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TECAN Scanner Manual

1. 6 1 Help Menu LS Download eene 6 108 Scanner Shell ssesse 6 88 wieter CC 6 47 I image FPreSCaN E 6 12 Area Gelechon cece ceccc cece ceneeeeeeeeeeeees 6 15 Images Stitching ME 6 57 Instrument CIS AI WAG m hone 8 1 8 6 Bon E 8 8 SE 1 1 Sall 2 1 Installaton ee 3 1 Sere m T 5 1 Instrument Menu LS Download eene 6 105 Instrument Options 6 74 Integration time ses 6 38 L Lamp Control 6 88 See also Laser Control Language EE 6 74 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 Index Index Laser Control 6 27 Lasers eege eege 1 4 Excitation wavelengths 2 3 Log Ole Interface n00nnnnaannnoennneanenennnnne 6 88 Logfile ON MH ETE 6 88 LS Download tele WEE 6 105 dE 6 102 Print Preview eeeeeeeeseee 6 104 Print Report cccccceccceeeeceeeceeeeseeeeaeees 6 103 PING SOUP EE 6 103 Save Henort 6 102 Se IG era 6 101 LS Scanner Interface UE 6 4 ir alle E r P 6 4 LS Series Scanner eene 2 1 LS Server File TYD S ccccccecesesececsseeeseseeseseeeneeeens 6 9 Locating files seeeesseseesseeeeesse 6 10 M Measurement control Image Hrescan 6
2. Select the communication port which is used to connect the Twister from the COM Port combo box Normally the Twister is connected using COM 2 because COM 1 is reserved for other instruments such as the Tecan LS SERIES SCANNER Clicking OK saves all entered data and closes the Port Setup dialog box The Port Setup dialog box contains the following elements Stacker In the Stacker combo box the Twister must be chosen as the combo box connected stacker instrument COM Port In the COM Port combo box the COM Port into which the Twister combo box is connected must be selected When using the Tecan LS SERIES SCANNER instrument the LS Scanner instrument is normally connected to COM 1 and the Twister is connected to COM 2 OK button Click OK to save the selected options and close the dialog box Cancel button Click Cancel to close the dialog box The selected options are not saved Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download 6 4 8 Scanner Shell Wizards General The Scanner Shell is equipped with a number of wizards These wizards represent workflow modules which define a sequential procedure and guide the user step by step to perform a specific activity Standard Elements of a LS Scanner Shell Wizard Every wizard consists of a number of windows that are displayed in succession They provide the user with the necessary information and optio
3. 2 The plate transport is moved into the correct position 3 The user is asked to insert the transportation shock absorber pad 4 Instrument is locked 5 The instrument door is closed As long as the instrument is locked the LSServer Measurement Control cannot be started Thus scanning is not possible For information unlocking instrument see 6 4 10 The Transport Unlock Wizard description in this manual 6 76 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Gain Calibration 6 LSServer Scanner Shell and Download To start the Gain Calibration wizard select Gain Calibration in the Service menu A wizard guides the user through the gain calibration procedure The Gain Calibration option is implemented in Scanner Shell as a wizard It represents workflow modules which define a sequential procedure and guide the user step by step to perform a specific complex activity The Gain Calibration is needed to take into account differences in sensitivity between PMTs used in Tecan LS SERIES SCANNER instrument It is NOT only necessary for dual channel instruments The deviation between PMTs can be up to 500 96 The LS SERIES SCANNER is provided with calibrated PMTs Data from the PMTs becomes less accurate over the course of its life span so gain calibration should be repeated regularly After 100 days the user will be requested to start gain calibration again Note Gi Gain calibration n
4. Gain Calibration X Prepare gain calibration Check for correct filter slide in channel 1 and 2 S Set device parameter Set Autofocus I Il Prepare P measurement Perform test scan Back Cancel Help Click Next to start the procedure and the user is guided to the next screen of the wizard The Measurement Gain Calibration window 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 99 6 LSServer Scanner Shell and Download TECAN The Measurement Gain Calibration window In the Measurement Gain Calibration window the gain calibration is done Intensity measurements are performed with gains between 255 and 70 and the calibration data is calculated Gain Calibration X Start gain calibration PMT channel 1 Gain eu Io r S Calculate gain calibration data P Back Cancel Help Gain The Gain static text box shows the maximum gain value Gain is static text box measured from 255 to 70 to The to static text box shows the current gain value just measured static text box It finishes at value 70 Measurement The Measurement progress bar indicates the progress of the Progress Bar ongoing process Stop Click Stop to stop the measurement A message box is shown button Click Cancel to continue the measurement Clicking Next starts gain calibration and guides the user to the next screen of the wizard The End Gain Calibration window The End Gain Calib
5. Insert slide s into slide adapter as shown below W 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 autofocus algorithm might fail to find a focal plane 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 a f Figure 5 5 b Note The adapter is semi disposable The clamps that secure the slide might wear and the slides might become too loose in the adapter Please call your Tecan sales representative to order new adapters 5 4 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download 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 e Connecting to LS Series Scanner e Preparing measurement parameters in order to get the best results in scanning e Scanning in different modes Scanner Shell Functions e Connecting to Tecan LS Series Scanner e Preparing measurement parameters in order to get the best results in scanning e Ca
6. Note See Disinfection Certificate below for an example of the disinfection certificate that must be completed before the instrument is returned to the distributor for servicing 8 7 Disinfection Certificate This disinfection certificate must be completed before the instrument is returned to the distributor for servicing The certificate must be attached to the top of the outer package in which the instrument is returned t must be visible from the outside of the shipping container declare that the instrument in this package has been decontaminated or disinfected to remove or inactivate any biological material which could be dangerous to the service personnel or that it has never been exposed to any hazardous biological material 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 8 7 8 Cleaning amp Maintenance e TECAN 8 8 Disposal of Instrument Because the LS SERIES SCANNERS are exposed to potentially infectious chemical samples toxic or corrosive chemicals or radioactive chemicals waste management of the complete instrument must be carried out to ensure that there is no risk of contamination WARNING DEPENDING ON THE APPLICATIONS PARTS OF THE LS SCANNER MAY HAVE BEEN IN CONTACT WITH BIOHAZARDOUS MATERIAL e MAKE SURE TO TREAT THIS MATERIAL ACCORDING TO THE APPLICABLE SAFETY STANDARDS AND REGULATIONS ALWAYS DECONTAMINATE ALL PARTS BEFORE DISPOSAL Follow laboratory and
7. 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 11 6 LSServer Scanner Shell and Download TECAN Time e Elapsed time static text box group box e Estimated run time static text box Gain control e Gain 1 slider spin control group box Use the slider or spin control to online adjust the gain in Channel 1 e 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 Please wait under the static text a progress bar progress bar indicates the progress of the ongoing process Shrink button Click Shrink to minimize the display of the Status dialog box Default button Click Default to maximize the display of the Status dialog box Break button Click Break to abort the current measurement Prescan Image Prescan In the Measurement Control dialog box click Prescan and select Image Prescan to start an overview measurement for the first selected scan area The mage 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 e Single Scan mode e 40 um scan resolution e Large pinhole e Optimize integration time selected e No autofocus e Scan Settings from Channel 1 onl
8. Cancel Click Cancel to close the dialog box without saving the options Help Click Help to display the online help associated with the dialog box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download General Tab 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 Measurement Parameter L5 SERIES SC ANNER Simulation X Scan Mode Single C Dual Sequential C Dual Parallel Stacker Use Stacker Lontiguration Plate Iv Move plate out after measurement Barcode v Read barcode The General tab contains the following elements e Scan Mode group box e Stacker group box e Plate group box e Barcode group box 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 29 6 LSServer Scanner Shell and Download TECAN Scan Mode Stacker Plate 6 30 Scan Mode group box Stacker group box Plate group box In the Scan Mode group box several scan modes can be selected e 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 expe
9. The End Gain Calibration window saves the gain calibration data and finishes the gain calibration 6 98 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download For further information refer to the chapter 6 4 6 Service Menu Gain Calibration description in this manual The Start Gain Calibration window The Start Gain Calibration screen asks the user to insert specific special slide s into the instrument e Scattered light glass slide e Calibration filter slide with different OD filters The Start Gain Calibration window Gain Calibration X Before starting gain calibration Ingen Scattered light glass slide into slide position 1 Insert calibration filter slide into channel 1 and standard filter slide into channel A Cancel Help Click Next to confirm that the special slides have been loaded and the user is guided to the next screen of the wizard The Prepare Gain Calibration window The Prepare Gain Calibration window In the Prepare Gain Calibration window the Tecan LS SERIES SCANNER instrument is prepared for gain calibration The following steps are carried out e Check for the correct filter slides e Set special device parameters e Perform an Autofocus scan e Prepare for gain calibration measurement e Perform test scan A Status Control bitmap shows the result of the operation The Prepare Gain Calibration window
10. 1mm x1mm 6 14 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download Autofocus Area option button Select the Autofocus Area option button to enable the Autofocus Settings group box Prescan 1 E Area Selection Please select a rectangular ALII Area OF Interest to specify the scan area respectively autofocus area Press Apply Button to set selection C Scan Area C AGC Scan Area t BarCode Autofocus Settings Autofocus Amplitude mm fi U Autofocus Selection No Autofocus f HS Autofocus C Wellmode C MIP Mode Apply selected Autofocus Area om 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 Ei rowo 533 A1 270203 18 tif 1 1 Legend barcode line autofocus lines scan area AGC area figure 6 2 Minimum distance between Autofocus lines 3 mm x 3mm 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 15 6 LSServer Scanner Shell and Downlo
11. 3101 1 C22 2 No 1010 1 Physical Outer dimensions Width 812 mm 31 7 inches Height 355 mm 13 9 inches Depth 566 mm 22 1 inches Weight approx 60 kg Environmental Ambient temperature Operation 15 C 30 C 59 F 86 F Non operation 20 C 60 C 4 F 140 F Relative humidity Operation 90 non condensing Overvoltage category II Pollution degree 2 Usage Commercial Noise level lt 75 dBA Method of disposal Electronic waste infectious waste 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 7 3 T Instrument Features e ECAN 7 1 1 Lasers The LS SERIES SCANNERS are rated as a Class 1 laser product The Instrument contains up to four lasers rated as Class 3 laser products Therefore it is strictly prohibited to open the housing when power is switched on Caution Never open the instrument when power is switched on WARNING LASER RADIATION DO NOT STARE INTO BEAM CLASS 3B LASER PRODUCT INSIDE WARNING CAUTION THE USE OF CONTROLS OR ADJUSTMENTS OR PERFORMANCE PROCEDURES OTHER THAN THOSE SPECIFIED HEREIN MAY RESULT IN HAZARDOUS RADIATION EXPOSURE 7 1 2 Optional Barcode Scanner 7 4 The barcode laser scanner optional is for the identification of barcode labels on a slide This should not be confused with the automatic identification of filter slides standard The barcode device is able to read more than 20 different barcodes as Code 128 EAN 8 an
12. 6 LSServer Scanner Shell and Download TECAN Image Prescan Dialog Box When the image prescan of the first selected area is complete the mage 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 Area Selection Please select a rectangular A01 Area Of Interest to specify the scan area respectively autofocus area Press Apply Button to set selection scan Ares C AGC Scan Area C Autofocus Area BarCode Autofocus Settings Autofocus Amplitude rm T Autofocus Selection C No Autofocus f HS Autofocus Wellmode C MIP Mode Apply selected Autofocus Area o The mage 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 AOI figure 6 1 Minimum scan area
13. 6 2 Tecan LS Scanner Interface eseeeeeeeeeenen nenne 6 4 OVC ee 6 4 Starting LS Scanner Interface hiiit 6 4 EIC a DEMEURE 6 6 Starting title tt 6 6 Measurement Control EE 6 6 File Types used in Leer 6 9 MUZE tege ee EE Eeer 6 11 zit E teedeake 6 26 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 5 6 3 6 6 3 7 6 3 8 6 3 9 6 3 10 6 4 6 4 1 6 4 2 6 4 3 6 4 4 6 4 5 6 4 6 6 4 7 6 4 8 6 4 9 6 4 10 6 5 6 5 1 6 5 2 Oe TECAN Measurement Harameier eese eene nnn nnn nnn nnns 6 28 Excitation Angle Tab siauasteri peser undiesutkxu kane Ros enc Futasu su Meu tais 6 49 cg 6 54 Slo Ee Ee ee EE 6 62 Slides to Drocess nnn hnnn nnn nnn nnn nhan nasa u ad 6 62 LS Scanner Shell 1eeeeeeeeeeeeeeene nennen nnne nnn nnn 6 64 Ecc EE 6 64 Starting Scanner Shell e serena erra a anra eta 6 64 Window et 6 64 File types used in Scanner Shell 6 66 Scanner Shell Ee 6 68 Service MaN E 6 75 Stacker Setup Tweeter 6 89 Scanner Shell Eeer 6 91 The Transport Lock Ward esses 6 92 The Transport Unlock Ward 6 95 BS OW Od Q E 6 101 Starting GSouwnload sees 6 101 LSDownl ad El 6 102 Instrument Features 7 1 7 1 1 7 1 2 d Specifications oir enm ae RUP RES oe eee een ee eee ee eee 7 1 CDS US Ee 4 Optional Barcode Zammer 7 4 Reproductio
14. 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 Focus image files are saved as Focus1 tif for first autofocus scan Focus2 tif for second autofocus scan Focus3 tif for third autofocus scan only created during MTP autofocus Log file data is saved in the following file log1 log5 format e SServer log A record of current measurement data L SServer log1 LSServer log5 A record of earlier measurement data Note Each time the LSServer is started the LSServer log file is overwritten old data is saved in LSServer logn file 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 9 6 LSServer Scanner Shell and Download TECAN 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 Type of File File Directory Extension Measurement Parameter parameter Slide adapter format RE Gain calibration CalData CSV Crosstalk CalData Temporary Files Temporary files needed for diagnostic and controlling purposes are stored in the directory C ADocuments and Settings user_logged_in Local Settings The file types are displayed below Type
15. Load certain predefined parameter files e he Settings group element with the Settings button to enter the filename and to select the scan areas e The Slide Adapter Format group element to load existing Slide Adapter Format saf files e The Slides to Process group element to display arrangement of the scan areas e File size of chosen slides Measurement The Measurement group contains the following elements Start button Click the Start button to start a measurement with the current measurement parameter The Status dialog box is displayed Prescan button Click the Prescan button to select three different prescan modes o Image prescan o Adapter prescan o Focus prescan Instrument The Instrument group contains the following elements Plate Filter button Click the Plate Filter button to open the Movements dialog box Plate and filter can be moved Laser Control button Click the Laser Control button to open the Laser Control dialog box Laser type can be selected and power control can be set changed Measurement Parameter The Measurement parameter group contains the following elements 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
16. Measurement Parameters Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 25 6 LSServer Scanner Shell and Download TECAN 6 3 5 Instrument Plate Filter 6 26 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 Filter slide 1 Ip Out Filter slide 2 In Out 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 The Plate group box consists of the following elements group box e Plate In button Click the Plate In button to close the door and to move in the plate transport e Plate Out button Click the Plate Out button to open the door and to move out the plate transport Filter Slide 1 The Filter Slide 1 group box consists of the following elements group box e 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 e Out button Click the Out button to move out Filter Slide 1 Filter Slide 2 The Filter Slide 2 g
17. The standard resolution is 10 um For larger sample features there is the option to scan with 20 uim or 40 um thus both increasing scan speed and decreasing the amount of data omaller structures can be better resolved with 6 uim or 4 um pixel resolution Scan widths for a single path scan are 22 mm for 10 um 20 um and 40 um 6 um pixels and 15 mm for 4 um 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2 3 2 General e TECAN 2 1 8 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 eith
