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NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 

Specifications, instrument ...............................................................................................................6 

Electrical........................................................................................................................................7 

Environmental..............................................................................................................................7 

Mechanical....................................................................................................................................6 

Optical...........................................................................................................................................6 

Performance .................................................................................................................................6 

Physical .........................................................................................................................................7 

Processing .....................................................................................................................................7 

Specifications, microarray slides .....................................................................................................8 

Speed/sensitivity, specifying for a scan .........................................................................................42 

Spills, cleanup .................................................................................................................................68 

Start menu.......................................................................................................................................26 

Starting the control unit, scanner, instrument software..............................................................25 

Symbol conventions ........................................................................................................................iv 

Technical support, contact information .......................................................................................80 

Text conventions..............................................................................................................................iv 

Trademarks .......................................................................................................................................ii 

Troubleshooting .............................................................................................................................73 

Unpacking the instrument .............................................................................................................19 

Voltage ranges, instrument............................................................................................................20 

Warranty ...........................................................................................................................................ii 

Workspace, instrument software...................................................................................................32 

Zooming in and out, images ..........................................................................................................61 

 

Summary of Contents for Nimblegen MS 200

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Page 3: ...the Control Unit 8 2 3 Specifications for Microarray Slides 8 B System Description 11 1 System Packages 11 2 System Description 12 2 1 Description of the Instrument 12 2 2 Slide Magazine 13 2 3 Slide Magazine Box 14 3 Installation 19 3 1 Installation Warning and Recommendation 19 3 2 Unpacking the Instrument 19 3 3 Space and Power Requirements 19 3 4 Environmental Requirements 20 3 5 Installation ...

Page 4: ...iewing Images 61 8 1 Displaying an Image 61 8 2 Zooming in and out 61 8 3 Displaying Intensity Data for a Feature 62 8 4 Adjusting Image Appearance 62 8 5 Displaying a Histogram or Line Profile 63 8 6 Choosing the Channel s to Display 66 D Maintenance and Care 67 1 ILC Test 67 2 Liquid Spill Cleanup 68 3 Ozone Filter Replacement 68 4 Instrument Relocation 68 5 Instrument Disinfection 70 E Appendix...

Page 5: ... directed to your Roche NimbleGen Account Manager or Roche Microarray Technical Support Go to www nimblegen com arraysupport for contact information Every effort has been made to ensure that all the information contained in the NimbleGen MS 200 Microarray Scanner Operator s Manual is correct at the time of printing However Roche NimbleGen Inc reserves the right to make any changes necessary withou...

Page 6: ...tive holders VI Intended Use The NimbleGen MS 200 Microarray Scanner is designed to read fluorescently labeled DNA microarrays on 1 x 3 inch standard glass laboratory slides for experiments in research laboratories This Microarray Scanner is intended for life science research only VII License Statements for the Instrument Any patents or patent applications are owned by the original equipment manuf...

Page 7: ...erview provides an introduction to the instrument s capabilities and specifications for the instrument control unit and microarray slides Chapter B System Description contains a description of the instrument s components and consumables and instructions on the installation of the instrument and software Chapter C Operation describes the operating procedures for the instrument Chapter D Maintenance...

Page 8: ...software Bold type Identifies buttons and menu names when operating the instrument software Underscore and brackets A placeholder for information such as in the actual name of a directory in a path is enclosed in brackets e g install path Placeholders for file names numbers dates etc are separated by an underscore _ e g Barcode _ User Text _ Laser WL Symbols The following types of notices may be u...

Page 9: ...n Contact Roche Microarray Technical Support for information on proper disposal Follow your institutional requirements for disposal of the accessories XII Warnings and Precautions Handling Requirements The Microarray Scanner must be used by only trained and skilled personnel It is essential that the following safety information required for installation and operation of the Microarray Scanner is c...

Page 10: ... procedures It is assumed that instrument operators due to their vocational experience are familiar with the necessary safety precautions for handling chemicals and biohazardous substances Adhere to the following laws and guidelines National industrial protection law Accident prevention regulations Safety data sheets of the reagent manufacturers Safety and Information Labels Safety and information...

Page 11: ...anner XIII Disposal of the Instrument and Consumables Disposal of the Instrument Because components of the Microarray Scanner could be exposed to potentially infectious chemical samples toxic or corrosive chemicals or radioactive chemicals perform appropriate waste management to ensure there is no risk of contamination ...

