Format

group box

The Filename Format group box contains the following elements:

• The

The user.

When using standard name (Use standard name check box is selected) the filename format is fixed to:

• Barcode - excitation wavelength - slide position - current date - image

• Excitation wavelength - slide position - current date - image counter, if no

If no check boxes are enabled, the Filename Format cannot be changed.

Clear and the

Filename Format is user-definable.

Barcode check box is automatically selected, if a barcode reader is

connected to the instrument and is enabled for use. If barcode reading fails, barcode is set to “xxx”.

Wavelength check box must be selected, if the excitation wavelength

is to be part of the image filename.

Position check box must be selected, if the slide position is to be part

of the image filename.

Counter check box is automatically selected and cannot be reset by the

counter, if a barcode reader is installed and the barcode option is selected.

barcode reader is installed.

Use standard name to enable the following check boxes / option buttons

Date Format group box:

Wavelength check box

•

Position check box

•

Date Format

group box

Stitching

Stitch resulting images

check box

• The Date Format is automatically selected and cannot be reset by the user,

but the type of date format can be selected:

▪ DDMMYY - Day Month Year ▪ YYMMDD - Year Month Day

Select the Stitch resulting images check box to combine all scanned slides together into one image.

The filenames used for parts of the stitched images are automatically set to standard name.

The filename of the stitched image is set to:

Format

, where barcode option and slide position are set to “xxx”.

Standard name + fixed Filename

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Rotate Images

Leave Images

Flip image up/down

For example, if selected, the result will be as follows:

Flip image left/right

Flip image up/down is

For example, if

Image is not changed

Flips image vertically.

Flips image horizontally.

Flip image left/right is selected, the result will be as follows:

When

resulting images

be as follows:

Flip image up/down and Stitch

are selected, the result will

When

Flip image left/right and Stitch resulting images are selected, the

results will be as follows:

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Rotate image

For example, if

When as follows:

Rotates image clockwise 180°.

Rotate image is selected, the result will be as follows:

Rotate image and Stitch resulting images is selected the results will be

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Files

AutoSave

check box

Select the AutoSave check box to save every scanned image automatically:

AutoSave on: all files will be stored in designated folder,

AutoSave off: all files will be stored in temp folder,

(see chapter Folder Options)

Filename = title of the image window = standard or special name according to the selected options in the

Directory =

\...

The images are saved as 16bit TIF format. Scanning of microplates or other slide adapter formats will open a lot of image

windows in the

AutoSave is automatically enabled in Stacker Mode; no user action

necessary.

To save memory and user time the first window will be closed after 10 scans.

(10 active pictures is the default setting). So the user won’t see all the scans

Tecan Array Pro Software subdirectory = Array Pro 45 \ Images

Tecan Array Pro Software.

Slide Settings tab

Note

at once, just the last 10.

Generate JPEG backup

check box

The image will also be saved as a .jpg file and saved in the same folder as the .tif file.

Note

There must be an equal number of pictures in each column and in each

row, (i.e. the pictures must form a complete rectangle,

e.g. 2 x 3, 4 x 6, etc.)

Improper selection of images to be stitched can cause an unexpected

stitched image result.

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Folder Options

In the Measurement Control dialog box, click Settings … to open the Slide Settings dialog box:

Select the Folder Options tab to view the current file storage paths.

By clicking the

• Images (*.tif; *.jpg)

• Parameters (*.lsp)

• Adapter (*.saf)

• Temp: all files (.tif, .jpg, .lsp, .saf, autofocus images) when

not been selected, (see Files on page 6-60).

Example:

After a scan is finished:

A folder with the current date is created, (Y_M_D).

In the date folder, a folder with the current time is created, (h_m_s).

The current .lsp file will be saved as _SCAN_Time.lsp) (e.g. _SCAN_141149.lsp; 2 pm, 11 minutes and 49 seconds).

Experiment Folders:

Browse button, paths can be defined for the following file types:

AutoSave has

Date

Scan Parameter and Image files:

6.3.9 Slide Adapter Format

The Slide Adapter Format group contains the following elements:

Load button Click the Load button to open the Open Slide Adapter Format

dialog box: SAF can be selected.

See Slide Adapter Format for more information.

6.3.10 Slides to Process

The Slides to process group gives a general view of the slide / plate format

Scanlist

used and the arrangement of available scanned after pressing scanned are dark gray.

The selection can be changed in the Measurement dialog box. Click on a slide to toggle its selection. For Prescan, only the first selected slide will be scanned.

Start / Prescan button are green, those that will not be

scan areas. Scan areas that will be

A scan list is a text file (.txt) for batch processing: (e.g.: created with Notepad or Microsoft Text Editor)

Example1:

S,160,0,633,670,0,0

Scan Mode: S ( Single ), DS ( Dual Sequential), DP ( Dual Parallel )

Gain Channel1:160, Gain Channel2: 0

Laser Channel1:633

Filter Channel1:670

Laser Channel2:0

Filter Channel2:0

In this example, a single scan is performed with a gain of 160, with red laser and red filter.