18. an individual Filename Format AutoSave Stitching of resulting images or Flipping can be selected if desired Under Measure select the slides to process The Slide Settings dialog box x Slide Settings Folder Options untitled Filename Format Barcode e Wavelength v Position Date Format GG DIM C AMDO Slide Process Filename Stitching untitled Stitch resulting images untitled untitled Rotate Images untitled Leave image F C Flip image up down F C Flip image lefteright E Rotate image F Files AutoS ave Generate JPEG backup Cancel Help The Slide Settings tab contains the following elements e Filename group box e Measure grid box e Filename Format group box e Date Format group box e Stitch resulting images check box e Rotate image group box e Files group box LL sl FT P W bw WM k 6 54 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download The Slide Settings tab also contains the following buttons OK Click OK to save the selected options and close the dialog box button Cancel Click Cancel to close the dialog box without saving the options button Help Click Help to display the online help for the dialog box button Filename Filename In the Filename group box a standard name for the scanned image can be group box selected This name will be
19. and the following dialog boxes appear in succession e The Start Setting Transport Lock window gives a short overview of the main focus of the wizard e nthe Position Transport window the plate is moved in and transports are initialized e Inthe Apply Absorber Pad window the user is asked to insert the shock absorber pad s In the End Setting Transport Lock window the transport lock procedure is completed Once the instrument is locked no further measurement is possible To unlock instrument the Transport Unlock wizard must be started This is done automatically at every attempt to connect to a locked instrument For further information about Transport Unlock wizard refer to 6 4 10 The Transport Unlock Wizard in this manual The Start Setting Transport Lock window The Start Setting Transport Lock screen gives a short overview of the main focus of the wizard The static text displays information about starting Transport Lock This is a purely informational window and no actions must be carried out in this window The Start Setting Transport Lock window Start setting transport lock x To prevent damage to intrument during transport transportation lock has to be set You will be led through this session in several steps Cancel Help The Next button guides the user to the next screen of the wizard the Position Transport window 6 92 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 200
20. 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 Measurement Parameter LS SERIES SCANNER Sin X General Geometry Parameters Scan Settings Excitation Angle Excitation Angle Defaut z optical axis C MTP Mode Image Scan Autofocus ho m mo Hanis object Cancel Help 6 50 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 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 Figure 6 9 Adjustable laser beam angle 0 1 increments High working distance 6 5 mm 6 5 mm max object depth absolut range of object height 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 valu
21. be saved to a file 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 7 6 LSServer Scanner Shell and Download TECAN 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 6 8 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 TECAN 6 LSServer Scanner Shell and Download 6 3 3 File Types used in LSServer The following file types are used with LSServer File Type File Description Extension Scanned image files are saved in a 16bit TIF format Tagged Image File Measurement Measurement data is saved as Isp files Parameter Slide adapter Slide adapter format data is saved as saf files ormat Gain calibration data is saved as
22. country specific procedures for bio hazardous or radioactive waste disposal Pollution degree 2 Method of Disposal Electronic waste Contaminated Waste infectious waste 8 8 1 Disposal of Packing Material According to Directive 94 62 EC on packaging and packaging waste the manufacturer is responsible for the disposal of packing material Returning Packing Material If you do not intend to keep the packing material for future use e g for transport and storage purposes Return the packaging of the product spare parts and options via the field service engineer to the manufacturer 8 8 2 Disposal of Operating Material WARNING BIOLOGICAL HAZARDS CAN BE ASSOCIATED WITH THE WASTE MATERIAL MICROPLATE OF THE PROCESS RUN ON THE SAFIRE ABSORBANCE READER TREAT THE USED MICROPLATE OTHER DISPOSABLES AND ALL SUBSTANCES USED IN ACCORDANCE WITH GOOD LABORATORY PRACTICE GUIDELINES INQUIRE ABOUT APPROPRIATE COLLECTING POINTS AND APPROVED METHODS OF DISPOSAL IN YOUR COUNTRY STATE OR REGION 8 8 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Index A Advanced Autofocus 6 32 6 44 AE ee e 6 35 dei EE 6 43 Scan lines eeeeenne 6 31 SEEC TO eonan EEE EE Ed de ERR T 6 47 B Ba OE MA 6 36 acie DOK se ensactetesnuennscesnscucueanceteans 6 31 Bi 6 31 C Channel 1 toab 6 79 Channel 2 tab eere
23. description in this manual Define Filter Slides In the Setup menu select Define Filter Slides The Define Filter Slides option is used to define the filter slides found in the currently connected instrument For example in Dual Channel Instruments two filter slides can be loaded simultaneously Parameters and comments for one two filter slides channel 1 channel 2 must be set before starting measurement The first time is done by a service engineer 1 Load the selected filter s into channel 1 slot by hand Caution You cannot define a filter slide that has been loaded into the channel 2 slot All filters must be defined in channel 1 slot 2 Inthe Setup menu select Define Filter Slides The Define current loaded filter slides dialog box is displayed KEEP IN MIND THIS OPTION IS NOT FOR GENERAL USE Caution The instrument can recognize predefined filter slides and the filter values should not be changed However if the filter in the filter slide have been changed by a service engineer or if a new undefined customized filter slide is to be used the filter slides need to be defined 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 71 6 LSServer Scanner Shell and Download TECAN The Define current loaded filter slides dialog box represents all filter slides found and defined in the currently connected instrument For each slide that is loaded a different tab dialog bo
24. for enabling the demo mode The Stacker Port group box contains the following elements e Select option button A list in which the appropriate communication port can be selected is shown e Find any option button The LSServer searches for any available port e 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 e None option button No Stacker available for the instrument 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 5 6 LSServer Scanner Shell and Download TECAN 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
25. 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 1 1 e TECAN 2 General 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 non confocal 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
26. is the standard Windows Print dialog box Click OK and the printing of the report of the current download is started Print Setup The Print Setup option in the File menu is used to select the desired printer and set the options for the printer Epson Stylus Photo 750 ESC P 2 Properties S Latus Ready Type Epson Stylus Photo 750 ESC P 2 Where LPT Comment Copies Number af copies D RER RER bk Collate Cancel C Selection See the Microsoft Windows manual for more details about the Print Setup dialog box When the required options are set click OK to close the dialog box 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 103 6 LSServer Scanner Shell and Download OTECAN Print Preview In the File menu select Print Preview and the program displays the Print preview screen and the first page of the report is shown ls PS Print Next Page Prey Page Tivo Page 1 Zoom Dut Close Instrument Connect instrument TECAN LS Firmware Download Report File Instrument Laserscanner Main CPL Open file Serial Number 12902000006 Date OF Aug 2002 Time 15 52 Instrumentname ee Filename 2 Hung Version e VW d O81 Previous Version W 1 10 Ur 7 02 Loxxx Mew Version Y AA 0804 il k Page 1 The Print Preview option has the following buttons Button Description Print Selects the print option to pri
27. of File File Extension me pee Temp leat to logn The default paths for saving files can be changed in the Slide Settings dialog box on the Folder Options tab See Folder Options for more information File Management 6 10 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 TECAN 6 LSServer Scanner Shell and Download 6 3 4 Measurement 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 Status LS SERIES SCANNER ml x Instrument i performing autofocus 1 Processing slide number amp 1 Time Elapsed time 00 00 54 dihhimm ss Estimated runtime 00 06 38 d hh mm ss Gain Control Gain 1 kon el 175 Gan 2 185 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
28. of Scanner Shell software shows that the connection is successful or unsuccessful Working in Scan Mode Connection Message in window area of Scanner Shell 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 Working in Demo Mode Message in window area of Scanner Shell 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 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 69 6 LSServer Scanner Shell and Download TECAN 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 dri
29. procedure This is a purely informational window and no actions must be carried out The Start Remove Transport Lock window Start remove transportation lock x Instrument is locked To activate instrument transportation lock has to be removed You will be led through this session in several steps Cancel Help The Next button guides the user to the next screen of the wizard the Remove Absorber Pad window 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 95 6 LSServer Scanner Shell and Download TECAN The Remove Absorber Pad window In the Remove Absorber Pad window the user is instructed to remove the transportation shock absorber pad found in instrument The Remove Absorber Pad window LT x Please remove the transportation shock absorber pad Back Cancel Help The Next button guides the user to the next screen of the wizard the Reset Transport Lock window Confirm that the transportation shock absorber pad has been removed Flap is closed automatically 6 96 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download Caution Do not try to open or close the instrument flap manually Instrument is initialized and Tecan Scanner Control is now available Caution Save packing materials and transport locks for further transportation purposes The LS series scanners must be
30. process The End Setting Transport Lock window End Transport Lock B X Transportation lack set To complete lock process please switch off instrument and close Tecan Imager Software Cancel Help Click Finish to complete the Transport Lock procedure and close the Transport Lock wizard 6 94 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 6 4 10 The Transport Unlock Wizard General The Transport Unlock wizard is designed to quickly guide the user through the transportation unlock procedure If the user tries to connect to a locked instrument or by selecting Instrument Connect from LS Scanner Shell menu the Transport Unlock wizard is displayed e The Start Remove Transport Lock window gives a short overview of the main focus of the wizard e Inthe Remove Absorber Pad window the user is asked to remove the shock absorber pad from the instrument e inthe Reset Transport Lock window lock status is removed and transports are initialized In the End Remove Transport Lock window the transport unlock procedure is completed Measurements are possible only after the transport lock has been successfully removed The Start Remove Transport Lock window The Start Remove Transport Lock screen gives a short overview of the main focus of the wizard A static text displays information about starting the Remove Transport Lock
31. second plane from the signal intensity profile in z direction e 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Autofocus Selection Autofocus Selection group box 6 LSServer Scanner Shell and Download e 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 e 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 de
32. shipped with the original packing and the transport locks must be installed CAUTION BEFORE TRANSPORTATION Place the instrument carefully in the indicated orientation before fixing the transportation locks otherwise the instrument will become damaged The Reset Transport Lock window In the Reset Transport Lock window lock status is removed from the instrument transportation lock is reset and transports are initialized Click Next to start the removal of the lock status and to initialize the transports A Status Control bitmap shows the result of the operation The Reset Transport Lock window Reset transportlock flag X Transportation lock will be removed Reset transportation lock v Initialize transports P The Next button guides the user to the next screen of the wizard the End Remove Transport Lock window 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 97 6 LSServer Scanner Shell and Download OTECAN The End Remove Transport Lock window In the End Remove Transport Lock window the static text informs the user that transport lock has been successfully removed and that the instrument is ready for use The End Remove Transport Lock window End remove transport lock X Transportation lock removed Instrument ready for use Cancel Help Click Finish to complete the Remove Transport Lock procedure and close Transport Unlock wizard The Gain Calibration Wiz
33. the current laser and filter combination selected in the Laser Channel 1 Channel 2 and Filter Channel 1 Channel 2 combo box Otherwise Crosstalk elements are not enabled and no crosstalk correction factor can be set The defined K factors for the current laser filter combination are displayed in the Crosstalk list box Clicking on a Crosstalk list item sets the K factor values appearing in K1 K2 static text box which will be used when starting the next measurement if the Crosstalk correction check box has been selected If the Crosstalk correction check box has not been selected no correction is done e heK1 static text box displays the current selected crosstalk factor K1 residual signal contribution from the first dye detected in the second channel will be corrected e he K2 static text box displays the current selected crosstalk factor K2 residual signal contribution from the second dye detected in the first channel will be corrected e Inthe Crosstalk list box all crosstalk factor records corresponding to selected laser filter combination are displayed Format K1 Dye 1 Name Date Format K2 Dye 2 Name Date For further information refer to the chapter 6 4 6 Service Menu Crosstalk in this manual Note In order to obtain reliable results it is strongly recommended to place reference spots with one dye only onto your sample These spots should represent every dye of your experiment and should be
34. 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 Caution When placing a sample into the sample carrier always make sure that the correct slide and slide carrier definitions are selected in the software Wrong definitions especially with special samples can lead to damage of the instrument or the sample 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 5 1 5 Operation e TECAN 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 STOP 5 1 2 Instrument Power On When switching the instrument ON the following actions are induced e The filter slides move into the reference position e The dichroic filter carrier moves into the reference position e he pinhole carrier moves into the reference position e The microplate
35. used for QC purposes 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 41 6 LSServer Scanner Shell and Download TECAN Integration time Sensitivity 6 42 Integration time group box Sensitivity group box Select the Optimize integration time OIT check box to increase the sensitivity of the scan due to longer integration of each pixel If the integration time is longer more photons i e more signal are gathered for each pixel resulting in higher intensity and better signal to noise ratio OIT not selected e Same Integration time for each scanning amplitude e Comparable signal values for all scanning amplitudes in the same resolution OIT selected e Increase sensitivity of scan due to longer integration time of each pixel e Longer integration time lead to more photons which can gathered for each pixel e Higher signal to noise ratio higher sensitivity e Not comparable signal values between scans with different amplitudes e Comparable range of amplitudes 22 mm 20 mm 15 mm 10 mm o mm Oversampling factor edit box Enter a certain Oversampling factor to average scan lines and to combine them into one pixel Oversampling factor can be a value between 1 10 For 4 um scan resolution n max 3 For 6 um scan resolution n max 4 For 10 um scan resolution n max 8 For 20 um scan resolution n max 10 For 40 um scan resolution n max 10 For exa
36. 004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 3 3 3 Installation Data cable to connector box 3 4 e TECAN 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 damaged 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 RS232 to computer Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN RS232 to instrument Connection for monitor cables Digital monitor Cu cables 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 3 Installation The pictures below show the connection of the interface cables to the back of the computer Connector box Data cable to instrument Analog monitor rahlac 3 5 3 In
37. 1 Filter combo box all filters found in filter slide loaded in slot 1 of current connected instrument are displayed The one used for crosstalk correction must be selected In Channel 2 Filter combo box all filters found in filter slide loaded in slot 2 of current connected instrument are displayed The one used for crosstalk correction must be selected The Date static box shows the current date Format DD MM YY In the Name edit box the user can type in his name or initials or some other comment 6 80 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 2004 11 K1 K2 list box OK button Cancel button Help button 6 LSServer Scanner Shell and Download The K1 K2 list box displays all data needed for crosstalk correction as a crosstalk factor record Format K1 Dye 1 Name Date Format K2 Dye 2 Name Date Special operations can be performed on a crosstalk factor record Add Click the Add button to collect all data entered button by the user in a crosstalk factor record calculate the crosstalk correction factor and add a new item to the list box Change Click the Change button to change the current button selected crosstalk factor record in list box Old record data is overwritten Delete Click the Delete button to delete the crosstalk button factor record of the selected list item Click the OK button to save the selected options in a data file called Crosstal