Page 12: ... and local regulations for waste disposal and management Directive 2002 96 EC on waste electrical and electronic equipment WEEE Negative environmental impacts associated with the treatment of electrical and electronic equipment waste Do not treat electrical and electronic equipment as unsorted municipal waste Collect waste from electrical and electronic equipment separately Pollution degree 2 Meth...

Page 13: ...ozone concentrations during operation The Microarray Scanner produces single or multi image Tagged Image File Format files TIFF tif that can be read by software packages available from Roche NimbleGen and other vendors Following is a description of the instrument s key functionality and components Autofocus Procedure Microarray slides can have a variable surface planarity which can affect the focu...

Page 14: ...Other dyes similar to Cy3 and Cy5 can also be used such as Alexa 555 and Alexa 647 or DY 547 and DY 647 Excitation intensity can be varied with neutral density filters located in a filter wheel behind the lasers so that each laser can be adjusted separately with its own filter device A reference photodiode is used for detecting the laser power Emission Filters The Microarray Scanner is equipped wi...

Page 15: ...d The Microarray Scanner can measure two fluorescent dyes simultaneously parallel mode at increased overall scan speed Alternatively the dyes can be read one at a time sequential mode In addition two scanning velocities are available 16 lines per second 8Hz and 24 lines per second 12Hz The overall processing time includes loading and unloading of a slide reading the barcode performing the autofocu...

Page 16: ...e you initiate the ILC run the ILC module runs fully automated with no user intervention The instrument software will automatically load and unload the ILC slide as required and perform and evaluate all tests The following tests are performed and results are reported refer to page 29 for information on how to save the results Actuators Test Performs a step loss check for each actuator e g slide tr...

Page 17: ...bsystem while performing several Z scans using different parameters on the ILC slide Optical Resolution Test Scans defined test structures i e line gratings with high low reflectivity parallel to the X and Y axes on the ILC slide to provide information on optical resolution Sensitivity Tests Check the overall performance of components that are relevant for sensitivity electronics detectors lasers ...

Page 18: ...hotomultiplier tubes Gain adjustment 0 01 1000 Optics High aperture collection optics NA 0 7 Emission filters One predefined filter per laser Dichroic beam splitter Two different beam splitters Pinholes Two pinholes of fixed size Reference detector Monitors laser power Autofocus Automatic user selectable slide types Barcode reader Capable of reading NimbleGen Code 39 and Code 128 barcode formats M...

Page 19: ...s 64 bit Interface Ethernet RJ45 Data acquisition High speed 16 bit A D conversion Samples to be measured Fluorescent features on microscope slides within the specified slide dimensions Slide magazine Holds up to 48 slides and allows automatic loading Environmental Ambient temperature Operation 18 28 C 64 82 F Non operation 20 60 C 4 140 F Relative humidity Operation 20 80 non condensing Storage 1...

Page 20: ...ard US layout Mouse 2 button optical scroll mouse Operating system Microsoft Vista Business 64 bit 2 3 Specifications for Microarray Slides Slide Formats Microarray slides to be processed using the Microarray Scanner should meet the nominal specifications of 25 4 x 76 2mm 1 x 3in for standard glass laboratory slides or following dimensions Width 24 6 26 0mm Length 75 0 76 5mm Thickness 0 8 1 2mm S...

Page 21: ... Microarrays To obtain reliable results it is strongly recommended that reference spots are placed onto the slide for quality control These spots should represent every dye used for the experiment and be distributed in a nonsymmetrical pattern across the slide It is also recommended that blank spots be placed on the slide to check for variation of the background in the experiment Figure 2 Scan Are...

Page 22: ...10 NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 Notes ...

Page 23: ...ipping agent before accepting the product Use only the original packaging for transportation or relocation of the equipment Quantity Component Microarray Scanner Catalog No 05394341001 1 MS 200 Microarray Scanner 1 Power cord European standard 1 Power cord North American standard 1 Ethernet cable 1 Slide magazine box 1 ILC slide Control Unit Catalog No 05394325001 1 19 LC display with sound 1 2 bu...

Page 24: ... v1 0 2 System Description 2 1 Description of the Instrument The following illustrations identify the outer attributes of the Microarray Scanner An overview of the Microarray Scanner s functions is provided in subsequent sections Figure 3 Front Figure 4 Rear ...