The text file must be located in the same folder as ArrayPro32.exe file. (Default folder

C:\ArrayPro4.5).

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When using a scanlist file the following dialog box will appear after clicking Start:

Click

Yes and the following dialog box will appear:

Click the button is not clicked the scan starts automatically after the wait time has expired.

Example2:

Scan Mode: S ( Single ), DS ( Dual Sequential), DP ( Dual Parallel ), Scan Mode, Gain Channel1, Gain Channel2, Laser Channel1, Filter Channel1, Laser Channel2, Filter Channel2

In this example, three different scans are performed:

First a single scan is performed on each scan area of the adapter with a gain of 180, with red laser and red filter.

Next a dual parallel scan is performed with a gain of 220 in the first channel with orange laser and orange filter and a gain of 190 in the second channel with blue laser and blue filter.

Then a dual sequential scan is performed with a gain of 120 in the first channel with red laser and red filter and a gain of 100 in the second channel with blue laser and blue filter.

Proceed button to skip the warm up time of the laser. If the Proceed

S,180,0,633,670,0,0

DP,220,190,594,635,488,535

DS,120,100,633,670,488,535

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6. LSServer, Scanner Shell and Download

6.4 LS Scanner Shell

6.4.1 General

The following chapters contain the description of the special LSServer options, which can be viewed and utilized in the Shell software is required for the following:

• Defining filter slides

• Locking and unlocking the instrument for transportation purposes

• Calibrating the gain of PMTs

• Defining crosstalk

• Setting up and calibrating the stacker

6.4.2 Starting Scanner Shell

Close all programs using Tecan LSServer.

Click the

The

Scanner Shell icon in the Tecan program group.

Scanner Shell window is displayed.

Scanner Shell program. The Scanner

6.4.3 Window Elements

The

Scanner Shell main window contains a menu bar, a toolbar, the window

and the status bar.

area

The

window area displays the type of the connected LSServer. For example: LS

SERIES SCANNER

Simulation.

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Menu Bar

Toolbar

6. LSServer, Scanner Shell and Download

Refer to chapter 6.4.5 Scanner Shell Menus for information of the menu options.

The following buttons are available on the toolbar:

Click the About button to show the About dialog box.

It contains the following elements:

• Program information

• Version number

• Copyright

Click the Help button to display the online Help for elements such as:

• Buttons

• Menus

• Windows

Status Bar

Click the Connect button to directly connect to an instrument.

Click the Measurement button to display the Measurement Parameter

dialog box.

The Start Measurement button appears gray, because measurements

cannot be started from the Scanner Shell software.

Click this button to show the Measurement Control panel.

The Status bar displays the following information:

• Help access: Press

• Current status of the keyboard toggles:

block lock),

SCRL (Scroll lock).

F1 for Help

CAP (caps lock), NUM (Numeric

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6. LSServer, Scanner Shell and Download

6.4.4 File types used in Scanner Shell

The following file types are used with Scanner Shell:

File Type File

Extension

Measurement Parameter

Slide adapter

ormat

Gain calibration

Crosstalk calibration

Log

.lsp Measurement data is saved as .lsp files.

.saf Slide adapter format data is saved as .saf

.dat

.cvs

.dat Crosstalk data is saved as CrosstalkCor.dat

.log

.log1 - .log5

Description

files.

Gain calibration data is saved as GainCalibration.dat files.

Gain calibration data is stored as a comma separated list (.cvs files). For analysis these files can be loaded in Excel or another calculation program.

files.

Log file data is saved in the following file format:

• LSServer.log:

A record of current measurement data.

• LSServer.log1 - LSServer.log5:

A record of earlier measurement data.

Note

Each time the Scanner Shell is started, the LSServer.log file is

overwritten; old data is saved in LSServer.logn file.

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6. LSServer, Scanner Shell and Download

Locating Files

Scanner Shell Files

By default, the files associated with Scanner Shell are stored as subdirectories in the directory where LSServer.dll is found:

C:\Program Files\Common Files\Tecan\Reader\….

The subdirectories are displayed in the table below:

Temporary Files

ype of File File

Extension

Measurement parameter

Slide adapter format

Gain calibration

Crosstalk

Temporary files needed for diagnostic and controlling purposes are stored in the directory:

C :\Documents and Settings\”user name”\Local Settings\

The file types are displayed below:

ype of File File Extension Directory

Focus

Log

.lsp Parameter

.saf SAF

.dat

.csv

.dat CalData

.tif Temp

.log

.log1 to .logn

File Menu

Exit

In the File menu, select Exit to exit the Scanner Shell software.

Edit Menu

Not implemented in this version of the Scanner Shell software.

View Menu

Toolbar

In the View menu, select the Toolbar option to show / hide the Scanner Shell software Toolbar.

When the Toolbar option is selected (√) the Scanner Shell software Toolbar will be shown.