38. 12 Ir E EE 6 7 Measurement cece eeeceeeceeeeeeeeeeeeeeees 6 7 Measurement poarameter 6 7 le E 6 8 Slides to process 6 8 Starting a Measurement 6 11 Measurement Control Panel Scanner hell 6 69 Measurement parameter CNA EE 6 28 Loading ies 6 52 er i lelizcu 6 53 Measurement Parameters Editing Scanner Shell 6 70 MTP Mode iec e 6 47 N Non confocal measurements 2 3 O Optical Method 6 43 P Packing Material PINS OOS a mM 8 8 aiziu nuo BE 8 8 MOOG EE 6 38 e TECAN Plate Move plate out after measurement 6 30 Plate and Filter Moving Scanner Shell 6 70 Plate Filter Movement 6 26 PMT Seilen EE 6 38 Pont olio ate 6 4 Power Requirements sssuss 3 9 PES a 6 12 R FRO SONU OT BE 2 3 S ors 1 1 Ser FES hots EE 6 31 6 34 Scan mode Dual Parallel 6 30 Dual Sequential 6 30 elsi zlii 0 g RINT 6 29 AG c 6 30 Scan Mode Scanner hell EE 6 69 Scan Resolution 6 38 6 43 Scanner Shell Connect Instrument 6 69 Disconnect Instrument 6 70 Edit Measurement Parameters 6 70 Measurement Control P
39. 4 11 e TECAN 6 LSServer Scanner Shell and Download The Position Transport window In the Position Transport window instrument transport is initialized and plate is moved into the Transport Lock position Click Next to move the plate in and initialize transports Status Control bitmaps show the results of the operations The Position Transport window Position transport x Instrument transport will be driven in lack position Move plate in and initialize transports v Move to tranport lock position P x Back Cancel Help The Next button guides the user to the next screen of the wizard the Apply Absorber Pad window The Apply Absorber Pad window 2004 11 In the Apply Absorber Pad window the user is instructed to put the transportation shock absorber pad into the instrument and informed that the transportation lock will be set The Apply Absorber Pad window Remove Absorber Pad X Please apply the transportation shock absorber pad Tranportation lock will be set Cancel Help The Next button guides the user to the next screen of the wizard the End Setting Transport Lock window Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 93 6 LSServer Scanner Shell and Download TECAN The End Setting Transport Lock window The End Setting Transport Lock window informs the user that the transportation lock has been set and instructs the user how to complete the
40. 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 Oe TECAN Asia Tecan Asia Pte Ltd 80 Marine Parade 7113 04 Singapore 449269 Singapore Tel 65 44 41 886 Fax 65 44 41 836 Germany Tecan Deutschland GmbH Theodor Strom Strake 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 Mannedorf Switzerland Tel 41 922 8 922 Fax 41 922 8 923 2004 11 OTECAN WARNING CAREFULLY READ AND FOLLOW THE INSTRUCTIONS PROVIDED IN THIS DOCUMENT BEFORE OPERATING THE INSTRUMENT 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 Untersbergstrake 1A A 5082 Gr dig Salzburg AUSTRIA EUROPE Telephone 0043 0 6246 8933 FAX 0043 0 6246 72770 E mail office austria tecan com Copyright Information The contents of thi
41. 6 80 Confocal measurements 2 3 Connect Instrument Scanner Shell 6 69 e NETT 6 78 COMO OIA E 6 38 6 41 Correction facorki 6 41 Correction facorki 6 41 D IJ8te OP E 6 57 Define Filter Slides 6 71 Demo Mode Scanner 9lell desseseudekaseu ere dei eatur 6 69 Demo Mode Allowed 6 76 Disconnect Instrument LS Download 6 108 ocannef lel cavix uiis tick emi Sat Las dai eaa 6 70 Disinfection Lerttcaie cc ccccccecceeceeeeeeeeeseeeeeeeeeeees 8 7 Jar Dunn ER 8 6 eier MEE 8 7 SONOS EE 8 6 Disposal Operating Material 8 8 Packing Material nnaannennnannnennennnnn ennen 8 8 Disposal of Instrument 8 8 Download File OPENING T 6 106 Dual channel instruments eeeeeeeeeeennnn 2 3 F File Menu LS DO WhO AG E 6 102 Index File types SC hile CIP EE 6 66 Filename Format 6 57 Files Locating Scanner Shell 6 67 Filter elle 3 8 ENEE Le UE 2 3 Filter Slide A 6 73 FIEF SN 6 74 Firmware Neie le Te Le Eo 6 107 Focal Plane rris ax oA ra p Fw eh rr menace 6 46 FocUsS Galf MM 6 46 Focus E 6 45 e 3 9 8 2 G Gain Calibration 6 77 6 78 6 99 Gain Calibration Wizard 6 99 H Hardware Requirements
42. 798 Rev No 1 5 2004 11 e TECAN Optics 2004 11 Optics group box 6 LSServer Scanner Shell and Download The appearance of the Optics group box is dependent on whether dual scan single scan or dual scan sequential is selected In dual scan sequential Channel 1 1 Run and Channel 1 2 Run will appear instead of Laser Channel 1 and Laser Channel 2 Laser Channel 1 combo box Select the appropriate laser from the Laser Channel 1 combo box for excitation The selection of lasers is dependent on the type of instrument connected Laser Channel 2 combo box Select the appropriate laser from the Laser Channel 2 combo box for excitation The selection of lasers is dependent on the type of instrument connected Laser Channel 2 is only activated if Dual Parallel Scan Mode has been selected in the General tab Filter Channel 1 combo box Select the appropriate filter from the Filter Channel 1 combo box to match with the selected excitation wavelength in Laser Channel 1 All filters that have been defined in the filter slide which is inserted into Filter Channel 1 can be selected from the Filter Channel 1 combo box Filter Channel 2 combo box Select the appropriate filter from the Filter Channel 2 combo box to match with the selected excitation wavelength in Laser Channel 2 All filters that have been defined in the filter slide which is inserted into Filter Channel 2 can be selected from the Filter Channel 2 combo box Filter C
43. 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 Shuttle o eight z5 D 2 emm i ixl Clamp Height Carrier Height Table MTP Adapter 6 22 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download Adapter Format Wizard 2 2 X Adapter Format z Dimensian Adapter 5 ample Height 11 5 mm Total Height 145 mm slide Thickness 1 em Skirt height Carrier 48 r mm Clamp ER mm Shuttle r7 E mm Back Finish Cancel 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 Click Back to save data temporally and perform the first part of button the wizard Finish Click Finish to save data and close the wizard button Click Cancel to close the dialog box The selected options are not saved After all the settings have been correctly entered click Finish to save the settings The Save dialog box will then appear ELLEN 31 xl Gave in E saf e amp ES 8 96 well Greiner 1x6 MPA saf an virtuel 3x4 saf e S wellMunc 1x6 saf e Standard sar Standard 22 saf e test sat sat el virtuel 12x8 saf Save as hype slide adapter files saf Can
44. Detector Autofocus Barcode reader Mechanical Scanner Scan table Front door Performance Sensitivity Dynamic Range Pixel resolution Reading speed Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 e TECAN Characteristics 2 4 Lasers 633 nm HeNe 532 nm solid state 594 nm HeNe 488 nm solid state Low dark current photo multiplier tube s 70 255 units High aperture collection optics NA 0 6 with high working distance max 6 5 mm User selectable Held in exchangeable filter slides Up to 28 different filters supported by the instrument Additional filters can be defined and added by the user Two different beamsplitters automatically selected An additional beamsplitter can be implemented 3 pinholes of different sizes user selectable by software Monitors laser power Automatic user selectable parameters Optional Scans 40 rows per second 5 axis high precision module for scanning and automatic alignment of exact focus position Opens automatically lt 0 1 Fluoequivalent um Cy5 5 orders of magnitude 40 um 20 um 10 um 6 um 4 um 40 lines per second lt 4 minutes for full slide two colors for dual channel instruments 2004 11 e TECAN T Instrument Features Parameters Characteristics Electrical Power supply Auto sensing 100 120 V 220 240 V 50 60 Hz Power consumption 250 VA Main fuse T 2 0A 250 V slow blow Approvals DIN EN 61010 1ff UL
45. Interface description in this manual The desired instrument will be connected using the selected communication port A message in the window area of the LSDownload software shows that the connection is successful or unsuccessful Connection Message in report area of LSDownload Unsuccessful No instrument connected Successful LS SERIES SCANNER V V 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 105 e TECAN 6 LSServer Scanner Shell and Download Open Download File In the Instrument menu select Open Download File to browse for a upd file The standard Windows Open dialog box appears e Morphok Convok Ca Scripts HASP ITemplate Help UBL Sco 110 upd IDBFiles Images File name Santi up Files of type Download files upd e Cancel Open as read only E In the Open dialog box all existing Download files files will be shown After selecting the requested file it will appear in the filename line Click OK to load the new firmware and close the dialog box The Open dialog box is the standard Windows file open dialog box It contains the following elements Look in combo box Workspace list box File name edit box Files of type combo box Open as read only check box Open button Cancel button 6 106 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 In the Look in combo box the folder from
46. K1 K2 data list box All data selected entered in the Crosstalk dialog box is stored as a crosstalk factor record CrosstalkCor dat This can be added to K1 K2 data list box Clicking on an item in the list box displays corresponding data Crosstalk factor records can be added changed or deleted at any time Click OK to save all K1 K2 list box data in a special file CrosstalkCor dat and close the dialog box The first part of Crosstalk dialog box is divided into individual tabs 1 Channel 1 tab Before calculating crosstalk correction a so called K factor must be determined This is done during a measurement without taking into account crosstalk correction Adjusted values in this measurement session must be entered in the Channel 1 tab The Channel 1 tab contains the following elements Dye 1 In the Dye 1 edit box the description of used dye must be entered edit box K1 In the K1 edit box the correction factor for contribution of dye with edit box shorter emission wavelength into the detection channel of dye with longer emission wavelength must be entered The K1 default value is set to 0 This means no crosstalk correction will be done no other parameters Dye gain must be specified Gain 1 In the Gain 1 edit box PMT Gain channel 1 must be entered edit box Gain 2 In the Gain 2 edit box PMT Gain channel 2 must be entered edit box 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 79 6
47. LSServer Scanner Shell and Download TECAN 2 Channel 2 tab Before calculating crosstalk correction a so called K factor must be determined This is done during a measurement without taking into account crosstalk correction Adjusted values in this measurement session must be entered in Channel 2 tab The Channel 2 tab contains the following elements Dye 2 In the Dye 2 edit box the description of used dye must be edit box entered K2 In the K2 edit box the correction factor for contribution of dye edit box with longer emission wavelength into the detection channel of dye with shorter emission wavelength must be entered The K2 default value is set to 0 This means no crosstalk correction will be done no other parameters Dye gain must be specified Gain 1 In the Gain 1 edit box PMT Gain channel 1 must be entered edit box Gain 2 In the Gain 2 edit box PMT Gain channel 2 must be entered edit box Next part of Crosstalk dialog box contains the following elements Channel 1 Laser combo box Channel 2 Laser combo box Channel 1 Filter combo box Channel 2 Filter combo box Date static box Name edit box In Channel 1 Laser combo box all lasers found in current connected instrument are displayed The one used for crosstalk correction must be selected In Channel 2 Laser combo box all lasers found in current connected instrument are displayed The one used for crosstalk correction must be selected In Channel
48. N 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 Caution The LS Series Scanners are precision instruments and are very heavy At least two people must carefully lift the instrument from the box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 2
49. OTECAN Operating Manual for the LS Series Scanner Document Part No 30001798 2004 11 Document Revision No 1 5 Tecan Affiliates and Service Centers ud Austria Tecan Austria GmbH Untersbergstrasse 1a A 5082 Gr dig 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 ltalia 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 Austria Tecan Sales International GmbH Untersbergstrasse 1a A 5082 Gr dig 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 M lndal Sweden Tel 46 31 75 44 000 Fax 46 31 75
50. S Series Scanner No 30001798 Rev No 1 5 Index
51. Slide Adapter Format X Path AHRATS T ImagersLSsereersRelease sa Comment Slides Number of columns Number of rows Area width Area height Lett margin Upper margin Right margir Lower margin Adapter height Skirt height carrier Skirt height clamp Skirt height shuttle Cancel Help The Open SAF dialog box is used to load special slide adapter files For further information about creating and editing Slide Adapter Format files refer to the chapter Advanced Menu Edit SAF on page 6 85 description in this manual In the Open Slide Adapter Format dialog box the last loaded adapter file and its contents are displayed A drop down list contains all of the available Slide Adapter Format files Selecting a file shows all file data in the Comment text and Slide group box Click OK to set the selected Slide Adapter Format file as the current file format and close dialog box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 83 6 LSServer Scanner Shell and Download TECAN The Open Slide Adapter Format dialog box contains the following elements File In the File combo box all Slide Adapter Format files found are combo box displayed File data is shown as Comment in the Slide group box Comment n the Comment static text box a comment describing the slide static text adapter format is displayed Slides In the Slide group box slide format data corresponding to s
52. Small confocal mode focal depth 70 um gt Medium less confocal focal depth 300 um gt Large non confocal focal depth 800 um The small pinhole gives high background rejection and better signal background ratio If samples are bulky or have a large volume larger pinholes and less confocality give better reproducibility and higher signals e AGC Mode checkbox Only available in Single Scan Mode Dual Sequential Scan Mode Not available in Dual Parallel Scan Mode due to Cross Talk problems e Noise Level amount of pixels in the percentage which will be discarded Range 0 01 1 e Signal Level Mean value of all pixels in the selected signal level range will be set to 50 000 Range 0 01 1 See AGC Scan Area option button on page 6 16 for more information Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Crosstalk Crosstalk group box 6 LSServer Scanner Shell and Download The Crosstalk group box contains the following elements The Crosstalk correction check box Select Crosstalk correction to select a correction factor K factor from the Crosstalk list box Dual channel instruments operated in Dual Parallel Scan Mode are corrected for the spectral crosstalk from the first dye into the second detection channel by applying K factors The Crosstalk correction check box is automatically available if a Gain Calibration file and a Crosstalk file are found for
53. ables the logging of LSServer data When the Log Ole Interface option is selected V the LSServer data log will be activated When the Log Ole Interface option is cleared the LSServer data log will be deactivated In the Instrument menu select Connect to connect the instrument In the Advanced menu select Show Logfile The Show Logfile option starts the standard Windows editor i e notepad and shows the LSServer log file When the Show Logfile option is selected V the LSServer log file will be opened When the Show Logfile option is cleared the LSServer log file will not be opened In the Instrument menu select Connect to connect the instrument In the Advanced menu select Lamp Control The Lamp Control dialog box is used to select lasers and laser power For further information refer to the chapter Laser Control description in this manual In the Lamp Control dialog box specific lasers 1 4 can be activated deactivated and laser power can be set Laser 4 In the Help menu select About Information about the Scanner Shell program the version number and Copyright are displayed in the About dialog box 6 88 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 TECAN 6 LSServer Scanner Shell and Download 6 4 7 Stacker Setup Twister General The Tecan LS SCANNER instrument can operate in manual and automatic mode For automation purposes a stacker instrument such as t
54. ad TECAN 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 Es Useable barcode area Total Slide Length mu m 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 Prescan NEN x r Area Selection Please select a rectangular ADI Area Of Interest to specify the scan area respectively autofocus area Press Apply Button to set selection C Scan ra y R CScanAred y Autofocus Area C BarCode M Autofocus Settings Autofocus Amplitude mm fi 0 m Autofocus Selection C No Autofocus HS Autofo
55. ad Save Help In the Slide Adapter Format dialog box all parameters defining a standard slide adapter or a microplate must be entered e Number of slides columns and rows max 14 x 9 e Geometry settings width min 9 mm height min 9 mm margins For determining squares and distances keep in mind that the point of origin is top left Enter values of distances in mm 2 digits may be included for the specific parameters 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 85 6 LSServer Scanner Shell and Download TECAN The Slide Adapter Format dialog box contains the following elements Title bar Comment edit box Slides group box Adapter In the Title bar the name of the loaded adapter file is displayed In the Comment edit box the user can enter special information relating to the provided slide adapter In the Slide group box the slide adapter format must be defined Rectangular areas must be partitioned in rows and columns The number of elements per row and columns must be typed in the e Number of columns controls e Number of rows controls The dimensions of individual areas are determined in the e Area width controls e Area height controls The overall dimensions of the scanned surface can be entered e Left margin controls e Upper margin controls e Right margin controls e Lower margin controls Select Use Standard Adapter to set all adapter height data to def