Page 25: ...re 6 Slide Magazine Accommodates up to 48 Microarrays For loading the slides the slide magazine contains rails with the slide positions numbered 1 48 from the top down The latch on top of the slide magazine ensures that the flap remains closed so that all slides are kept safely in position and do not slip out For instructions on how to unlock and lock the latch refer to the Inserting Slides into t...

Page 26: ...magazine box can be used as a storage device for the slide magazine to provide protection against dust Figure 7 This box is also suitable for placing the slide magazine reclined in the foam slot so that slides can be inserted from above Figure 9 Figure 7 Slide Magazine Box Inserting Slides into the Slide Magazine STOP Wear powder free gloves or equivalent when handling slides Avoid touching the mi...

Page 27: ... each slide by its edges with the microarray facing up Insert the slide into the slide magazine slot using the same rail profile Insert slides with a barcode with the barcode area first Figure 8 Numbered slots provide spacing for inserting slides 3 When finished inserting slides release the flap s flange which causes the latch to automatically lock so that slides do not slip out of the slide magaz...

Page 28: ...azine Insertion and removal of the slide magazine is achieved manually and should be done gently and with care Figure 10 A green light in the upper left corner of the insert eject magazine button indicates that the slide magazine is accessible whereas a locked stacker cover is indicated by a red light Figure 10 Inserting the Slide Magazine into the Microarray Scanner ...

Page 29: ...ine to determine which slots are occupied STOP Do not start the instrument software during the initialization process that the Microarray Scanner performs after slide magazine insertion Doing so may cause the software to shut down unexpectedly To remove the slide magazine 1 Press the insert eject magazine button to open the stacker cover 2 Wait for the slide magazine to eject from the stacker unit...

Page 30: ...de magazine s flap to ensure the slides do not slip out left image Avoid tilting or wedging microarrays in the slide magazine right image STOP Never force or wedge a slide into the slide magazine Be careful when carrying and when inserting the slide magazine into the Microarray Scanner Do not unlatch the flap or slides could slip out ...

Page 31: ... instructions to unpack the instrument Visually inspect the instrument for loose bent or broken parts Report any damage immediately 3 3 Space and Power Requirements Space Requirements Ensure that the designated site meets the dimension and weight requirements of the Microarray Scanner Place the instrument on a rigid and level surface that can support 50 0kg 110 0lb The instrument is 46 6cm 18 5in ...

Page 32: ... sensing and able to operate without any manual adjustments within the following voltage ranges 100 120V AC 50 60Hz 150VA 220 240V AC 50 60Hz 150VA 3 4 Environmental Requirements The Microarray Scanner is intended for indoor operation under controlled laboratory conditions For optimal operation and smooth running of the relevant applications operate the Microarray Scanner only in the specified con...

Page 33: ...ng to a place with changed environmental conditions Humidity for operation 20 80 non condensing Humidity for storage 10 80 non condensing 3 5 Installation of the Control Unit To install the control unit and connect it to the Microarray Scanner 1 Connect the mouse keyboard and monitor to the computer as instructed in the computer s documentation 2 Connect the Microarray Scanner to the computer s PC...

Page 34: ... safety instructions of the hardware devices controlled with the software described here are strictly observed and followed Therefore all relevant reference materials must always be available to all users working with the instrument software What Users Must Know Users must be qualified and trained to run the instrument and the instrument software In particular they must fulfill the following quali...

Page 35: ...dministrator rights 3 6 5 General Installation Considerations Pay attention to the following If a previous version of the instrument software is installed on the target computer uninstall it before installing the new one Install the new instrument software Create the necessary user accounts 3 6 6 Saving User Defined Data Roche NimbleGen recommends that you save all user defined data and output fil...

Page 36: ... local administrator Use the following user account and password for the installation procedure Account msInstall Password 1 msInstall For instructions on using or creating a user account that has administrative permissions refer to the To add a new user to the computer topic in Windows Help or contact your system administrator At the first log in you will be prompted to change the password The pa...

Page 37: ...s Click Install Software to continue The instrument software and all necessary components will be installed by an automatic setup program Wait while the setup process is performed Figure 13 Welcome Window 8 After successful installation carefully read the release notes if provided to learn about the latest changes and functionality 3 7 Starting the Control Unit Microarray Scanner and Instrument So...

