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tecan ls series Operating Manual

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TECAN
Operating Manual for the
LS Series Scanner
Document Part No.: 30001798
2004-11
Document Revision No.: 1.5

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Summary of Contents for tecan ls series

  • Page 1 TECAN Operating Manual for the LS Series Scanner Document Part No.: 30001798 2004-11 Document Revision No.: 1.5...
  • Page 2 UK-Reading RG7 5AH United Kingdom Tel.: +1 919 361 5200 Tel.: +44 11 89 300 300 Fax: +1 919 361 5201 Fax: +44 11 89 305 671 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 3 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.
  • Page 4 OF LIFE OR EQUIPMENT DAMAGE IF THE INSTRUCTIONS ARE NOT FOLLOWED. WARNING INDICATES LASER. DO NOT STARE INTO THE BEAM! WARNING INDICATES THE POSSIBLE PRESENCE OF BIOLOGICALLY HAZARDOUS MATERIAL. PROPER LABORATORY SAFETY PRECAUTIONS MUST BE OBSERVED. Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 5: Table Of Contents

    LSServer..................6-6 6.3.1 Starting the First Time ..............6-6 6.3.2 Measurement Control ..............6-6 6.3.3 File Types used in LSServer ............6-9 6.3.4 Measurement................. 6-11 6.3.5 Instrument..................6-26 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...
  • Page 6 8.5.1 Disinfection Solutions ...............8-6 Disinfection Procedure ..............8-7 Disinfection Certificate ..............8-7 Disposal of Instrument ..............8-8 8.8.1 Disposal of Packing Material ............8-8 8.8.2 Disposal of Operating Material ............8-8 Index Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 7: Safety

    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.

  • Page 9: General

    The design allows the use of standard microplate equipment to load very high numbers of slides automatically. For instance, with a Connect, up to 200 slides or 50 microplates can be loaded and processed automatically within one run. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 10: Samples

    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.

  • Page 11: Modes Of Operation

    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.

  • Page 12: Automation Friendliness

    It is also recommended to place ‘blank’ spots onto your arrays in order to check for the variation of the background in your experiment. Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 13: 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 causing a short circuit 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...
  • Page 14 Remove transportation locks. 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...
  • Page 15 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...
  • Page 16 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 Data cable to connector box Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 17 The pictures below show the connection of the interface cables to the back of the computer: RS232 to instrument Connection for monitor cables Connector Digital monitor Data cable to cables instrument Analog monitor cables 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...
  • Page 18 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. Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 19: Remove Transport Lock

    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...

  • Page 20: Filter Installation

    2 (horizontal orientation) and make sure that the filters are oriented properly, (see pictures below). Filter Channel 2 Filter Channel 1 Note Both filter slides are only necessary in dual channel instruments. • Close the filter compartment Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 21: Power Requirements

    May either become damaged or May no Longer be Able to perform Its Procedures correctly and the Accuracy of the instrument can no longer be guaranteed. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 23: Technical Description

    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...
  • Page 24 (PMT’s). The two different filters are located on two different filter slides in that case. A reference diode monitors laser power before each measurement. Figure 4.2 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 25: Autofocus

    - 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.

  • Page 27: Operation

    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...

  • Page 28: General Operating Features

    5. Operation 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.

  • Page 29: Connect To Instrument

    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...

  • Page 30: Insert Slide(S) Into Slide Adapter

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

  • Page 31: Lsserver, Scanner Shell And Download

    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.

  • Page 32: Software Requirements

    It is necessary that the person who installs the software has administrator rights on a PC with a Win 2000 operating system. Step Procedure Place the LS Driver for Tecan LS V2.2 Setup CD in the CD-ROM drive. Open the CD drive folder and start LSServer.exe. The installation procedure begins.
  • Page 33 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...

  • Page 34: Tecan Ls Scanner Interface

    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: •...
  • Page 35 Cancel button Click Cancel to close the dialog box. The selected options are not saved. Help button Click Help to display the online help for the dialog box. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 36: Lsserver

    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.
  • Page 37 Measurement parameters can be loaded from a file. Save button Click the Save button to open the Save As dialog box: Measurement parameters can be saved to a file. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 38: Slide Adapter Format

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

  • Page 39: File Types Used In Lsserver

    LSServer.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...