56. allevel 2 0 01 Pinhole Small x m Crosstalk Crosstalk correction K1 o K2 Im m Integration time Optimize Integration Time m Sensitivity 3 Resolution Oversampling factor 1 Scan Resolution um 10 D Cancel Help 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 l Signal level Noise level E Ou X Q Me O c O E et E Signal intensity 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 6 18 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download A good starting point to find the right settings for the AGC will be 0 196 Noise level and 0 1 Signal level To increase the overall signal the noise level and or signal level must be exten
57. anel 6 69 MIS DO SNR RR SR P 6 69 Move Plate and Filter 6 70 Si a ro TT 6 64 Status EE 6 65 je TUR 6 65 NVI Zan Cl cM 6 91 SL E 2 3 6 38 Oversampling factor 6 42 Setup Port 6 71 Slide PAC OLN RPM RM 2 2 5 4 Slide Adapter Format 6 33 E OUN BEE 6 85 80 WEE 6 83 SIS ANG Aasen dad emp QUEUE EE DUNG 6 12 elle es ii e 6 54 Filename Format 6 55 Slide Thickness 6 31 6 33 Slides to porocess nonnnnennnennnnnnnnennnnennennnni 6 62 Index Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Software Automatic Hemoval 6 3 Installation Procedure 6 2 Heourements 6 2 Stacker qiie iore RR 6 30 POM OSUD E t 6 90 SED eee m 6 82 sj tsetse 6 11 Status bar Scanner hell ess 6 65 T Test COMMONS EN 6 75 Toolbar Index Scanner Shell ss 6 65 Transport ee 6 76 Transport Lock Wizard 6 92 Transport Unlock Wizard 6 95 Twister POM SC WIP ME 6 90 V View Menu LS Download 6 105 W Well Mode eeeeeeeeeeeeeeeee 6 47 Z Z ocan Height rore einn nn 6 45 2004 11 Operating Manual for the L
58. ant to use parameters From scanlist File All slides will be activated For reading Click Yes and the following dialog box will appear Wait until laser reached warm up time E X Tecan Connect starts mr 19 min and 52 sec Click the Proceed button to skip the wait dialog 1 0 Eeer Click the Proceed button to skip the warm up time of the laser If the Proceed button is not clicked the scan starts automatically after the wait time has expired Example2 S 180 0 633 670 0 0 DP 220 190 594 635 488 535 DS 120 100 633 670 488 535 scan Mode S Single DS Dual Sequential DP Dual Parallel Scan Mode Gain Channel Gain Channel Laser Channel Filter Channel 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 63 e TECAN 6 LSServer Scanner Shell and Download 6 4 LS Scanner Shell 6 4 1 General The following chapt
59. anual for the LS Series Scanner No 30001798 Rev No 1 5 3 9 e TECAN 4 Technical Description 4 Technical Description 4 1 Optical System Laser 4 4 Srat Fir Beam Cambier Laser 3 59420 mer Laser 2 54 310m F Pam Comber Laser 1 6 33ram 4 Beam Can bier Reference Diode BT Focus Lers 4 Focal Flare sample 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 4 Technical Description e TECAN 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 um resolution 4 mm are scanned within 10 s 4 mm 40 lines s 100 lines mm 10 um pixel size 10 s For this second direction the scanning speed is reciprocal to t
60. ard The Gain Calibration is needed to take into account the differences in sensitivity between PMTs used in Tecan LS SERIES SCANNER instrument For each PMT found in instrument the Gain Calibration must be done Tools needed for gain calibration are delivered with each instrument e Scattered light glass slide e Calibration filter slide with different OD filters e Normal filter slide Pay attention when loading the filter slides e Gain Calibration PMT 1 Put the calibration filter slide in filter slot 1 and the normal filter slide in filter slot 2 Gain Calibration PMT 2 Put the calibration filter slide in filter slot 2 and the normal filter slide in filter slot 1 Note To prevent damage to a PMT which has not been calibrated a normal filter slide must be loaded in the corresponding filter slot The Gain Calibration wizard is designed to quickly guide the user through the gain calibration procedure The following dialog boxes appear in succession The Start Gain Calibration window asks the user to put special slide s into the instrument The Prepare Gain Calibration window prepares the instrument for performing the gain calibration The Measurement Gain Calibration window carries out the gain calibration The Start Gain Calibration window the Prepare Gain Calibration window and the Measurement Gain Calibration window are repeated during gain calibration depending on the number of PMTs available in instrument
61. atch run has finished Demo Mode Humber of plates H Cancel Help Plates group box Laser Handling Demo Mode combo box OK 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 43 6 LSServer Scanner Shell and Download TECAN Cancel button Click the Cancel button to close the dialog box The selected options are not saved Help Click the Help button to display the online help for the dialog button box Advanced Autofocus To edit the Autofocus parameters select the Geometry Parameter tab in the Measurement Control dialog box and select Autofocus option button to ma
62. ault values equivalent to the Standard Tecan Slide Adapter Adapter Sample Height spin control In the Adapter Sample Height spin control the adapter height must be entered JubieH e OL The height of the Standard Tecan Slide Adapter is 11 5 mm The thickness of the slide that is inserted into the adapter must be edited as well Total Height spin control In the Total Height spin control the total adapter height must be entered Caution A Total Height outside of the recommended range can damage the sample and or the instrument 6 86 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Skirt height Preview group box Figure 6 11 Skirt heights Close Load Save Help 6 LSServer Scanner Shell and Download In the Skirt height group box the skirt dimensions of the slide adapter must be entered Carrier controls Enter the carrier skirt height A in Figure 6 11 Skirt heights Clamp controls Enter the clamp skirt height B in Figure 6 11 Skirt heights Shuttle controls Enter the shuttle skirt height C in Figure 6 11 Skirt heights Click the Load Standard Adapter button to set all adapter data to default values equivalent to the Standard Tecan Slide Adapter In the Preview group box the adapter format which corresponds to the entered parameters is displayed The Preview window displays the adapter format according to the data entered A
63. cel ZA To save the Slide Adapter Format file type in the desired filename of the newly created saf file and click Save 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 23 6 LSServer Scanner Shell and Download OTECAN 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 Optical Method Reflection Default C Fluorescence Focus Pinhole Small 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 Focus Prescan ES s 2 x m Focal Plane Position R Offset Focus Offset D ae ER Example of HS and well mode auto focus The Focus Prescan dialog box has the following butto
64. cess 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 9 and correct for angles of tilt of the sample or tolerances of the adapters Precisions for the axis are in the range of 1 2um 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 4 3 e TECAN 5 Operation 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
65. ct The Port Setup dialog box x Instrument Select Is SERIES SLAMMER C Find any Cancel Help NNI Fort Select Find any C Find any Demo mode Stacker port Select Find anu C Find ary C None Ce Demo mode 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 6 4 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download The Port Setup dialog box contains the following elements Instrument group box Port group box Stacker Port group box OK button Cancel button Help button The Instrument group box contains the following elements e Select option button A specific instrument can be selected choose in instrument type combo box e Find any option button The LSServer searches for available instruments automatically The Port group box contains the following elements e Select option button A list in which the appropriate communication port can be selected is shown e Find any option button The LSServer searches for any available port e 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
66. ction Please select a rectangular 40 Area OF Interest to specify the scan area respectively autofocus area Press amp pply Buttan ta set selechinn Scan Area Autofocus Arma BarCode Autofocus Settings Autofocus Amplitude mm U Autofocus Selection No Autofocus Bottom mm 44 24 E Advanced Autofocus HS Autofocus Slide Slide Adapter Format Wellmade C MiP Mode Slide Thickness pm i UU Load Load Standard Adapter Apply selected Autofocus Area zm 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 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 17 6 LSServer Scanner Shell and Download TECAN 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 x General Geometry Parameters Scan Settings Excitation Angle Optics Channel 1 1st run Channel 1 2nd run Laser nm 633 543 m Filter nm 670 Cy5 PMT Gain 130 130 AGC r DILL Ir Noiselevel 0 01 Sign
67. cus C Wellmode C MIP Mode Apply selected Autofocus Area TH 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 6 16 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 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 e Single Scan Mode e 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 Measurement Parameter L5 SERIES SCANNER Simulation xX General Geometry Parameters Scan Settings Excitation Angle Geometry Standard Top mm 52 28 Scan drea C Autofocus Left mm Right mm 8 16 est 15 52 est Area Sele
68. d EAN 13 For detailed information on barcodes please consult the corresponding manufacturer Note Depending on whether your instrument is configured for barcode top or barcode bottom reading the bar code label needs to be placed on the upper or the lower side of the slide Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN T Instrument Features 7 1 3 Reproduction of labels placed on the instrument Labels placed on the rear front of the instrument Complies with FDA radiation performance standards 21CFR Subchapter J Labels placed inside the instrument when housing is opened LASER RADIATION AVOID DIRECT EXPOSURE TO BEAM CLASS Ip LASER PRODUCT Label placed underneath lid 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 7 5 e TECAN 8 Cleaning amp Maintenance 8 Cleaning amp Maintenance 8 1 Introduction Caution Ensure that the sample is removed from the instrument before it is prepared for shipment If a sample is left in the instrument liquids may spill onto the optical parts and damage the instrument The cleaning and maintenance procedures are important in order to prolong the instrument s life and to reduce the need for servicing This section contains the following procedures e Liquid Spills e Replacing the Fuse e Instrument Disinfection 8 2 Liquid Spills Wipe up the spill immediately with absorbent material Dispos
69. ded Amount of pixels E eb X Q um O c O E et Signal intensity Signal intensity Before AGC scan After 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 e No Autofocus HS Autofocus e Wellmode e 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 Apply Click Apply to confirm the defined areas of the AOI button OK Click OK to save data and close the dialog box button Cancel Click Cancel to close the dialog box button The selected options are not saved Help Click Help to display the online help for the dialog box button 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 19 6 LSServer Scanner Shell and Download TECAN 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 us
70. 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 e Measurement group e Instrument group e Measurement Parameter group e Settings group e Slides to Process group Measurement control x Measurement Instrument Plate Filter nm Ga esit eee Measurement parameters Edi Ge Load ig Save Settings rey Settings Slide Adapter Format M Load Slides to process Standard Total Height 14 50 mm 5 ampleH eight 11 50 mm Filesize 4 18 53 MByte 6 6 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download The Measurement Control dialog box consists of the following elements e he Measurement group element with the Start and Prescan button e he Instrument group element to move plate and filters and to switch on lasers e he Measurement Parameter group element to Edit parameters or to Save and
71. displayed Or press F1 to view the online help for the current dialog box In the Help menu select About and the About dialog box appears E LSDownLoad MA Version E 3 05b beta zi Copyright 1333 by Tecan Austria GmbH The software version and copyright information can be viewed Click OK to close this dialog box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN f 7 1 2004 11 7 Instrument Features Instrument Features Specifications The table below lists the technical specifications for the instrument Parameters Characteristics Measurement Image processing PC Operating system Interface Data acquisition Samples to be measured Slide adapter Software controlled by external PC Integrated Software package Array Pro Delivered together with the instrument Windows 2000 Serial interface RS 232 and high speed data acquisition connector High speed 16 bit A D conversion Biochips on microscope slides and user defined substrates up to the size of microplates Holds 4 slides and allows automatic loading with microplate handling equipment Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 7 1 7 Instrument Features Parameters Optical Light sources Fluorescence Detector s Gain adjustment Optics Working distance Emission Filters Dichroic Beamsplitter Dual channel instruments only Pinholes Reference
72. dministrator rights on a PC with a Win 2000 operating system 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 A Welcome window informs the user about the beginning of the installation process Click Next to continue A Read Me File window informs the user about the new features of the setup 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 6 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download Automatic Software Removal Scanner Shell LSDownload can be removed using the Windows standard uninstall routine Make sure the ScannerShell LSDownload application is closed Select Add Remove software from Settings Control Panel in the Start menu Select the ScannerShell LSDownload icon and click Remove The Uninstall wiza
73. e determined as optimum for your samples 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 51 6 LSServer Scanner Shell and Download Load 6 52 e TECAN In the Measurement Control dialog box click Load to open existing Measurement Parameter Isp files The standard Windows Open dialog box 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 OK to 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 in which all slides are selected see Slide Settings The Open dialog box Open EE 2 xl File name MTP1 Isp Files of type Measurement parameter files lsp Cancel Open as read only E The Open dialog box is the standard Windows file open dialog box It contains the following elements Look in In the Look in combo box the folder from which the combo box measurement parameter file can be opened is selected Workspace The Workspace list box shows the files and folders selected in list box File name edit box Files
74. e of contaminated material appropriately Clean the instrument surfaces with a mild detergent For biohazard spills clean with a 5 10 solution of bleach in de ionized water o Wipe cleaned areas dry ee e 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 8 1 8 Cleaning amp Maintenance e TECAN 8 3 Replacing the Fuse e Turn the instrument OFF and unplug the main power cable from the instrument The fuse is located to the right of the main power cable connection in the rear of the instrument e Open the fuse compartment by inserting a screwdriver into the slot in the top of the cover and push the fuse holder out Main power socket Fuse compartment On Off Switch 12 ON 0 OFF e Pull the fuse out and replace the defective fuse s with the spare fuse s e Ensure that the fuse s has have the correct rating T 2 0 A 250 V slow blow WARNING RISK OF FIRE REPLACE ONLY WITH FUSES OF THE SAME TYPE AND RATING e Replace the fuse holder e Reconnect the mains cable e Turn the instrument on Caution If the fuse continues to blow call for service 8 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 8 Cleaning amp Maintenance 8 4 8 4 1 8 4 2 2004 11 Remote Control and Data Exchange FTP up download For exchange of large data sets between Tecan and your company Tecan offers an ftp site It is accessible through ft
75. e option button Select the Barcode option button to specify the reading position of the barcode by dragging the blue line by mouse or by typing in the distance in mm from the lower margin 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 This option is not available if your instrument is equipped with a barcode bottom reader The reading area is fixed in that case See Barcode on page 6 36 and Barcode Area option button on page 6 16 for more information e AGC option button Select the AGC Scan Area option button to start automatic gain control scan area selection AGC is only available in e Single Scan Mode e 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 See AGC Automatic Gain Control on page 6 37 and AGC Scan Area option button on page 6 16 for more information 6 32 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Slide Slide group box Slide Adapter Format 2004 11 Slide Adapter Format group box 6 LSServer Scanner Shell and Download The Slide group box contains the following elements e Slide Thickness box In the Slide Thick
76. ecan ch Please download Citrix ICA web client for 32 bit windows Contact your local dealer or email helodesk at tecan com to receive login information user name and password to access the conference ftp server When Citrix conferencing manager is activated and you have entered the meeting organized by the Tecan administrator please make sure that you have shared information about the according telephone connection on both sides for voice conversation At the very beginning of the application meeting the cursor on your screen have to be moved once by yourself in order to show it online on everybody desktop 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 8 5 8 Cleaning amp Maintenance e TECAN 8 5 Instrument Disinfection All parts of the instrument that come into contact with biological samples or other hazardous material must be treated as potentially infectious areas Caution It is very important that the instrument is thoroughly disinfected before it is removed from the laboratory or any servicing is performed on it Before the instrument is returned to the distributor for servicing it must be disinfected and a disinfection certificate completed If a disinfection certificate is not supplied the instrument may not be accepted by the servicing center or it may be held by the customs authorities 8 5 1 Disinfection Solutions If the laboratory has no specific disinfection procedure the fol