Page 38: ...ck All Programs and locate the NimbleGen folder Open the folder and select the program icon to launch the instrument software 4 The instrument software workspace opens Figure 14 Make sure that the instrument software has completely loaded before continuing 5 Click the Green Laser and Red Laser buttons to switch on the lasers Allow them to warm for at least 10 minutes Refer to Chapter C Operation f...

Page 39: ...the ILC slide Avoid touching or damaging the featured slide surface 1 If necessary switch on the Microarray Scanner using the main power switch on its rear and the on off button on its left side You will notice that the internal fans switch on The blue initialize function light indicates that the instrument is ready for operation 2 Start the instrument software to connect to the Microarray Scanner...

Page 40: ... procedure button When prompted load the ILC slide into slot 48 of the slide magazine Figure 17 Insert the slide magazine into the Microarray Scanner Figure 10 Figure 17 Inserting the ILC Slide 5 Click OK in the instrument software The Microarray Scanner removes the ILC slide from the slide magazine and places it in the ILC bay ...

Page 41: ... the ILC test refer to ILC Module on page 4 Keep the ILC slide in the Microarray Scanner and remove it only when transporting or moving the instrument to another site Make sure that slot 48 of the slide magazine is empty before instructing the Microarray Scanner to remove the ILC slide Click the Remove ILC slide button in the Integrated Laser Check window to move the ILC slide from the ILC bay to ...

Page 42: ...30 NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 Notes ...

Page 43: ...Safety section on page 22 2 Using the Instrument Software A Typical Scanner Experiment Following are typical steps in a scanner experiment Before starting the software start the control unit and Microarray Scanner refer to page 25 and load the slides into the scanner refer to page 14 1 Start the instrument software refer to page 25 2 Start the scanner s lasers to allow for proper warmup refer to p...

Page 44: ...strument software workspace opens and provides menus and functionality for viewing and editing scan specifications and acquiring and viewing images Figure 19 The Instrument Software Workspace The instrument software consists of various input and output options Its workspace is arranged to help you focus on specifying scan parameters Figure 19 top figure and viewing images Figure 19 bottom figure ...

Page 45: ...NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 33 Figure 19 Components of the Instrument Software Workspace ...

Page 46: ...s and viewing images QC tab Displays the ILC button to initiate testing of the Microarray Scanner s performance Scan Control Displays the Start Stop Scan button and a progress bar During initialization at startup and scanning the current task that is being performed is identified above the progress bar Laser Control Displays buttons for turning on and off the Microarray Scanner s lasers Click the ...

Page 47: ...h scan grid to display a more detailed view in the Image View Do not use the resizable magenta rectangle when scanning at 2μm resolution Image View Displays the currently scanned or loaded image Refer to the Reviewing Images section on page 61 for more information 3 1 Understanding Sessions Session is the term used when the slide magazine is loaded with slides to scan in a user defined run Like th...

Page 48: ...session files Click the Roche button to display the Application menu Figure 20 and select the appropriate command Parameter file parax Stores user inputs such as slide type resolution speed channels gain and laser intensity as well as image file definition and scan areas can be saved A parameter file can be loaded into a session and assigned to one or more slides For instance you can create parame...

Page 49: ...t make any restrictions on overwriting deleting or modifying files Use care when performing file handling tasks 3 2 Using the Help Viewer The Help Viewer provides background information functionality overviews and procedural assistance for the Microarray Scanner and instrument software Click the Help button or press F1 to access the Help Viewer Figure 22 Help Viewer At the top of the Help Viewer y...

Page 50: ... The Search tab allows you to type in the word or phrase for which you want to search for and then click List Topics Double click a search result to display the corresponding topic 3 3 Setting Software Options The instrument software provides options for specifying the default storage location for image files how long the lasers will remain on during periods of non use before the instrument softwa...

Page 51: ...n the text box 4 Review the default file format Currently Roche Format is the only available format 5 Click OK to save any changes Or click Cancel to exit without saving changes 4 Specifying Parameters In this section you learn how to Work with the magazine control to identify the slides to scan Set the parameters to use to scan the slides Specify scan barcode and autogain areas 4 1 Working with t...

