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Version 7.0.0 User's guide

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1. Save zx Save in BE Desktop vi ete MW Computer me Se Network Comments Recent Items a A be BE Desktop gt gt di iaa Separated TIFF files p My Documents p V Use TIFF LZW compression lossless Ph 77 p r V Prefix File Name 3 d F User Name F Date amp Time Computer ci es Barcode Pixel size a Text Area i Network Suffix File Name Counter Reset File name tif Save Files of type Tagged Image File Format tif tiff z Cancel A For Windows users If you use Windows and want to save your images or results in Windows folders named My documents My images you have to check first if those directories are not read only which is the default of these folders Mapix indeed checks if directories are writable or not To modify read write attributes of folders right click on the folder then click on Properties and in the Attributes area uncheck the read only attribute For information about saving parameters refer to the table below INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561971 975 support innopsys fr Mapix V7 0 0 User s guide 26 ITEM DESCRIPTION You can use the comments box to add specific experiment Comments parameters or other comments about your slides For two color slide scans you can save the image as A single TIFF file containing both
2. Validation code i put X Please type the provided code and insert the new verification slide Insert the new validation slide and then click ok The validation process will proceed as usual NNOPSYSI Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr SNe ae eee A A A E E E GR Sen Came S Mapix V7 0 0 User s guide 84 8 Preferences Using the Preferences menu you can Define the language and the appearance of Mapix Define the generic file name by which the image will be saved when created Define the format of results files and customize the results table Choose a user as the account manager Choose a password to protect your account RK Click on the Users option to display the Preferences menu Preferences INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 8 1 General settings 85 Use this section to define different MAPIX options Preferences General settings Image Files Results files Gridding Folders rose LEE Fer Multi access user Single access user Look amp Feel Windows ei Skin Do not show preventative messages J Enable Disable the scanner buzzer User Account Control J Automatic scanner disconnection after 30 v minutes of inactivity vi Automatic check at
3. 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide ITEM Save results Refresh Mirai Scatter plot Automatic flag H Normalization Display 50 DESCRIPTION You can save your results in txt or gpr format Note If the grid a block or a spot is modified after the quantification process an asterisk will appear in the display window title and the icon Refresh becomes active to indicate that the data is not in accordance with the grid Use the refresh button to re quantify the spots Opens the scatter plot window Opens the automatic flag window Opens the normalization window Changes the display into the data viewer window as well as the form in which data is saved in the results files Counts the number of spots flagged in each category good bad not found absent as stated in the flagging spots section INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 51 5 3 1 The scatter plot window Click on the scatter plot icon to open the scatter plot window This window allows you to draw plots from generated data You can generate either a scatter plot of all spots on the array a histogram or a MA plot analysis Scatter Plot waved jd J 44 MA Pot Optic 3 Tele E E B LSJ la kaj kal Navigation ze l
4. Circularity measure from 0 to 100 100 is most circular O is most non circular A Mapix manages only circular features this value is always 100 The ratio of the median intensities wavelengths w1 and w2 with the median background intensity subtracted INNOPSYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Ratio of Means w1 w2 Median of Ratios w1 w2 Mean of Ratios w1 w2 Ratios SD w1 w2 Sum of Medians w1 w2 Log Ratio w1 w2 60 The ratio of the arithmetic mean intensities wavelengths w1 and w2 with the median background intensity subtracted The median of pixel by pixel ratios of pixel intensities for wavelengths w1 and w2 with the median background intensity subtracted Note Ratios greater than 100 and less than 0 01 are excluded when calculating this value The mean of the pixel by pixel ratios of pixel intensities for wavelengths w1 and w2 with the median background intensity subtracted Note Ratios greater than 100 and less than 0 01 are excluded when calculating this value The standard deviation of the log of pixel intensity ratios for wavelengths w1 and w2 Note Ratios greater than 100 and less than 0 01 are excluded when calculating this value The sum of the median intensities for wavelengths w1 and w2 with the median background intensity at each wavelength subtracted Log2