77. ect New or press Ctrl N to clear all fields In the File menu select Save Report or press Ctrl S and the Save as dialog box appears saveas Dave mt Cy Reports t EN Dave as type Test Documents tt Cancel AnotherD ownloadF eport Ext fansi E 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 select the drive and the folder in which the download report should be saved The Workspace list box shows the files and folders selected in the Save in combo box Enter the File Name for the download report or select one from the list The download report will be saved as a text file txt Click the Save button to save the current download report as a text file extension txt Click the Cancel button to close the dialog box without saving Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 TECAN 6 LSServer Scanner Shell and Download Print Report To print the report of the current download select the Print Report option in the File menu or press Ctrl P The following dialog box is displayed Print Epsen Stylus Photo 750 ESC P 2 Properties Status Ready Type Epson Stylus Photo 750 ESC P 2 Where LPT2 Comment Copies Humber of copies ji A Pages from 1 pl C Selection RES RER bk Collate Cancel This
78. elected group box files in File combo box are shown e Number of columns e Number of rows e Area width e Area height e Left margin e Upper margin e Right margin e Lower margin e Adapter height e Skirt height carrier e Skirt height clamp e Skirt height shuttle OK Click the OK button to set the selected file as current file and close button the dialog box Cancel Click the Cancel button to close the dialog box The selected button options are not saved Help Click the Help button to display the online help for the dialog box button 6 84 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download Edit SAF The Slide Adapter Format dialog box is used to edit or create Slide Adapter Format files Each file consists of data which represents a copy of a standard slide adapter or microplate MTP for example GREINER 96 well or NUNC 96 well To enter and save adapter parameters the Slide Adapter Format dialog box must be displayed In the Advanced menu select Edit SAF and the Slide Adapter Format dialog box appears Slide Adapter Format 545 Ei Comment New aun Slides Number of colurnns S Humber of rows Adapter Use Standard Adapter Adapter 5 ample Height 11 5 Area width Area height Total Height Skirt height Left margin Carrier Upper margin Clamp Right margin Shuttle Lower margin Preview Lo
79. ent Laser 4 Select Laser 4 check box to activate the 488 nm laser and check box the blue LED is switched on at the rear of the instrument The blue laser can be power controlled OK button Click OK to save the selected options and close the dialog box Cancel button Click the Cancel button to close the dialog box The selected options are not saved Help button Click the Help button to display the online help for the dialog box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 27 6 LSServer Scanner Shell and Download TECAN 6 3 6 Measurement Parameter Fdit 6 28 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 Measurement Parameter L5 SERIES SCANNER Simulation l x Scan Mode Single C Dual Sequential C Dual Parallel Stacker Use Stacker Sontiguration Plate Je Move plate out after measurement Barcode v Read barcode Cancel Help The Measurement Parameter dialog box contains the following elements e General Tab e Geometry Parameter Tab e Scan Settings Tab Depending on the installed hardware features a fourth element can also appear e Excitation Angle See 6 3 7 Excitation Angle OK Click OK to save the selected options and close the dialog box
80. er 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 2 4 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 3 3 1 Installation Unpacking amp 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 3 Installation 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 2004 11 causing a short circuit Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 3 1 e TECA
81. ers contain the description of the special LSServer options which can be viewed and utilized in the Scanner Shell program The Scanner Shell software is required for the following e Defining filter slides e Locking and unlocking the instrument for transportation purposes e Calibrating the gain of PMTs e Defining crosstalk e Setting up and calibrating the stacker 6 4 2 Starting Scanner Shell Close all programs using Tecan LSServer Click the Scanner Shell icon in the Tecan program group The Scanner Shell window is displayed 6 4 3 Window Elements Ws untitled ScannerShell Bl x Menu Bar File Edit View Instrument Setup Service Advanced Help Toolbar a W En a Pk eM Ss Cc Scanner server Version E 2 00 Mo Instrument connected Window Ares tatus Bar For Help press F1 The Scanner Shell main window contains a menu bar a toolbar the window area and the status bar The window area displays the type of the connected LSServer For example LS SERIES SCANNER Simulation 6 64 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Menu Bar Toolbar Status Bar 2004 11 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 3 Click the About button to show the About dialog box It contains the
82. fo ok this operation will Pas 3 on nm o nm ho fail Pos 4 nm po Pm DES Pas 5 535 nm js nm Fu Eos B br nm po nm EN Cancel Help The Filter Slide 2 tab window consists of the following elements Pos 1 Pos 6 This static text corresponds to the filter positions on the filter static text slide loaded in filter slot 2 e Pos 1 is reserved for focus measurement e Pos 2 5 are free for filter definition e Pos 6 is reserved Instrument Options Language The Instrument Options option is not available in this version of the Scanner Shell software In Setup menu select Language The Language option shows the available languages of the LS Scanner Shell software When the Language is selected V the LS Scanner Shell software menus windows comments will be displayed in this language 6 74 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 6 4 6 Service Menu Test Commands In the Service menu select Test Commands and the Test Command dialog box is displayed Test Commands X Command Ir Answer v Empty command input field after sending Cancel In the Test Command dialog box commands can be sent to the connected instrument These commands must be typed in the Command edit box Click Send to transmit the commands to the instrument The instrument answer is immediately displayed in the Answer edit bo
83. following elements Program information Version number Copyright X Click the Help button to display the online Help for elements such as Buttons Menus Windows E Click the Connect button to directly connect to an instrument M Click the Measurement button to display the Measurement Parameter dialog box SI The Start Measurement button appears gray because measurements cannot be started from the Scanner Shell software C Click this button to show the Measurement Control panel The Status bar displays the following information e Help access Press F1 for Help e Current status of the keyboard toggles CAP caps lock NUM Numeric block lock SCRL Scroll lock Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 65 6 LSServer Scanner Shell and Download TECAN 6 4 4 File types used in Scanner Shell The following file types are used with Scanner Shell File Description Extension Measurement data is saved as Isp files Slide adapter format data is saved as saf 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 lide adapter ormat Crosstalk Crosstalk data is saved as CrosstalkCor dat alibration files log Log file data is saved in the following file log1 log5 format e LSServer log A rec
84. for the LS Series Scanner No 30001798 Rev No 1 5 6 35 6 LSServer Scanner Shell and Download OTECAN Barcode Select the Barcode option button to define the barcode reading position The Geometry Parameters tab appears as follows Measurement Parameter LS SERIES SCANNER Simulation X General Geometry Parameters Scan Settings Excitation Angle Geometry Standard Scan Area C Autofocus C AGC Scan Advanced Autofocus Slide Slide Adapter Format Slide Thickness um 1000 Load Load Standard Adapter Cancel Help The Barcode window contains the following elements Top Use the Top control or type in a value to set the barcode spin control reading position blue line The barcode position is centered on the slide and must be at least 37 5 mm from the bottom line The barcode reading position can not be adjusted when using a barcode bottom reader Note Barcode must be defined in the upper half of the slide due to limited traveling distances in the y direction Note 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 6 36 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download AGC Automatic Gain Control Select the AGC Scan Area optio
85. frame is generated with single sub areas called scan areas The parameters of a single scan area are represented in the Geometry Parameter Tab of the Measurement parameter dialog box of LSServer interface Click the Close button to save the entered slide data and close dialog box Click Load to open the standard Windows Open dialog box Slide Adapter Format saf files already available are shown in the file area To select a file to be loaded click on the item or enter its name into the File name edit box Click OK to load the SAF file One Adapter Format file corresponding to the Standard Tecan Slide Adapter is already installed standard saf All special adapter format files are loaded from saved in e the default directory created after the installation of the SServer software C Program Files Common Files Tecan Reader SAF e or in a user defined directory Click the Save button to open the standard Windows Save dialog box After entering the file name and clicking OK all adapter data is saved Click the Help button to display the online help for the dialog box 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 87 6 LSServer Scanner Shell and Download TECAN Log Ole Interface Show Logfile Lamp Control Help Menu About In the Instrument menu select Connect to connect the instrument In the Advanced menu select Log Ole Interface The Log Ole Interface option disables en
86. hannel 2 is only activated if Dual Parallel Scan Mode has been selected in the General tab PMT Gain Channel 1 edit box Set PMT Gain to a value between 70 and 255 to regulate the detector sensitivity in Channel 1 The PMT Gain can also be adjusted online during the measurement via the Status control dialog box window The Status dialog box is displayed after clicking the Start button PMT Gain Channel 2 edit box Set PMT Gain to a value between 70 and 255 to regulate the detector sensitivity in Channel 2 The PMT Gain can also be adjusted online during the measurement via the Status control dialog box window The Status dialog box is displayed after clicking the Start button PMT Gain Channel 2 Channel 1 2 Run when Dual Scan Sequential is selected is only activated if the instrument is a Dual Channel Instrument and if Dual Parallel Scan Mode has been selected in the General tab Unusable filter laser excitations are signaled by red exclamation marks Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 39 6 LSServer Scanner Shell and Download TECAN 6 40 AGC e Pinhole combo box Select the appropriate pinhole for measurement from the Pinhole combo box Tecan LS Series Scanners have three different pinholes Small Medium and Large that can be changed using the software The size of the pinhole determines the grade of confocality Select between confocal and non confocal measurements gt
87. he Twister must be connected For further information about using the Twister refer to Twister manuals The Twister User s Guide and The Twister Service Manual Twister connected to LSx00 scanner The following modifications have to be performed 1 Set up the Twister Bottom Plate as described in the Twister Manual 2 Unscrew the instrument feet from bottom of the scanner add spacers to instrument feet see figure below and mount both back into the original position Instrument foot 3 The Twister arm has to be slightly modified by adding Extended fingers to the Twister arm see figure below Extended fingers Before starting the Twister the user must adjust some settings in order to ensure that the Twister is the stacker instrument used and that it functions optimally The Stacker Setup dialog box offers all of the necessary options for setting up the Twister 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 89 6 LSServer Scanner Shell and Download TECAN Port Setup Twister 6 90 In the nstrument menu select Connect to connect the instrument In the Service menu select Stacker Setup and then click Port Setup The Port Setup dialog box appears in which the stacker instrument and communication port can be selected Port Setup X Stacker Twister T COM Port Seran COM Cancel In the Port Setup dialog box select Twister from the Stacker combo box
88. he 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 t
89. ically 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 Standard name fixed Filename Format where barcode option and slide position are set to xxx 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 57 6 LSServer Scanner Shell and Download OTECAN Rotate Images Leave Images Image is not changed Flip image up down Flips image vertically For example if Flip image up down is When Flip image up down and Stitch selected the result will be as follows resulting images are selected the result will be as follows Flip image left right Flips image horizontally For example if Flip image left right is selected the result will be as follows 6 58 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 TECAN 6 LSServer Scanner Shell and Download Rotate image Rotates image clockwise 180 For example if Rotate image is selected the result will be as follows When Rotate image and Stitch resulting images is selected the results will be as follows PFELDIETUE TITL III 2004 11 Operating Manual for the LS Series Sca
90. idered in displaying the slide scheme and needs to be defined for searching the focal plane within an appropriate range e Z Scan End controls Use the Z Scan End controls um to enter the End value of the autofocus z scan scan in vertical direction Use the arrows or type in the value manually e Z Scan Start controls Use the Z Scan Start controls um 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 um 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 e Focus Offset controls Use the Focus Offset controls um 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 c
91. ing the following default measurement parameters e Single Scan mode e 40 um scan resolution e Large pinhole e Optimize integration time selected e No autofocus e 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 Insert Plate Heigthts X ls current adapter sample height corect mm lz current total plate height corect mm 45 Cancel Help 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 6 20 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 2004 11 6 LSServer Scanner Shell and Download After clicking OK on the nsert Plate Heights dialog box the instrument starts the p
92. kCor dat and 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 81 6 LSServer Scanner Shell and Download TECAN Stacker Setup Stacker Setup is only used when Tecan LS Scanner is connected to a special autoloader the Twister If the Tecan Connect is associated with the LS Scanner than a special XConnect software which is delivered with the instrument is responsible for the calibration and configuration of the connected autoloader Connect For further information about using Connect refer to the Connect manual In the Service menu select Stacker Setup and the Stacker Setup dialog box is displayed x Stacker Configuration Stacker Settings Stacker Calibration The Tecan LS SCANNER instrument can operate in manual and automatic mode For automation purposes a stacker instrument such as the Twister must be connected For further information about using Twister refer to the Twister manuals The Twister User s Guide and The Twister Service Manual The Stacker Setup dialog box helps the user select calibrate and configure the installed stacker instrument For further information about Stacker Setup refer to the chapter 6 4 7 Stacker Setup Twister description in this manual In the Stacker Setup dialog bo
93. ke Advanced Autofocus available Click the Advanced Autofocus button and the Advanced Autofocus dialog box appears Window Elements The Advanced Autofocus dialog box m Z Scan Height Slide Thickness pm fi 000 Z Scan End um fod 3 9 oe Z Scan Start um Lon Ei Focus Offset um o Autofocus Selection Focal Plane C No Autofocus Plane HS Autofocus C Plane 2 C Wellmode C MTP Mode nee Focus Gain H 40 Cancel Help 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 OK Click the OK button to save the selected options and to close the button dialog box Cancel Click the Cancel button to close the dialog box The selected button options are not saved Help Click the Help button to display the online help for the dialog box button 6 44 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Z Scan Height Z Scan Height group box Focus Offset 2004 11 Focus Offset controls 6 LSServer Scanner Shell and Download e 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 cons
94. l 1 vertical orientation and Filter Channel 2 horizontal orientation and make sure that the filters are oriented properly see pictures below Filter Channel 2 Filter Channel 1 e Close the filter compartment 3 8 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 0A 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 M