Page 52: ... number of times to scan the slide Refer to page 45 for information on how to add cycles Slide Present Each position in the slide magazine is automatically identified as empty or occupied An occupied position is identified by a green box an empty position by a light gray box A red box indicates the instrument software is in the process of checking the status of the slide position Select Scan Selec...

Page 53: ... Image View Parameters Scan parameters are assigned to a letter code in alphabetical order The same letter corresponds to same applied parameter settings For information on how to change parameters refer to the Specifying Scan Parameters section below Resolution Displays the selected scan resolution Laser Red and green dots represent selected laser channels 4 2 Specifying Scan Parameters 1 Go to t...

Page 54: ...de Type The only selection available is Roche NimbleGen Additional selections could be available in the future Resolution Select from 2 5 10 20 and 40μm resolutions Speed Sensitivity Adjusts the scan speed Your selection has an impact on the overall results based on the speed and sensitivity of the scan Click the slider in the following locations to select one of these settings ...

Page 55: ... at 0 1 1 10 25 50 75 or 100 for each channel It is recommended to keep the laser intensity set to 100 and adjust the PMT gain setting if necessary Autogain Select this checkbox to activate the autogain procedure During the autogain procedure the instrument software scans the specified autogain area and equalizes the intensity values for the channels Apply to slide number x and cycle x Select this...

Page 56: ...eter Control button Figure 25 2 Go to the row of the slide with the preferred parameters in the Magazine Control right click and select Copy from the menu 3 Highlight the rows for the slides to process using the same parameters right click and select Paste Parameter Settings from the menu To highlight multiple slide rows hold down the Ctrl key and click each slide s row Or click a row and then hol...

Page 57: ...e a maximum of 12 times Each time the slide is processed is referred to as a cycle To create a cycle 1 If open close the Parameter Control by clicking the Close Parameter Control button Figure 25 2 Go to the slide row in the Magazine Control Figure 24 right click and select Add Cycle 3 Specify parameters for the cycle as described in Specifying Scan Parameters on page 41 To delete a cycle 1 If ope...

Page 58: ...onsistency and avoids naming conflicts across a batch scan 1 Highlight the slide row in the Magazine Control Figure 24 2 If necessary open the Parameter Control Figure 25 by clicking the slide s Open Parameter Control button in the Magazine Control 3 In the Parameter Control click the Open Close File Settings button to open the File Settings Control Figure 26 Figure 26 File Settings Control 4 Choo...

Page 59: ...ft arrow button Make sure to select the Barcode annotation i e include it in the right list box to read the barcode label information on the slide 7 Once your selection is complete optionally change the order of the annotations in the file name Click the annotation in the right list box and click Up or Down to adjust its position If you will be using NimbleScan software for data analysis order the...

Page 60: ...ning because the settings can be saved for future use To display the Area Definition Control 1 Highlight the slide row in the Magazine Control Figure 24 2 If necessary open the Parameter Control Figure 25 by clicking the slide s Open Parameter Control button in the Magazine Control 3 In the Parameter Control click the Open Close Area Definition Control button to open the Area Definition Control Fi...

Page 61: ...ckboxes allows for the definition of the barcode and autogain areas To activate the barcode functionality specify Barcode as part of the image file name using the File Settings Control Figure 26 To activate the autogain functionality select the Autogain checkbox in the Parameter Control Figure 25 STOP Do not adjust the barcode area if using NimbleGen arrays The default location and size of the bar...

Page 62: ...K and 12x135K arrays use the default settings for the scan region For NimbleGen 385K and 4x72K arrays it is recommended that you reduce the scan area to reduce the scan time To define and adjust a single scan area on your microarray 1 If necessary highlight the slide row in the Magazine Control Figure 24 2 If necessary open the Parameter Control Figure 25 3 If necessary open the Area Definition Co...

Page 63: ...cursor 6 Drag the rectangle over the desired feature region Adjust the size of the rectangle by dragging a corner side handle 7 Click Apply to confirm your settings 8 If desired click Save to save settings to an area file for future use To use an existing array image as a template for your area layout Choose between the following To load an image from a file click the Roche button select Open Imag...

Page 64: ...your selection 6 2 Specifying Multiple Scan Areas If you are using NimbleScan software for data analysis Roche NimbleGen recommends specifying a single scan area instead of multiple scan areas For NimbleGen multiplex arrays you use the software s burst functionality to create individual image files for the arrays To identify multiple areas 1 If necessary highlight the slide row in the Magazine Con...