  • Page 40: File Management

    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. 6-10 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 41: 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 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-11...
  • Page 42 Single Scan mode • 40 µm scan resolution • Large pinhole • Optimize integration time selected • No autofocus • Scan Settings from Channel 1 only 6-12 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 43 Default Click the Default button to maximize the display of the button Status dialog box. Click the Break button to abort the current measurement. Break button 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-13...
  • Page 44 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.
  • Page 45 Autofocus area is centered automatically to the scan area. Legend: barcode line autofocus lines scan area AGC area figure 6-2 Minimum distance between Autofocus lines: 3mm x 3mm. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-15...
  • Page 46 The barcode is always read centered to the slide width and must be set within the useable barcode area. The Barcode Area button is enabled only if a barcode top reader is available to the Tecan LS Series Scanner and Read barcode has been selected from the Measurement Parameter dialog box. Figure 6-3 The total slide area must be at least 37.5 x 15.0 mm, otherwise there is no...
  • Page 47 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-17...
  • Page 48 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...
  • Page 49 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 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-19...
  • Page 50 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...
  • Page 51 After the instrument has performed the prescan, the first page of the adapter format wizard appears. Table MTP adapter Adapter Prescan = Non confocal scan of the complete transport-table-area. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-21...
  • Page 52 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 Height Clamp Height Carrier Height MTP Adapter Table 6-22 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 53 The Save dialog box will then appear. To save the Slide Adapter Format file, type in the desired filename of the newly created .saf file and click Save. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-23...
  • Page 54 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...
  • Page 55 Focus Offset radio button: The green line represents the focus offset. Example of focus prescan for MTP autofocus After clicking OK, the following dialog box appears: 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-25...

  • Page 56: Instrument

    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.

  • Page 57: Laser Control

    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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-27...

  • Page 58: Measurement Parameter

    Click OK to save the selected options and close the dialog box. 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. 6-28 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 59: General Tab

    The General tab: The General tab contains the following elements: • Scan Mode group box • Stacker group box • Plate group box • Barcode group box 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-29...

  • Page 60: Scan Mode

    Move plate out after measurement check box: group box Selecting Move plate out after measurement opens the door and moves out the plate transport after the measurement is finished. 6-30 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 61 The Slide Thickness is entered respectively. The Geometry Parameter tab: The Geometry Parameter tab window contains the following elements: • Geometry group • Slide group • Slide Adapter Format group 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-31...
  • Page 62 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...
  • Page 63 • Load Standard Adapter button Click the Load Standard Adapter button to load the Standard.saf file and to reset default Geometry Parameters. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-33...

  • Page 64: Scan Area

    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). 6-34 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 65 Autofocus entered in Well or HS-Mode. Autofocus Amplitude (width of Autofocus line) from 3mm to 22mm Distance (between Autofocus lines): from 3mm to slide length 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-35...
  • Page 66 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...
  • Page 67 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...

  • Page 68: Scan Settings Tab

    The Scan Settings tab window contains the following group boxes: • Optics group box • AGC group box • Crosstalk group box • Integration time group box • Sensitivity group box • Resolution group box 6-38 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 69 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-39...
  • Page 70 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. 6-40 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 71 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 used for QC purposes. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-41...
  • Page 72 In theory, the signal to noise ratio is increased by n (n= oversampling factor). For example, a factor of 4 will increase the signal to noise ratio by a factor of 2. 6-42 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 73 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 button the dialog box 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-43...
  • Page 74 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...
  • Page 75 113 µm, - calculated according to following formula: Formula for the offset: d-[(n-1)/n]*d n= refractive index of the cover glass (= 1,5) d= thickness of cover glass 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-45...
  • Page 76 Focus.tif images. The measurement is performed on the selected third plane of the signal profile in z. 6-46 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 77 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.
  • Page 78 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 Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 79: Excitation Angle Tab

    Default It is recommended to select Default for all ‘flat‘ samples (e.g. slides). Angle is set to 25° for both the image scan and for autofocus. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-49...
  • Page 80 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 6-50 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 81 MTP mode or another value determined as optimum for your samples. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-51...
  • Page 82 Click the Open button to load a selected measurement button parameter file (*.lsp). Cancel button Click the Cancel button to close the dialog box without loading a file. 6-52 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 83 Click the Save button to save the current measurement parameters in a file with the extension *.lsp. Cancel button Click the Cancel button to close the dialog box without saving. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-53...