95. l and Download TECAN Geometry Geometry group box The Geometry group box contains the following elements e The static text which appears after Geometry displays the name of the currently loaded saf file e Scan area option button Select the Scan area option button to set the appropriate scan area either by dragging the four red borderlines by mouse or by typing in the distances measured from the lower left corner Units are given in mm Minimum Scan area 1mm x 1mm See Scan Area on page 6 34 and Scan Area option button on page 6 14 for more information e Autofocus option button Select the Autofocus option button to specify the position of autofocus scan lines The Autofocus is a scan in vertical direction Z scan measuring the reflection light of the 633 nm laser in order to bring the sample exactly into the right focal plane For this purpose z scans are performed along the autofocus scan lines that can be positioned either by dragging green lines by mouse or by typing in the distances units in mm measured from the lower margin The width of the autofocus scan lines is given by the Amplitude unit in mm For more information see Autofocus on page 6 35 Select Autofocus to make the Advanced Autofocus button available and to change autofocus parameters or to select a different autofocus and or autofocus mode For more information see Advanced Autofocus Minimum Autofocus 3mm x 3mm e Barcod
96. librating LS Series Scanner instruments e Creating special formats for scanning different plates and slides e Filter Definition e Stacker Setup LSDownload is a software tool needed for downloading new firmware versions to LS SERIES SCANNER instruments For details on e data analysis see the corresponding Array Pro 4 5 operating manual e 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 Ween Recommend Pentium IIl 4 GHz Pentium IV 1 7 GHz 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 1 6 LSServer Scanner Shell and Download TECAN 6 1 3 Software Requirements The following software requirements are needed for LSServer and Scanner Shell Microsoft Windows Windows 2000 Windows 2000 Additional supported software Array Pro 4 5 for microarray image analysis Note G Microsoft amp Excel and Microsoft amp 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 a
97. lide position in alohanumerical order The first character represents the row the second character the column position in the defined slide adapter For example using a slide adapter with slide positions arranged in 2 columns and 2 rows the Slide grid column shows A1 slide on position column 1 row 1 B1 slide on position column 1 row 2 A2 slide on position column 2 row 1 B2 side on position column 2 row 2 e he Process grid column displays check boxes for each slide defined All slides selected are processed during next measurement Select the check boxes of the corresponding slides to be processed Select several rows and press Insert Key Delete Key to mark the selected slides to be processed not to be processed Click the heading of the Process column to select all of the rows in this column Press Insert Key Delete Key to mark all of the slides to be processed not to be processed e Inthe Filename grid column the image name must be entered The 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 standard name edit box is used creating image filename The Filename grid column is enabled if Use standard name check box is cleared The name entered in Filename grid column is used creating the image filename Operati
98. lowing procedure should be used to disinfect the instrument The instrument should be disinfected using a solution such as Lysetol Manufacturer Schulke amp Mayr Ges m b H Aseptisol Manufacturer Bode Chemie Hamburg If neither of these solutions are available 70 ethanol should be used as an alternative Caution The disinfection procedure should be performed by authorized trained personnel in a well ventilated room wearing disposable gloves protective glasses and clothing Please note that the disinfectant can influence the performance of your instrument if it is applied inside the instrument 8 6 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 8 Cleaning amp Maintenance 8 6 Disinfection Procedure The following procedure should be used to disinfect the outside surfaces of the instrument 1 Disconnect the instrument from the main power supply 2 Disconnect the instrument from any accessories that are used Ensure that you are wearing disposable gloves 3 Carefully wipe all the outside surfaces of the instrument with a wad of cotton wool that has been soaked in the disinfecting solution 4 Ensure that the same disinfection procedure is performed with the plate carrier 5 Repeat the disinfection procedure on any accessories that are also being moved or returned 6 After the disinfection procedure has been performed ensure that the disinfection certificate is completed
99. mple with an oversampling factor of three one pixel is scanned three times and the average of these values is calculated Oversampling therefore reduces noise but increases scan time by the factor The average will be calculated during scanning In theory the signal to noise ratio is increased by yn n oversampling factor For example a factor of 4 will increase the signal to noise ratio by a factor of 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Resolution 6 LSServer Scanner Shell and Download Resolution Scan Resolution combo box displays a selection of possible resolution of 4 group box 6 10 20 and 40 um The Scan Resolution is the number of um per pixel in the x and y directions The smaller the value the higher is the resolution of the image but the more time it takes to perform a scan and the larger is the image file 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 Connect Configuration X Plates Read plate barcode Don t read top most plate Besteck after last plate Laser handling warm up tima GG Start batch run only after all lasers reached Switch off laser after b
100. n button to start automatic gain control scan area selection The Geometry Parameters tab appears as follows Measurement Parameter L5 SERIES SCANNER Simulation xj General Geometry Parameters Scan Settings E citation Angle Geometry Standard E Top mm 52 280 est C Grandes C Autofocus C Barcode Left mm Right mm 8160 E 15 520 E Botton mm 44 240 E Advanced Autofocus Slide Slide Adapter Format Slide Thickness pm 1000 Load Load Standard Adapter Cancel Help The AGC window contains the following elements Top Use the Top spin control or type in a value to set the upper spin control border of the scan area The value is measured in mm from the lower left corner 0 0 Left Use the Left spin control or type in a value to set the left border spin control of the scan area The value is measured in mm from the lower left corner 0 0 Right Use the Right spin control or type in a value to set the right spin control border of the scan area The value is measured in mm from the lower left corner 0 0 Bottom spin Use the Bottom spin control or type in a value to set the bottom control border of the scan area The value is measured in mm from the lower left corner 0 0 AGC is only available in e Single Scan Mode e 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 C
101. n of labels placed on the instrument 7 5 Cleaning amp Maintenance 8 1 8 2 8 3 8 4 8 4 1 8 4 2 8 4 3 8 5 8 5 1 8 6 8 7 8 8 8 8 1 8 8 2 Index Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 Jud Le Te TORN terc 8 1 Be Ire Ke UE 8 1 Replacing the Fuse ooscnsvenet nene tzxxexwevasirxv ax Duvxe lot E pd aua u ite Ea 8 2 Remote Control and Data Exchange 8 3 uUo 7 QOW MOA EE 8 3 Working with pcAnywhere esses eene nnns 8 3 Working with CITRIX web conferencing manager 8 5 Instrument DISINFECTION eee eee eere ee eene nnn 8 6 Disinecion Ree EE 8 6 DISINFECTION EOF uiris opone ienix eco eege chu eda Ripa ED E EO ER 8 7 Disinfection Certificate eeeseee eee rc eere eene nnn 8 7 Disposal of Instrument eeeseee rere eee nenne nnn 8 8 Disposal of Packing Material esses 8 8 Disposal of Operating Material eren 8 8 2004 11 TECAN 1 Safety 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
102. ness box the thickness of a sample i e a slide must be entered in order to allow the instrument to search for the focal plane within an appropriate range If the Slide Thickness is entered incorrectly the algorithm might be unable to find the right surface The Slide Thickness ranges from 0 to 2000 uim and must be adjusted respectively to the Adapter height defined in saf files see Advanced Menu Edit SAF on page 6 85 1 Ifthe Adapter height is measured from the surface of the plate transport to the surface of the spots the Slide Thickness must be set to O 2 Ifthe Standard Tecan Slide Adapter is used with the default height of 11 5 mm the thickness of the slide that is inserted into the adapter must be edited as well The Slide Adapter Format group box contains the following elements e Load button Click Load and the Open Slide Adapter Format dialog box appears Select a Slide Adapter Format saf file from the drop down list and it will be loaded automatically e Load Standard Adapter button Click the Load Standard Adapter button to load the Standard saf file and to reset default Geometry Parameters Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 33 6 LSServer Scanner Shell and Download TECAN Scan Area 6 34 The Geometry Parameter tab appears differently depending on which option button has been selected Select the Scan Area option button to define the scan area that i
103. ng Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Filename Format Filename Format group box Date Format Date Format group box Stitching Stitch resulting images check box 6 LSServer Scanner Shell and Download The Filename Format group box contains the following elements e he 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 e The Wavelength check box must be selected if the excitation wavelength is to be part of the image filename e The Position check box must be selected if the slide position is to be part of the image filename The Counter check box is automatically selected and cannot be reset by the user When using standard name Use standard name check box is selected the filename format is fixed to e Barcode excitation wavelength slide position current date image counter if a barcode reader is installed and the barcode option is selected e Excitation wavelength slide position current date image counter if no barcode reader is installed If no check boxes are enabled the Filename Format cannot be changed Clear Use standard name to enable the following check boxes option buttons and the Date Format group box Wavelength check box e Position check box Filename Format is user definable e he Date Format is automat
104. nner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 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 7 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 accep
105. nner No 30001798 Rev No 1 5 6 59 6 LSServer Scanner Shell and Download TECAN Files AutoSave Select the AutoSave check box to save every scanned image automatically check box 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 Slide Settings tab Directory Tecan Array Pro Software subdirectory Array Pro 45 Images Josz 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 Tecan Array Pro Software AutoSave is automatically enabled in Stacker Mode no user action necessary Note 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 at once just the last 10 Generate JPEG The image will also be saved as a jpg file and saved in the same folder as the backup tif file check box 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 2x 3 4x 6 etc Improper selection of images to be stitched can cause an unexpected stitched image result 6 60 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Folder Op
106. ns Click OK to save the settings The focus values are stored for the 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 Cancel Click Cancel to close the dialog box button The selected options are not saved Help Click Help to display the online help for the dialog box button 6 24 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 2004 11 6 LSServer Scanner Shell and Download 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 r pvp gii E midi DITE CEN REN Focus Prescan EM E x Focal Plane Fosition Manuell Focus Focus 2 8 R Focus 1 Focus 3 500 pm 800 tum Offset C Focus Offset Example of focus prescan for MTP autofocus After clicking OK the following dialog box appears LS rb Mois es d Do vau want to store the actual amp uboFaus Offset Value permanently to current
107. ns to enter data To help the user navigate from one window to another the following buttons are used in the individual windows of a wizard Back The Back button can be used to navigate back to the previous button window within a wizard In the first window of a wizard the Back button is not active Next The Next button can be used to navigate forward to the next window button within a wizard In the last window of a wizard there is no Next button Finish The Finish button is only found in the last window of a wizard It button must be used to close the wizard save all changes made and finish the procedure Cancel The Cancel button can be clicked to close wizard All changes made button in the wizard are cancelled Help The Help button can be clicked to display the online help of the button wizard The Status Control bitmaps display the status of operation P Operation in progress Wait until finished wi The operation has finished with no errors Ka During operation an error occurred The user is informed about the reason for the error in a message box 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 91 6 LSServer Scanner Shell and Download TECAN 6 4 9 The Transport Lock Wizard General The Transport Lock wizard is designed to quickly guide the user through the transportation lock procedure From the Service menu select Transport Lock and the Transport Lock wizard is started
108. nt the report Next Page Displays the next page of the report Prev Page Displays the previous page of the report Two Page Displays two pages of the report simultaneously Zoom In Zooms in so that a part of the report is displayed larger Zoom Out Zooms out so that a part of the report is displayed smaller Close Closes the Print Preview option and returns to the main screen 6 104 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download Exit In the File menu select Exit and the LSDownload software will be exited View Menu Status Bar In the View menu select Status Bar to show hide the LSDownload software Status Bar When the Status Bar option is selected V the LSDownload software Status Bar will be shown The status bar displays following information e Help access Press F1 for Help e Activity of the keyboard toggles CAP caps lock NUM Numeric block lock SCRL Scroll lock When the Status Bar option is cleared the LSDownload software Status Bar will be hidden Instrument Menu Connect This option allows an instrument to be connected In the Instrument menu select Connect or in the nstrument group box click Connect Instrument or press Shift F5 and the Setup Port dialog box appears Select the desired instrument and communication port from the drop down lists For further information refer to the chapter 6 2 Tecan LS Scanner
109. o AN PRECAUTIONS MUST BE OBSERVED 4 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN Table of Contents 2004 11 1 Safety 1 1 Instrument Safety E 1 1 General 2 1 Instrument Features s oasixeon on an osxV cual vM EN CS RSV RUN aoaaa 2 1 Chl o ee 2 2 212 Modes of operaliON DE 2 3 E19 Aulomalion ee ele 2 4 2 1 4 Integrated Image Analysis Software Array Pro 2 4 Installation 3 1 Unpacking amp Inspection eese eee rennen nnn 3 1 3 2 Remove Transport Lock 1eeeeeeee seen ee nennen nnn 3 7 3 3 SITE UEL Le NEE 3 8 3 4 Power e UE UE E 3 9 Technical Description 4 1 BIL E 4 1 4 2 AUTOFOCUS C 4 3 4 3 Data Processi i ME 4 3 Operation 5 1 General Operating Features eeeeeeeeen eee 5 2 NN E ege Slan UP EEN 5 2 5 1 2 Instrument Power On 5 2 543 Connec fo Ee 5 8 5 1 4 Finish a Measurement Geseion esee nee 5 8 5 2 Insert Slide s into Slide Adapter 5 4 LSServer Scanner Shell and Download 6 1 6 1 1 6 1 2 6 1 3 6 1 4 6 2 6 2 1 6 2 2 6 3 6 3 1 6 3 2 6 3 3 6 3 4 6 3 5 BENET OCLC de BEE 6 1 OVO ON ee 6 1 Hardware FREQUuIreIMentts eese essen nnns 6 1 Software Requirements sees sesso nna 6 2 Software Installation PDrocedure cec
110. o longer valid after 100 days Tools needed for gain calibration are delivered with each instrument e Scattered light glass slide e Calibration filter slide with different OD filters For further information refer to the chapter The Gain Calibration Wizard on page 6 77 in this manual During the Gain Calibration procedure 1 Door opens and filter slides are moved out The user is asked to prepare the instrument for Gain Calibration Instrument parameters are set for Gain Calibration Gain Calibration PMT1 is done Gain Calibration PMT2 is done Gain Calibration data PMT1 PMT2 is saved as GainCalibration cvs in the CalData folder Door is closed and filter slides are moved out M NM c s Note G The gain calibration must be done for all PMTs found in instrument 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 77 6 LSServer Scanner Shell and Download OTECAN Crosstalk In the Service menu select Crosstalk and the Crosstalk dialog box is displayed Cross Talk 1 x Laser And Filter Selection Channel 1 Channel 2 Laser b33 nm 543 s an Filter 670 Filter slide 1 nm 590 Filter slide 2 nm Channel 1 Channel 2 Dyed Lui KL D 0556 Gain 1 175 Gain 2 175 Date 17 07 02 Mame Release DO D I e g username Lui Release Cys Cyh 1 Cph Release Cys Cyh CO GeSc ui Cys 2 1 GeSc_ Cys Dyb 2 13 Cy3 GeSc Cys Cult GeSc Cys CyS 1 13 i Y
111. oceed with step 5 If this message isn t displayed continue to step 7 5 Create a new caller On the Callers tab click the Create button in the Caller list button is marked by the red circle on the image below z Bic EET NET Mee pcAnywhere Host Properties MODEM Connection Infa Settings Callers Security Options Conference Protect Item Authentication type Nee Callback Cancel Apply Help 8 4 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 8 Cleaning amp Maintenance 6 A new message box pop s up For new caller identification type in Login Name tecan Password tecanls and confirm the password pcAnywhere Caller Properties New Caller E x Identification Callback Privileges Protect Item Login Name tecan Password mm Confirm Password Cancel Apply Help PcAnywhere s login identification is case sensitive Please use lower case letters If you use a different login and password as suggested provide Tecan service with this information before each planned start of a remote session 7 Click OK and the pcAnywhere icon appears in taskbar pcAnywhere is launched and is waiting for a remote call from Tecan service 8 4 3 Working with CITRIX web conferencing manager For online demo training and troubleshooting between Tecan and your company Tecan offers an ftp site It is accessible through http travel t