Page 65: ...orner of the microarray features 6 Drag the merged rectangles to the top left segment of the printed area to identify the area to scan Adjust the size of the magenta rectangle by dragging a corner handle 7 Use the white scan area rectangle to enclose the top left feature segment on the array This is used to set size and shape of all other scan areas Drag a corner handle or a side handle until that...

Page 66: ...strument software automatically scales all other areas to the same dimension Clear the Link to Geometry checkbox to disable this functionality In each corner and side of a scan area handles will appear to adjust each scan area individually 11 Click Apply to confirm your settings 12 If desired click Save to save settings to an area file for future use To use an existing array image as template for ...

Page 67: ...if using NimbleGen arrays The default location and size of the barcode area has been designated specifically for these arrays 1 If necessary highlight the slide row in the Magazine Control Figure 24 2 If necessary open the Parameter Control Figure 25 3 If necessary open the Area Definition Control Figure 29 4 Ensure the Barcode area checkbox is selected 5 Position the mouse pointer inside the resp...

Page 68: ...t the slide row in the Magazine Control Figure 24 2 If necessary open the Parameter Control Figure 25 3 If necessary open the Area Definition Control Figure 29 4 Ensure the Autogain area checkbox is selected 5 Position the mouse pointer inside the respective rectangle and click to enable the move cursor 6 Drag the rectangle to the desired location As a recommendation ensure the rectangle is approx...

Page 69: ...NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 57 Figure 30 Examples of Setting the Autogain Area for NimbleGen Arrays 8 Click Apply to confirm your settings ...

Page 70: ... selected in the Magazine Control Figure 24 7 2 Starting a Scan Click the Start Stop Scan button in the Scan Control Figure 19 Specify the folder and file naming to save the session file The scan process is then initiated If the lasers are not fully warmed up the Laser Warmup Time Active window opens asking you to wait After the necessary warmup time this window closes and the scan starts automati...

Page 71: ...ly loaded slide As the image is acquired it appears from the bottom upward in the Slide View For 5 10 20 and 40μm scans the Image View mirrors the Slide View and the Spot View is functional during the run For 2μm scans the Image View and Spot Views are not functional during the run After the scanning experiment is completed the light in the upper left corner of the insert eject magazine button bec...

Page 72: ... or above the signal intensity of the surrounding experimental features to help to ensure proper grid alignment Features with saturated pixels are drawn in magenta on the image Saturated fiducial controls can cause poor alignment quality 7 3 Aborting a Scan At any time you can stop the scan or batch run Click the Start Stop Scan button in the Scan Control Figure 19 It can take some time to stop th...

Page 73: ...isplaying an Image Choose between the following Click the Display Images button in the Magazine Control Figure 24 or open another session and click the Display Images button The Display Images button links to the directory in which the image was originally saved for the session If the image s file name is modified or if the file is moved clicking the Display Images button will result in an error C...

Page 74: ...d crosshair in the Spot View can be placed over a specific feature by moving the cursor within the Image View This will render intensity data for both channels and the coordinates for that feature 8 4 Adjusting Image Appearance You can adjust contrast and brightness using the Image Control Figure 35 to have a better view of features on the image Adjusting these settings allows faint features to be...

Page 75: ...ings does not modify the pixel values in the saved image They only adjust the way in which the image is displayed 8 5 Displaying a Histogram or Line Profile Using the Image Control Figure 35 you can generate histograms or line profiles Histograms show an intensity frequency profile for a specified region Line profiles show an intensity profile for a specified vertical or horizontal section To disp...

Page 76: ...ogram to reflect the changes in pixel intensity Histogram mode is not available for 2μm scans during the run but is available post run The following figure shows a histogram generated during a scanner experiment in which the channels are unbalanced The Gain 1 and Gain 2 spin boxes enable you to adjust the gain during the scan Figure 36 Histogram Generated During the Run Figure 37 shows a histogram...

Page 77: ...ow opens Figure 38 A magenta defining line is placed within your image in the selected channel mode Use the mouse to position the defining line over the pixels to measure The line can be drawn to any length by dragging either endpoint You can zoom the boundaries of the line profile plot range by dragging the slider bars in the Line Profile window Linear and Logarithmic Base 10 option buttons allow...