When the Toolbar option is cleared the Scanner Shell software Toolbar will be hidden.

Status Bar

In the View menu, select the Status Bar option to show / hide the Scanner Shell software Status Bar.

When the Status Bar option is selected (√) the Scanner Shell software Status Bar will be shown.

When the Status Bar option is cleared the Scanner Shell software Status Bar will be hidden.

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6. LSServer, Scanner Shell and Download

Instrument Menu

Connect

In the Instrument menu, select Connect or on the toolbar click the Connect button or press

This option allows the connection to an instrument. Before connecting the desired instrument the communication port must be chosen. To do this select

Port…

Setup on page 6-4 in this manual.

The desired instrument will be connected using the selected communication port. A message in the connection is successful or unsuccessful:

Working in Scan Mode

from the Setup menu. For further information refer to the chapter Port

Connection Message in window area of Scanner Shell

Shift + F5.

Setup

window area of Scanner Shell software shows that the

Unsuccessful

Successful

Working in Demo Mode

Connection Message in window area of Scanner Shell

Unsuccessful

Successful

Measurement Control Panel…

In the Instrument menu, select Measurement Control Panel… and the

Measurement control dialog box appears. In the Measurement control dialog box several groups, each containing

individual buttons, are shown that offer special operations for preparing and scanning data. Measurement parameters and measurement options are defined. The Start and Prescan buttons are not available in the Scanner Shell software.

For further information refer to the chapter 6.3 LSServer description in this manual.

Scanner Server Version: V 2.20 No instrument connected!

Scanner Server Version: V 2.20

LS SERIES SCANNER (+LS) 12902000004

V 3.00 08/03 IMAGING

V1.00 08/01 MEAS IMAGE iV 1.10……………….

Scanner Server Version: V 2.20 No instrument connected!

Scanner Server Version: V 2.20 LS SERIES SCANNER Simulation (+LSSim) 12345Sim V 2.20 12 / 02 SIMULATION V2.20 (RV1) iV 2.20……………….

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6. LSServer, Scanner Shell and Download

Move Plate and Filter…

In the Instrument menu, select Move Plate and Filter… and the Movements dialog box appears.

In the

Movements dialog box, specific In and Out buttons can be used to drive

the plate carrier or filter slides into or out of the LS Series Scanner. Click close the dialog box.

For further information refer to the chapter Plate/ Filter on page 6-26 description in this manual.

OK to

Edit Measurement Parameters…

In the Instrument menu, select Edit Measurement Parameters… or on the toolbar click the

Parameter

In the

Measurement Parameter dialog box general options like Scan Mode,

Stacker and/or Barcode as well as Geometry Parameters and Scan Settings can be defined.

For further information refer to the chapter Edit… on page 6-28 in this manual.

Edit Parameter button or press Ctrl + F5 and the Measurement

dialog box appears.

Start Measurement

Disconnect

The Start Measurement option is not available in the Instrument menu of the

Scanner Shell software.

In the Instrument menu, select the Disconnect option to disconnect the currently connected instrument. Another instrument can then be connected.

Note

This option is only available, if an instrument is already connected.

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tecan ls series, LS300 Operating Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

1.1 Instrument Safety

Slide adapters

Other formats

2.1.2 Modes of operation

Confocal or non-confocal

Excitation wavelengths

Emission wavelengths

Dual scanning

Resolution

Optimize sensitivity

2.1.4 Integrated Image Analysis Software Array Pro

3.2 Remove Transport Lock

4. Technical Description

5.1.1 Instrument Start Up

5.1.2 Instrument Power On

5.1.3 Connect to Instrument

5.1.4 Finish a Measurement Session

Disconnect from Instrument

Instrument Shut Down

5.2 Insert Slide(s) into Slide Adapter

6. LSServer, Scanner Shell and Download

6.1.4 Software Installation Procedure

Automatic Software Setup

Automatic Software Removal

6.2 Tecan LS Scanner Interface

6.2.2 Starting LS Scanner Interface

Port Setup

6.3.1 Starting the First Time

In the Measurement control dialog box, several groups, each containing

Measurement

Instrument

Measurement Parameter

Settings

Slide Adapter Format

Slides to Process

6.3.3 File Types used in LSServer

Locating Files

Start

Prescan

Adapter Prescan

Focus Prescan

Plate/ Filter

Laser Control

Edit…

Scan Settings and Autofocus Settings. The Measurement Parameter dialog box

Tecan Connect Configuration

Advanced Autofocus

6.3.7 Excitation Angle Tab

Default

MTP Mode

Set Beamshift

Load…

Save…

Slide Settings

Folder Options

6.3.9 Slide Adapter Format

6.3.10 Slides to Process

Scanlist

6.4 LS Scanner Shell

Menu Bar

Toolbar

Status Bar

6.4.4 File types used in Scanner Shell

Locating Files

File Menu

Edit Menu

View Menu

Instrument Menu