112. of type combo box Open as read only check box Open button Cancel button 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 Look in 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 Isp Select Open as read only to view the file and protect it from being changed Click the Open button to load a selected measurement parameter file Isp Click the Cancel button to close the dialog box without loading a file Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Save 2004 11 6 LSServer Scanner Shell and Download 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 Isp 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 overwrit
113. ommands can be entered immediately If the same command needs to be repeated several times this box should not be selected Send button Click the Send button to send the command which is in Command combo box edit field to the connected instrument Cancel button Click the Cancel button to close the dialog box Demo Mode Allowed Transport Lock To enable the Demo Mode option button in the Setup Port dialog box select Demo Mode Allowed from the Service menu In Demo Mode the Tecan LSServer can be simulated no instrument needs to be connected This option is used for training purposes For further information refer to the chapter 6 2 Tecan LS Scanner Interface description in this manual To start the Transport Lock wizard select Transport Lock from the Service menu A wizard guides the user through the transport lock procedure The Transport Lock option is implemented in Scanner Shell as a wizard It represents workflow modules which define a sequential procedure and guide the user step by step to perform a specific complex activity For transportation purposes it is recommended to lock the connected instrument A transportation shock absorber pad is inserted between the plate transport and the optic chassis to avoid damage to the optical parts For further information refer to the chapter 6 4 9 The Transport Lock Wizard description in this manual During the Transport Lock procedure 1 The instrument door is opened
114. ord of current measurement data L SServer log1 L SServer 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 6 66 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Locating Files 6 LSServer Scanner Shell and Download Scanner Shell Files Temporary Files File Management 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 ype of File File Directory Extension Measurement Parameter parameter Slide adapter format e oo Gain calibration CalData CSV Crosstalk CalData Temporary files needed for diagnostic and controlling purposes are stored in the directory C ADocuments and Settings user name Local Settings The file types are displayed below ype of File File Extension a Des Temp wei to logn Note To see the user name of the person logged on press Ctrl Alt Delete and the user name will be shown in the Logon dialog box The default paths for saving files can be changed in the S ide Settings dialog box on the Folder Options tab See Folder Options 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 67 6 LSServer Scanner Shell and D
115. ort after the measurement is finished Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download Barcode Barcode e Read barcode check box group box Read barcode will be available if the instrument is equipped with a barcode reader By selecting Read barcode the barcode is read prior to each measurement at the user specified reading position The barcode appears automatically as part of the filename see Slide Settings Geometry Parameter Tab In the Geometry Parameters tab the Scan area the location of the Autofocus scan lines as well as the Barcode line are determined within a certain Slide Adapter Format saf Different safs can be loaded using the Load button The Slide Thickness is entered respectively The Geometry Parameter tab Measurement Parameter LS SERIES SCANNER Simulation X 3eametry Standard 22 ps Top mm 70 000 lex Scan Area C Autofocus C Barcode C AGC Scan Lett mm Hight mm 4 699 d 13 595 a Bottom mm 5 000 Ge Advanced Autofocus Slide Slide Adapter Format Slide Thickness pm 1000 Load Load Standard Adapter Cancel Help The Geometry Parameter tab window contains the following elements e Geometry group e Slide group e Slide Adapter Format group 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 31 6 LSServer Scanner Shel
116. over glass with a thickness of 170 um the correct focus offset would be 113 um 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 45 6 LSServer Scanner Shell and Download TECAN Focus Gain Focus Gain controls Focal Plane Focal Plane group box 6 46 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 e raue 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 e 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
117. ownload OTECAN 6 4 5 Scanner Shell Menus File Menu Exit Edit Menu View Menu Toolbar Status Bar 6 68 In the File menu select Exit to exit the Scanner Shell software Not implemented in this version of the Scanner Shell software In the View menu select the Toolbar option to show hide the Scanner Shell software Toolbar When the Toolbar option is selected V the Scanner Shell software Toolbar will be shown When the Toolbar option is cleared the Scanner Shell software Toolbar will be hidden 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 V 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 Shift F5 This option allows the connection to an instrument Before connecting the desired instrument the communication port must be chosen To do this select Setup Port from the Setup menu For further information refer to the chapter Port Setup on page 6 4 in this manual The desired instrument will be connected using the selected communication port A message in the window area
118. p ftp tecan com Contact your local dealer or email helpdesk at tecan com to receive login information user name and password to access the ftp server Working with pcAnywhere When pcAnywhere is activated for the first time the software asks you to register the software Please follow the step by step wizard registration refer also to chapter 2 page 25 of the pcAnywhere 10 5 User s Guide Setting up host connection STEP PROCEDURE 1 Connect your analog phone line with the Tecan LS PC internal modem The connector is on the rear of the Tecan LS 2 Start pcAnywhere The software is installed in lt programs gt Symantec pcAnywhere gt 3 The pcAnywhere Manager dialog box appears Click the Hosts button Double click Modem in the Hosts window a pcAnywhere Manager E 1 Bl xl File Edit wiew Tools Help g Hozta Xe S S E amp amp Add Host DIRECT i i NETWORK NETWORK CABLE DSL Remotes Option Sets Packages Exit For Help press F1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 8 3 8 Cleaning amp Maintenance e TECAN 4 The fist time the software is started the following warning appears B B Host Security Warning E m No callers are defined Far this host ou must define at least one Gees caller before vau can use this host tem Would you like to define a caller now Do you wish to set caller privileges now Click Yes and pr
119. part of the image filename shown later as the title of the image window The Filename group box contains the following elements e Select the Use standard name check box to enter the name in 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 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 e Inthe 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 Use standard name box to enable the Filename grid column see Measure grid box Filename grid column 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 55 6 LSServer Scanner Shell and Download TECAN Measure 6 56 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 e The Slide grid column displays the s
120. pter 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 Scanlist 6 62 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 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 A scan list is a text file txt for batch processing e g created with Notepad or Microsoft Text Editor Example 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 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 2004 11 6 LSServer Scanner Shell and Download When using a scanlist file the following dialog box will appear after clicking Start Do wou w
121. ractions are performed in separate windows that are displayed if a menu is selected or if a toolbar button is clicked The LSDownload dialog box contains the following elements Instrument e Connect instrument button group box Click the Connect instrument button to open the Setup Port dialog box The Setup port dialog box serves to set up options for connecting instruments the desired instrument and the communication port are chosen e Status text box In the Status text box the currently connected instrument is displayed The Firmware Version and the Serial number of the instrument are shown as well File e Open File button group box Click Open File to select existing Download files files with the extension upd from the Open dialog box Confirm by clicking Open e Open File text box The Open File text box displays the selected Download file upd file as well as the instrument name and the version number Download Click the Download button to download the selected download file button Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 101 6 LSServer Scanner Shell and Download OTECAN 6 5 2 LSDownload Menus File Menu New Save Report 6 102 My Network P My Computer e tel COE Encoding Save in combo box Workspace list box File Name edit box Save as type combo box Save button Cancel button File name In File menu sel
122. ration Window When the End Gain Calibration window appears gain calibration has been finished successfully All calculated gain data is saved in files called GainCalibration dat and Gaincalibration cvs To view the gain calibration file load the Gaincalibration cvs file in a spreadsheet program such as Microsoft Excel The Gain Calibration window Gain Calibration l x Gain calibration finished successfully Data will be saved in file GainCalibration dat Back Cancel Help Click the Finish button to complete the Gain Calibration procedure and close the Gain Calibration wizard 6 100 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download 6 5 6 5 1 Menu bar Status bar 2004 11 LSDownload The LSDownload Software is used to download firmware to the instrument Starting L5Download Close all programs using Tecan LSServer Click the LSDownload icon in the Tecan program group The LSDownload window is displayed Muntitled isDowntoad ini x File View Instrument Help nstrument Connect instrument File Open file TECAN LS Firmware Download Report The LSDownload Report Window contains a menu bar the report area and the status bar The window area displays the Tecan Firmware Download Report For example LS SERIES SCANNER Download User inte
123. rd is started Select the preferred uninstall method Automatic or Custom and click Next to continue In the next window press Finish to uninstall ScannerShell LSDownload A message box pops up asking if shared components should be 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 3 6 LSServer Scanner Shell and Download TECAN 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 e Set Communication port e Choose Instrument type e 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 e In Tecan LSA Software Acquire menu select Tecan Scanner or e In Scanner Shell Software Setup menu select Setup Port or e InLSDownload Instrument menu select Conne
124. rescan EL CONNU JO Instrument iz performing prescan Time Elapsed time 00 00 03 dhh mm ss Estimated runtime 00 0752 dhhmmss Shrink Default Break 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 Adapter Format Wizard ER ES xj Adapter Format and 5can Positions Left margin BE H mm Number of columns 4 3 Right margin 75 mm Numberatrows 1 H Upper margin i m mm Lower margin 21 4 mm Slide Values Area widths 22 H mm Amaheg 75 SE 11 5 mm 12 5 mm Table MTP adapter Adapter Prescan Non confocal scan of the complete transport table area Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 21 6 LSServer Scanner Shell and Download TECAN The first page of the Adapter Format Wizard has the following buttons Click Reset to return all the values to the default settings 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
125. riments e 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 e 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 e 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 See also Tecan Connect Configuration e Move plate out after measurement check box Selecting Move plate out after measurement opens the door and moves out the plate transp
126. rough 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 23o0r4 T Dichroic Pinko lela RER l or 2PMT s BS m tics m d l or JF iberslides Scanner K Autofocussysiem Maun PU 5 amis zept Sen kummt door Figure 4 2 4 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 pro
127. round 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 e The LS Scanner can be equipped with up to 4lasers e Every Scanner has a HeNe laser with 633nm e 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
128. roup box consists of the following elements group box e In button The In button is disabled See the description for Filter slide 1 e Out button Click the Out button to move out Filter Slide 2 OK button Click OK to close the dialog box Help button Click the Help button to display the online help for the dialog box Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Laser Control 2004 11 6 LSServer Scanner Shell and Download 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 Lamp Laser control X JW Laser 1 E33 nm Cancel v Laser 2 543 nm Help M Laser 3 594 nm mp Iv Laser 4 488 nm 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 Select Laser 1 check box to activate the 633 nm laser check box Red LED is switched on at the rear of the instrument Laser 2 532 nm Select Laser 2 check box to activate the 532 nm laser check box Green LED is switched on at the rear of the instrument Laser 3 Select Laser 3 check box to activate the 594 nm laser and check box the orange LED is switched on at the rear of the instrum
129. s displayed as a light gray area within the red borderlines Minimum Scan area 1mm x 1mm anywhere on the slide The Geometry Parameters tab appears as follows Measurement Parameter L5 SERIES SCANNER Simulation l x Geometne Standard 27 Fe Top mm L QOL T Scan Area Autofocus Barcode AGC Scan Lett mm Right mm 4 699 m 13 598 Bottom mm 5 000 m Advanced Autofocus Slide Slide Adapter Format Slide Thickness pm 1000 Load Load Standard Adapter The Scan Area contains the following elements Top Use the Top spin control or type in a value to set the upper spin control border of the scan area The value is measured in mm from the lower left corner 0 0 Left Use the Left spin control or type in a value to set the left border spin control of the scan area The value is measured in mm from the lower left corner 0 0 Right Use the Right spin control or type in a value to set the right spin control border of the scan area The value is measured in mm from the lower left corner 0 0 Bottom spin Use the Bottom spin control or type in a value to set the bottom control border of the scan area The value is measured in mm from the lower left corner 0 0 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Autofocus 2004 11 6 LSServer Scanner Shell and Download Select the Autofocus option button to define the autofocus po
130. s 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 Copyright Tecan Austria GmbH All rights reserved Printed in Austria 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 e Installing the instrument e Operating the instrument e Cleaning and maintenance routines 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 3 Oe TECAN 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
131. sition and to make the Advanced Autofocus button available The Geometry Parameters tab appears as follows Measurement Parameter L5 SERIES SCANNER Simulation E X General Geometry Parameters Scan Settings Excitation Angle Scan Area C Barcode C AGC Scan Geometry Standard Slide Slide Adapter Format Slide Thickness pm 1000 Load Load Standard Adapter eal Top mm BU 000 Gi Amplitude mrm ES 20 000 E Bottom mm 10 000 Advanced Autofocus Cancel Help The Autofocus contains the following elements Top spin control Bottom spin control Amplitude spin control Advanced Autofocus button MTP Autofocus Use the Top spin control or type in a value to set the autofocus scan line for Focus 2 The value is measured in mm from the bottom line 0 0 Use the Bottom spin control or type in a value to set the autofocus scan line for Focus 1 The value is measured in mm from the bottom line 0 0 Use the Amplitude spin control or type in a value to set the width of autofocus scan line for both Focus 1 and 2 Click Advanced Autofocus to select a different autofocus mode or to change autofocus parameter For detailed information please refer to the Advanced Autofocus description in this manual Autofocus entered in Well or HS Mode Amplitude width of Autofocus line from 3mm to 22mm Distance between Autofocus lines from 3mm to slide length Operating Manual
132. stallation e TECAN 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 3 6 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 Caution Do not try to open or close the instrument flap manually Caution Save packing materials and transport locks for further transportation purposes The LS series scanners must be shipped with the original packing and the transport locks must be installed Caution Before Transportation Place the instrument carefully in the indicated orientation before fixing the transportation locks otherwise the instrument will become damaged 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 3 7 3 Installation e TECAN 3 3 Filter Installation Insert the Filter Slides into Filter Channe
133. tection points a focal plane will be determined l e 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 Y x 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 47 6 LSServer Scanner Shell and Download OTECAN Measurement Parameter L5 SERIES SCANNER Simulation E x General Geometry Parameters Scan Settings Excitation Angle Geometry Standard E Top mm 60 523 m C Scan Area Autofocus C Barcode C AGC Scan 3 Left mm Fight mm ER E Plateview E Amplitude mm P Bottom mm 20 578 Advanced Autofocus Slide Slide Adapter Format Slide Thickness um food Load Load 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 6 48 Operating Manual for the LS Series Sca