  • Page 84: Settings

    Measure grid box • Filename Format group box • Date Format group box Stitch resulting images check box • • Rotate image group box • Files group box 6-54 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 85 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...
  • Page 86 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. 6-56 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 87: Date Format

    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...
  • Page 88 For example, if Flip image left/right is selected, the result will be as follows: When Flip image left/right and Stitch resulting images are selected, the results will be as follows: 6-58 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 89 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: 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-59...
  • Page 90 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 \... The images are saved as 16bit TIF format.
  • Page 91 The current .lsp file will be saved as _SCAN_Time.lsp) (e.g. _SCAN_141149.lsp; 2 pm, 11 minutes and 49 seconds). Experiment Folders: Date Time Scan Parameter and Image files: See also Filename Format on page 6-57. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-61...

  • Page 92: Slide Adapter Format

    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 ). 6-62 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 93 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-63...

  • Page 94: Ls Scanner Shell

    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...

  • Page 95: Menu Bar

    The Status bar displays the following information: • Help access: Press F1 for Help • Current status of the keyboard toggles: CAP (caps lock), NUM (Numeric block lock), SCRL (Scroll lock). 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-65...

  • Page 96: File Types Used In Scanner Shell

    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...
  • Page 97 Logon dialog box. File Management The default paths for saving files can be changed in the Slide 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...

  • Page 98: Scanner Shell Menus

    When the Status Bar option is selected (√) the Scanner Shell software Status Bar will be shown. When the Status Bar option is cleared the Scanner Shell software Status Bar will be hidden. 6-68 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 99 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...
  • Page 100 In the Movements dialog box, specific In and Out buttons can be used to drive the plate carrier or filter slides into or out of the LS Series Scanner. Click OK to close the dialog box. For further information refer to the chapter Plate/ Filter on page 6-26 description in this manual.

  • Page 101: Setup Menu

    (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...
  • Page 102 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 box 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.
  • Page 103 Name edit box 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-73...

  • Page 104: Instrument Options

    The Language option shows the available languages of the LS Scanner Shell software. When the Language is selected (√) 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...

  • Page 105: Service Menu

    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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-75...
  • Page 106 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.
  • Page 107 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 %.
  • Page 108 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...
  • Page 109 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 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-79...
  • Page 110 The Date static box shows the current date. Format = DD.MM.YY Name edit box 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...
  • Page 111 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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-81...
  • Page 112 6. LSServer, Scanner Shell and Download 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 .

  • Page 113: Advanced Menu

    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. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-83...
  • Page 114 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...
  • Page 115 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...
  • Page 116 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...
  • Page 117 After entering the file name and clicking OK all adapter data is saved. Help Click the Help button to display the online help for the dialog box. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-87...

  • Page 118: Lamp Control

    About 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...

  • Page 119: Stacker Setup - Twister

    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...
  • Page 120 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 .

  • Page 121: Scanner Shell Wizards

    The operation has finished with no errors. 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...

  • Page 122: The Transport Lock Wizard

    Lock. This is a purely informational window and no actions must be carried out in this window. The Start Setting Transport Lock window: 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 2004-11...
  • Page 123 The Apply Absorber Pad window: The Next button guides the user to the next screen of the wizard: the End Setting Transport Lock window. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-93...
  • Page 124 The End Setting Transport Lock window: 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...