Page 78: ...ner Operator s Manual v1 0 Figure 38 Line Profile Window 8 6 Choosing the Channel s to Display The Overlay Channel 1 and Channel 2 option buttons in the Image Control Figure 35 enable you to view images in single channel or overlay mode ...

Page 79: ...ore detailed instruction Roche NimbleGen recommends you perform an ILC test every 2 weeks 1 Switch on the Microarray Scanner 2 Start the instrument software 3 Click the QC tab and then ILC in the instrument software The Integrated Laser Check window opens Figure 16 4 Click the Start stop ILC procedure button After the ILC test is completed the instrument software produces and displays a comprehens...

Page 80: ... spill occurs inside of the instrument a service technician is required 1 Switch off the Microarray Scanner 2 Wipe up the spill immediately using absorbent material 3 Dispose of contaminated material appropriately 4 Clean the instrument surfaces with a mild detergent 5 Disinfect the instrument as described in the Instrument Disinfection section on page 70 6 Wipe dry all cleaned areas 3 Ozone Filte...

Page 81: ...ed in the Instrument Disinfection section on page 70 Treat all parts of the instrument that come into contact with biological samples or other hazardous material as potentially infectious areas STOP Thoroughly disinfect the instrument before it is removed from the laboratory 3 Pack the instrument Use the original packaging to ensure that no damage occurs to the instrument STOP Remove the slides fr...

Page 82: ...ld be performed according to national regional and local regulations Perform the disinfection procedure when cleaning up a spill and when relocating the instrument 1 Disconnect the instrument from the main power supply 2 Disconnect the instrument from any accessories 3 Carefully wipe all the outside surfaces of the instrument with a clean lint free cloth that has been soaked in the disinfecting so...

Page 83: ...his package has been decontaminated or disinfected to remove or inactivate any biological material which could be dangerous to personnel or that it has never been exposed to any hazardous biological material Contact person Company Function Phone Fax Email Date of decontamination Method of decontamination applied Date Signature ...

Page 84: ...72 NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 Notes ...

Page 85: ...r Possible Cause s Corrective Measure s Instrument Level Troubleshooting Communication error occurred Power is not on Switch on power to the Microarray Scanner using the main power switch on its rear and using the on off button on its left side Power communication was interrupted Check cable s and plug to ensure they are securely connected Switch off then switch on power to the Microarray Scanner ...

Page 86: ...o the Microarray Scanner Carefully push back the stacker flap and lower the slide magazine beyond the mechanical hold point Switch on power to the Microarray Scanner and wait for initialization to complete If the problem persists contact Roche Microarray Technical Support Load unload of slide could not be done successfully Mechanical failure occurred Follow the instructions in the Removing a Slide...

Page 87: ...s present in the slide magazine Particles dust or finger prints are present on the slide Check the slide surface If possible remove dust and or particles from the slide by appropriate methods For NimbleGen arrays refer to the NimbleGen Arrays User s Guide for instructions Repeat scan If the problem persists run the ILC test If the problem persists contact Roche Microarray Technical Support The arr...

Page 88: ...g s Poor fluorescence was realized Avoid degradation of labeled samples on the array due to exposure to light ozone and or humidity Correct settings for PMT gain and or laser intensities Run the ILC test Barcode reading failed No barcode is on slide Verify the slide has a barcode Barcode is misplaced Check the position of the barcode area Slide inserted in the wrong direction Check the insertion d...

Page 89: ...oubleshooting Missing array images No Display Images button is available Array images were removed from the default file location or renamed Check the assigned directory in the File Settings Control Instrument software shuts down unexpectedly The Microarray Scanner may be performing the initialization process for the slide magazine After inserting the slide magazine into the Microarray Scanner wai...

Page 90: ...gure 40 Opening the Front Cover 3 If accessible manually remove the slide or slide fragments from the slide transport Figure 41 Use vacuum to remove all slide fragments if necessary Figure 41 Removing the Slide from the Slide Transport 4 Close the instrument s front cover Figure 42 Gently push the front cover into place making sure to push it all the way into place Two bolts and a pin secure the c...

Page 91: ...n Account Manager Go to www nimblegen com arraysupport for contact information The following items are included with the purchase of a NimbleGen MS 200 Microarray Scanner system Catalog No Product 05394341001 MS 200 Microarray Scanner 1 magazine included 05394325001 MS Control Unit 05394309001 MS 200 Operator Manual 05394333001 MS 200 Software The following accessory can be purchased Catalog No Pr...