134. ted by the scanner is 10 If your sample has high walls we recommend using the lowest possible value 710 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 flatt samples e g slides Angle is set to 25 for both the image scan and for autofocus Measurement Parameter L5 SERIES SCANNER Simulation X General Geometry Parameters Scan Settings Excitation Angle Excitation Angle E z optical aus C MTP Made Set Beamshilt Image Scan Autofocus Leo 50 y amp axis object Cancel Help 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 49 6 LSServer Scanner Shell and Download TECAN MTP Mode Select MTP Mode for most MTP applications Angle is set to 0 normal incidence for image scan and 10 for autofocus x General Geometry Parameters Scan Settings Excitation Angle Excitation Angle C Default z optical axis C Set Beamshitt Image Stan Autofocus joo A uo A 4 ae object Cancel Help Set Beamshift Set Beamshift may be a useful optimization parameter if your sample has only flat walls with a relatively low
135. ten The Save As dialog box SS 24 xl Save in c LSP amp Dies EZ an AK AFFy lsp File name Mi Save as type Measurement parameter files nl Cancel E The Save As dialog box is the standard Windows file Save As dialog box It contains the following elements Save in In the Save in combo box select the drive and the folder in combo box which the measurement parameter file should be saved Workspace The Workspace list box shows the files and folders selected in list box the Save in combo box File Name edit Enter the File Name for your measurement parameter file or box select one from the list Save as type All Tecan measurement parameter files are saved with the file combo box extension Isp Save button Click the Save button to save the current measurement parameters in a file with the extension Isp Cancel button Click the Cancel button to close the dialog box without saving Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 53 6 LSServer Scanner Shell and Download OTECAN 6 3 8 Settings Slide Settings In the Measurement Control dialog box click Settings to display the slide setting options e The filename s of the scanned image s e The slides to be processed e If the scanned image s should be saved automatically or not e lf the images should be stitched or not e lf the stitched image should be flipped or not The Filename can be either a standard name or
136. tion The signals measured for crosstalk correction depend on PMT gains If a valid Gain Calibration has been performed the instrument takes the PMT gains automatically into account For further information refer to the chapter 6 4 6 Service Menu Gain Calibration description in this manual 6 78 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download All data needed for calculating crosstalk correction must be entered selected in the Crosstalk dialog box For information about how to get special data needed for crosstalk correction and how to perform the correction refer to the LSServer Beginners Guide manual In the Crosstalk dialog box all data needed for crosstalk correction must be set The requested options must be entered in the corresponding edit boxes selections must be made in combo and list boxes The Crosstalk dialog box is divided into four areas Channel 1 Channel 2 tab In the Channel 1 Channel 2 tab data must be entered which has been previously determined through special measurement e g using Tecan LSA Software for microarray analysis Dye 1 Dye 2 K1 K2 Gain 1 and Gain 2 Laser Filter selection In the Laser Filter combo box laser and filter combinations for crosstalk must be selected Current Date and Name edit box In the Date field the current date is displayed In the Name edit box name or initials must be entered
137. tions 2004 11 6 LSServer Scanner Shell and Download In the Measurement Control dialog box click Settings to open the S ide Settings dialog box Slide Settings x Slide Settings Folder Options Images Parameters CAPROGRATISCOMMONTT Browse Browse Browse Adapters Temp OK Cancel Help Select the Folder Options tab to view the current file storage paths By clicking the Browse button paths can be defined for the following file types e Images tif jpg e Parameters Isp e Adapter saf e Temp all files tif jpg lsp sat autofocus images when AutoSave has 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 Isp file will be saved as SCAN Time Isp e g SCAN 141149 Isp 2 pm 11 minutes and 49 seconds Experiment Folders EH Experiment 2003 12 04 DS 2004 D 03 2004 04 14 EC 2004 04 15 Date t 14 11 49 Time Scan Parameter and Image files el SCAM 141149 1sp Es untitled 543 42 150404 2 tif bel untitled 633 42 150404 1 tif See also Filename Format on page 6 57 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 61 6 LSServer Scanner Shell and Download TECAN 6 3 9 Slide Ada
138. transport moves into the reference position e 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 Note 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 5 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 Note Please remove the recently measured sample before disconnect Instrument Shut Down 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 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 5 3 5 Operation TECAN 5 2 Insert Slide s into Slide Adapter
139. ully finished a dialog box appears instructing the user to switch the instrument off The result is shown in the report area of LSDownload software ES Lexxxv110 upd LSDownLoad E Bl xj File View Instrument Help m Instrument Connect instrument TECAN LS Firmware Download Report Instrument LaserScanner Main CPU LS SERIES SCANNER Serial Number PT1 Date 06 Aug 2002 Serial number PT1 Time 13 26 Filename LSxxxV110 upd Previous Version w 1 10 07 02 LSxxx New Version V XXX 06 01 File Open file LSxxxV 110 upd a Instrumentname LaserScanner Main CPU Version V 252 08 01 Firmware download successfully finished A message in the window area of the LSDownload software shows that the download was successful or unsuccessful Message in report area of LSDownload Firmware download failed Firmware download successfully finished 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 107 6 LSServer Scanner Shell and Download TECAN Disconnect Help Menu Contents About 6 108 In the Instrument menu select Disconnect to disconnect the currently connected instrument Another instrument can then be connected This option is only available if an instrument is already connected In the Help menu select Contents and the Online Help for LSServer Scanner Shell amp Download is
140. ve the plate carrier or filter slides into or out of the LS Series Scanner Click OK to close the dialog box For further information refer to the chapter Plate Filter on page 6 26 description in this manual Edit Measurement Parameters In the Instrument menu select Edit Measurement Parameters or on the toolbar click the Edit Parameter button or press Ctrl F5 and the Measurement Parameter dialog box appears 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 Start Measurement The Start Measurement option is not available in the Instrument menu of the Scanner Shell software Disconnect 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 6 70 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 6 LSServer Scanner Shell and Download Setup Menu Setup Port In the Setup menu select Setup Port This option allows an instrument to be connected The Setup Port dialog box is displayed where the desired instrument and communication port can be selected For more information refer to the chapter 6 2 Tecan LS Scanner Interface
141. very high numbers of slides automatically For instance with a Connect up to 200 slides or 90 microplates can be loaded and processed automatically within one run 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2 1 2 General e TECAN 2 1 1 Samples Slide adapters lts 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 2 2 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN 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 backg
142. w contains all data definitions for the filter slide loaded in channel 1 slot The Filter Slide 1 tab window Define current loaded filter slides l X Filter slide 1 Filter slide 2 Wavelength Bandwidth Name ES a P3 ES m po nm fad Pos 635 m 5 mwbs EDEN NES EE The Filter Slide 1 tab window consists of the following elements Pos 1 Pos 6 static text Wavelength edit box Bandwidth edit box Name edit box This static text corresponds to the filter positions on the filter slide loaded in filter slot 1 e Pos 1 is reserved for focus measurement e Pos 2 5 are free for filter definition e Pos 6 Is reserved In this field the Wavelength of corresponding filter must be entered In this field the Bandwidth of corresponding filter must be entered In this field the Name for a specific dye used for detection of corresponding filter must be entered No spaces are allowed in the name 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 73 6 LSServer Scanner Shell and Download OTECAN Filter Slide 2 tab The Filter Slide 2 tab contains all data definitions for the filter slide in channel 2 The tab is disabled in this version of the Scanner Shell software The Filter Slide 2 tab window Define current loaded filter slides X Wavelength Bandwidth Name Pos 1 must be Fu fo nm fo nm Autofocus defined as Autofocus otherwise Pos 2 o nm
143. which the Download files 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 Download files can be selected Either type the name of the file or use the Look in selection to obtain a list of file names from which the Download files can be selected All Tecan Download files have the file extension upd Select Open as read only to view the file and protect it from being changed Click the Open button to load a selected Download file upd Click the Cancel button to close the dialog box without loading a file 2004 11 OTECAN 6 LSServer Scanner Shell and Download ESL SxxxV110 upd LSDownLoad File View Instrument Help M Instrument TECAN LS Firmware Download Report Connect instrument LS SERIES SCANNER Serial number PT1 File Open file LS5xxxV110 upd a Instrumentname LaserScanner Main CPU Version Y x x 08 01 m Download Ready The Open File text box displays the selected Download file upd file as well as the instrument name and the version number Download This option allows firmware to be downloaded to an instrument In the Instrument menu select Download and a dialog box appears which recommends to stop all programs that are currently running The desired data will be sent to the connected instrument After the download has successf
144. x Click Cancel to close the dialog box The Test Command dialog box is used in case of errors and for testing purposes Including but not limited to the following e Noor faulty communication between PC INSTRUMENT e Noocorrect instrument function e Testing new instrument features e Setting new instrument parameter Sending commands directly to the instrument is an easy way of changing viewing instrument parameters and testing nearly all functions independent of special driver applications such as LSServer software KEEP IN MIND THIS OPTION IS NOT FOR GENERAL USE Caution Sending wrong data to an instrument can cause crashes of transports or damage the instrument Only service engineers should use this option 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 75 6 LSServer Scanner Shell and Download TECAN The Test Command dialog box contains the following elements Command combo box Use the Command combo box edit field to type in the command that should be sent to the instrument Each command entered is automatically added to the Command combo list All commands sent can be repeated by clicking on the corresponding list item Answer edit box The Answer edit box shows answers received from connected instrument Empty command input Selecting this box deletes commands typed in field after sending Command combo box after they have been sent to check box the instrument New c
145. x is displayed When connected to a Tecan LS SERIES SCANNER instrument two tabs Filter slide 1 filter in channel 1 slot and Filter slide 2 filter in channel 2 slot are shown The Wavelength Bandwidth and a Name for the specific dye used for detection can be defined Click OK to save the filter definition changes and close the dialog box Each filter slide contains 6 filter positions Position 1 is reserved for focus measurement Positions 2 5 are free for filter definition Position 6 is reserved Note Position 1 is always reserved for focus measurement and cannot be changed Note Position 6 is reserved for future functions and cannot be changed Note Empty filter slide positions Wavelength Bandwidth must be set to 0 No spaces are allowed in the filter name o A The Define current loaded filter slides dialog box is divided into individual tabs e Filter Slide 1 tab e Filter Slide 2 tab The Define current loaded filter slides dialog box contains the following buttons OK Click the OK button to save the selected options and to close the dialog box Cancel Click the Cancel button to close the dialog box The selected options are not saved Help Click the Help button to display the online help for the dialog box 6 72 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Filter Slide 1 tab 6 LSServer Scanner Shell and Download The Filter Slide 1 tab windo
146. x the user can choose between several options setting up the connected stacker instrument Click the Port Setup button to display the Port Setup dialog box Stacker type and communication port can be selected Click the Stacker Configuration button to display the Stacker Configuration dialog box the corresponding to the connected stacker instrument Click the Stacker Settings button to display the Stacker Settings dialog box the corresponding to the connected stacker instrument Click the Stacker Calibration button to display the Stacker Calibration dialog box which corresponds to the connected stacker instrument The Stacker Setup dialog box contains the following elements Port Setup button Click the Port Setup button to display the Port Setup dialog box Stacker Configuration Click the Stacker Configuration button to display the button Stacker Configuration dialog box Stacker Settings Click the Stacker Settings button to display the button Stacker Settings dialog box Stacker Calibration Click the Stacker Calibration button to display the button Stacker Calibration dialog box 6 82 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 e TECAN Advanced Menu Open SAF 2004 11 6 LSServer Scanner Shell and Download In the Instrument menu select Connect to connect the instrument In the Advanced menu select Open SAF and the Open Slide Adapter Format dialog box is displayed Open
147. y 6 12 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 2004 11 OTECAN 6 LSServer Scanner Shell and Download On clicking the Image Prescan option the Status dialog box appears and an overview measurement is started Status LS SERIES SCAMMER B m x Instrument is performing prescan Time Elapsed time 00 01 08 d hhimm ss Estimated runtime 00 02 22 dbrmm zs Gain Control Gain 2 I Please wait CTT Shrink Default Break The Status dialog box contains the following elements Instrument is The static text gives information about the actual process static text e g Instrument is performing prescan Instrument is measuring dark Time e Elapsed time static text box group box e Estimated run time static text box Gain control e Gain 1 slider spin control group box Use the slider or spin control to online adjust the gain in Channel 1 e Gain 2 slider spin control Channel 2 is disabled in Prescan mode Please wait Please wait under the static text a progress bar indicates progress bar the progress of the ongoing process Shrink Click the Shrink button to minimize the display of the button Status dialog box Default Click the Default button to maximize the display of the button Status dialog box Break Click the Break button to abort the current measurement button 2004 1 1 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 13
148. y5 where signal from one channel will be detected in the other channel and can therefore lead to incorrectly calculated gain values See AGC Scan Area option button on page 6 16 for more information 2004 11 Operating Manual for the LS Series Scanner No 30001798 Rev No 1 5 6 37 6 LSServer Scanner Shell and Download OTECAN Scan Settings Tab In the Scan Settings tab the excitation and emission wavelengths can be selected The gain for the PMT is set respectively in one or two channels Pinhole Crosstalk correction Integration time Sensitivity and Scan Resolution can be defined Click OK to save the changes and close the dialog box The Scan Settings tab window Measurement Parameter L5 SERIES SCANNER Simulation l X General Geometry Parameters Scan Settings Excitation Angle Optics Channel 1 1st run Channel 1 2nd run Laser nm 533 Y Filter nm 670 C5 PMT Gain 130 AGC AGC Mode Noiselevel 3 0 01 Signallevel SI Om Finhale Smal Crosstalk Crosstalk comection Integration time Optimize Integration Time Sensitivity Resolution Oversampling Factor H Scan Resolution pm 10 Cancel Help The Scan Settings tab window contains the following group boxes e Optics group box e AGC group box e Crosstalk group box e Integration time group box e Sensitivity group box e Resolution group box 6 38 Operating Manual for the LS Series Scanner No 30001
149. yo RaDa Alann CAF 194 Ze cn flea 0 BE rnc 3 Delete Spectral crosstalk can occur in dual label experiments when residual signal contributions from the first dye can be detected in the second detection channel For example if there is a strong signal of dye with shorter emission wavelength e g Cy3 there will typically be a weak but detectable contribution of this dye s Signal in the dye with longer emission wavelength e g Cy5 detection channel as well This is especially true for simultaneous dual color measurements In principle crosstalk can occur in both directions For example a Cy3 contribution can be found in the Cy5 channel and vice versa a Cy5 contribution can be found in the Cy3 channel Typically the shorter wavelength dye into the longer wavelength dye s detection channel is much stronger In our example of Cy3 and Cy5 there is a significant contribution from Cy3 to Cy5 that needs to be calibrated but there is a negligible contribution from Cy5 to Cy3 The latter one needs no calibration The LS SERIES SCANNERS have an automatic correction algorithm implemented for simultaneous dual color measurements Correction takes place on a pixel level during data acquisition In order to function correctly this algorithm needs a valid set of K factors for the dye combination to be measured The quantitative amount of crosstalk depends on the filters laser used the K factors are specific for individual filter laser combina

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