  • Page 125: 6.4.10 The Transport Unlock Wizard

    The Start Remove Transport Lock window: 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...
  • Page 126 Transport Lock window. Remove the transportation shock absorber pad (see picture below) 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...
  • Page 127 A Status Control bitmap shows the result of the operation. The Reset Transport Lock window: 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...
  • Page 128 The Gain Calibration Wizard 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: •...
  • Page 129 The Prepare Gain Calibration window: 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...
  • Page 130 To view the gain calibration file, load the Gaincalibration.cvs file in a spreadsheet program such as Microsoft Excel. The Gain Calibration window: 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...

  • Page 131: Lsdownload

    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 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-101...

  • Page 132: Lsdownload Menus

    Click the Save button to save the current download report as a text file (extension *.txt). Cancel Click the Cancel button to close the dialog box without saving. button 6-102 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 133: Print Report

    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...

  • Page 134: Print Preview

    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...

  • Page 135: View Menu

    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...
  • Page 136 Click the Open button to load a selected Download file (*.upd). Cancel button Click the Cancel button to close the dialog box without loading a file. 6-106 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 137 A message in the window area of the LSDownload software shows that the download was successful or unsuccessful: Download Message in report area of LSDownload Firmware download failed! Unsuccessful Firmware download successfully finished! Successful 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 6-107...

  • Page 138: Help Menu

    In the Help menu, select About and the About dialog box appears: The software version and copyright information can be viewed. Click OK to close this dialog box. 6-108 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 139: Instrument Features

    Biochips on microscope slides and user defined measured substrates up to the size of microplates Slide adapter Holds 4 slides and allows automatic loading with microplate handling equipment 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...
  • Page 140 40 µm, 20 µm, 10 µm, 6 µm, 4 µm Reading speed 40 lines per second < 4 minutes for full slide (two colors for dual channel instruments) Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 141 -4°F - +140°F Relative humidity Operation 90 % non-condensing Overvoltage category Pollution degree Usage Commercial Noise level < 75 dBA Method of disposal Electronic waste (infectious waste) 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 142: Lasers

    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.

  • Page 143: Reproduction Of Labels Placed On The Instrument

    Labels placed on the rear front of the instrument Labels placed inside the instrument when housing is opened. LASERSTRAHLUNG NICHT DEM STRAHL AUSSETZEN LASER KLASSE 3B Label placed underneath lid 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 145: Cleaning & Maintenance

    Dispose 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. Wipe cleaned areas dry. 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 146: Replacing The Fuse

    OF THE SAME TYPE AND RATING. • Replace the fuse holder. • Reconnect the mains cable. • Turn the instrument on. Caution If the fuse continues to blow, call for service. Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 147: Remote Control And Data Exchange

    Remote Control and Data Exchange 8.4.1 FTP up / download For exchange of large data sets between Tecan and your company, Tecan offers an ftp site. It is accessible through ftp://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.
  • Page 148 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). Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 149: Working With Citrix Web Conferencing Manager

    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...

  • Page 150: Instrument Disinfection

    Please note that the disinfectant can influence the performance of your instrument if it is applied inside the instrument. Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...

  • Page 151: Disinfection Procedure

    Name:........................Firm: ........................Address: ......................................................................... Country:........................ Signature:......................2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5...

  • Page 152: Disposal Of Instrument

    8. Cleaning & Maintenance 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.
  • Page 153 Opening ..........6-106 Integration time..........6-38 Dual channel instruments ....... 2-3 Lamp Control..6-88. See also Laser Control File Menu Language ............. 6-74 LS Download........... 6-102 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 Index...
  • Page 154 Optical Method ..........6-43 Slide Area ............. 6-12 Slide Settings..........6-54 Packing Material Filename Format........6-55 Disposal ............8-8 Slide Thickness ........6-31, 6-33 Returning.............8-8 Slides to process .......... 6-62 Pinhole............6-38 Index Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 2004-11...
  • Page 155 View Menu Start .............. 6-11 LS Download .......... 6-105 Status bar Scanner Shell..........6-65 Well Mode ............ 6-47 Test Commands ........... 6-75 Z-Scan Height ..........6-45 Toolbar 2004-11 Operating Manual for the LS Series Scanner No. 30001798 Rev. No. 1.5 Index...

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