Page 92: ...er control unit and instrument software Loading microarray slides Specifying parameters Scanning Analyzing images It also describes the instrument software workspace Refer to chapters noted for more details 3 1Starting the Scanner Control Unit and Instrument Software 1 Start the control unit and log into your user account 2 Start the Microarray Scanner Chapter B System Description 3 Start the inst...

Page 93: ...upied position Slide Present in the slide magazine Choose a slide to scan during the next run by selecting the Select Scan checkbox Specify scan parameters using the Parameter Control Adjust the output file format path for data storage and the name generation setting using the File Settings Control Define the scan barcode and autogain areas using the Area Definition Control Chapter C Operation For...

Page 94: ...sibility of features Use the Zoom function in the Area Definition Control to change the magnification in the Area Definition View In addition to the histogram of this potentially magnified area the instrument software offers data assessment with vertical and horizontal line profiles Chapter C Operation 3 6 Instrument Software Workspace The instrument software workspace offers menus and a variety o...

Page 95: ...NimbleGen MS 200 Microarray Scanner Operator s Manual v1 0 83 ...

Page 96: ...eshooting 75 Autogain Activating the autogain functionality 43 Dimensions of the autogain area 56 Specifying the autogain area 56 Barcode Acceptable formats 6 Activating the barcode reader functionality 47 Dimensions of barcode area 9 80 Location of the barcode area for NimbleGen arrays 55 Specifying the barcode area 55 Troubleshooting 76 Barcode reader test 4 Blank spots non NimbleGen microarrays...

Page 97: ...cription 2 Environmental specifications instrument 7 Features displaying intensity data 62 File Settings Control components 46 Files Area files 37 48 Parameter files 36 Saving log files 60 Session files 36 Setting the default format for image files 38 Setting the default storage location for image files 38 Specifying naming conventions for image files 46 Gain See PMT gain Gamma adjusting 63 Geomet...

Page 98: ...ILC slide into the slide magazine 28 Performing the initial ILC test 27 Proper handling of the ILC slide 27 Removing the ILC slide from the instrument 29 ILC test Example report 29 How often to perform the ILC test 27 Images Adjusting contrast brightness and gamma 62 Choosing the channe s to display 66 Displaying intensity data for a feature 62 Reviewing Images 61 Specifying file naming convention...

Page 99: ...ety instructions 22 Saving user defined data 23 Setting defaults options 38 Target computer 23 Typical scanner experiment 31 What users must know 22 Who should install 23 Workspace description 32 Intended use instrument ii Intensity data displaying 62 Keyboard specifications 8 Lasers Laser excitation description 2 Laser timeout setting 38 Laser s test 5 Specifying the laser intensity for a scan 43...

Page 100: ...of parameter files 36 Relationship between session parameter and area files 36 Saving parameter files 43 Specifying scan parameters 41 Password requirements 24 Performance specifications instrument 6 Photobleaching 3 Photodetectors 2 Photomultiplier tubes See PMTs PMT gain Adjusting the PMT gain during a scan 60 Specifying the PMT gain for a scan 43 PMTs 2 Pollution degree viii Positioning test 5 ...

Page 101: ... and opening session files 36 Description of session files 36 Relationship between session parameter and area files 36 Slide Barcode dimensions 9 80 Inserting the ILC slide into the slide magazine 28 Recommendations for non NimbleGen microarrays 9 Slide dimensions 8 Slide mishandling handling 17 Specifying a single scan area 50 Specifying multiple scan areas 52 Specifying the autogain area 56 Spec...

Page 102: ...icroarray slides 8 Speed sensitivity specifying for a scan 42 Spills cleanup 68 Start menu 26 Starting the control unit scanner instrument software 25 Symbol conventions iv Technical support contact information 80 Text conventions iv Trademarks ii Troubleshooting 73 Unpacking the instrument 19 Voltage ranges instrument 20 Warranty ii Workspace instrument software 32 Zooming in and out images 61 ...

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Page 104: ...Published by Roche NimbleGen Inc 504 S Rosa Road Madison WI 53719 USA 2009 Roche NimbleGen Inc All Rights Reserved 05394309001 0409 ...

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