5. grid algorithm settings configuration icon on the tools window or on the Analyse tab of the Main Menu The following window is opened Algorithms parameters a rGridding _ Fixed Diameter Dth Max position offset pitch 30 Min diameter Dth 50 Max diameter Dth 200 Photometric c alculatic ns 5 B border width pixels 21 gt Background diameter pitch 2 ie In the gridding panel you can adjust parameters related to automatic spot search whereas in the photometric calculations panel parameters are used to produce the results of the image quantification Refer to the table below for information IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Panel Gridding Photometric Calculations ITEM Fixed Diameter Max position offset pitch Min diameter Dth Max diameter Dth S B border width pixels Background diameter pitch 46 DESCRIPTION Use this option when you want to keep a defined spot diameter theoretical diameter defined in the gal file or the manually defined diameter The real spot diameter will not be measured but stated as the defined spot diameter Each spot has a mean position defined by the geometric parameters of the block in which it is located and an actual position observed This parameter
6. 158 i 00 501071 54 b092 192 168 0 171 00 50 c2 54 4b0 b3 710017 gi Ng 192 168 0 186 T 00 50 23 54 boras 710016 r My If you work with multiple scanners connected to the same computer you can recognize a scanner by its IP Address If you do not know this address you can use the icon to identify the scanner Click on the 4 beep select icon to connect to the selected scanner I INNOPSYS a Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide The Connect to the scanner icon in the tools window connects to the scanner used in the last session as defined by its IP address image RON KJES ti measurement PSN i ia The Scanner parameters icons become visible once the scanner is connected measurement ZEN Al Use the disconnect from the scanner icon to disconnect the scanner A 4 J A A A A 4 A J Pi A NNOPSYSI Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 10 3 2 Scanner Warm up To get optimal performance the scanner has to warm up for around 10 minutes after being connected to Mapix The scanner operating temperature is from 19 C to 26 C air conditioning recommended Laser warm up and scanner temperature are tested before each scan If
7. 33 561 971974 Fax 33 561971 975 support innopsys fr Mapix V7 0 0 User s guide 2 Starting Mapix 2 1 User workspace When the program starts the following dialog box is displayed NING ZE SE When using the software for the first time you need to create a user account by clicking on the button Create Note If this feature is unnecessary for your work environment a single user mode is available which does not ask you to log on whenever the program is run See the Preferences section Use the button Start to access the program from the workspace of the selected user INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr x a a a Se A A E E YY a a A A A Mapix V7 0 0 User s guide 2 2 The software application main window Once a user s workspace is selected the user interface displays the Main Window on the monitor screen This is your starting point for sending commands entering information or receiving scan status information This is also where scanned images and quantification results are displayed Image information Tools window window D splays These icons control general informaton __ scanner status Main menu This menu about image scanning image display and provides access tp all the and specific analysis software s features information for each color channel A
8. Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide selection too big you can only save it Click on the icon save and select the file where you want to save the new image 36 I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 37 4 6 The grid To determine the position of each spot a grid containing the parameters spot spacing diameter etc used at slide creation must be assigned To assign a grid you can use either a GAL file which is a standard ATF file generated by the spotter itself or the grid creation tool 4 6 1 Open an existing grid file GAL file d da You can import an existing GAL file by using the icon Open a grid Import a grid from a GAL file at the tool window or at the Analyze tab of the Main Menu If the image corresponds only to a part the slide and the GAL file contains the complete grid a message will ask to confirm for loading the grid A part of the grid is invisible Do you want to select only some blocks to load No Select Yes to continue then select the block corresponding to the image Selecting the Apply option Mapix will automatically open the part of the grid corresponding to the selected block With the option Open whole grid th
9. SO A SA SA A GE GG en Sen Oe Ga O Mapix V7 0 0 User s guide 6 1 4 Ouantification 74 GAL File Display lt Default display gt find all automatically 9 Grid Blocks Spots Blocks Spots Grid Spots Grid Blocks Spots only Gridding Fixed Diameter Dth Max position offset pitch Min diameter Dth Max diameter Dth Photometric calculations S B border width pixels 25 Background diameter pitch 2 Save results Sortresultdataby Block Dl nk File Format GenePix Results files Sap All blocks in a file Each block in a separate file Selected spots in a file _ Save a JPEG image containing analyzed spots Decimal separator ig Point Comma gt Ascending Use this step to define the parameters to be used for feature quantification and analysis Each panel corresponds to a specific step in the quantification process as defined below Step in the quantification For details please go to Panel l process section T GAL file Selection of the GAL file SE SAE E IME 1G Find all automatically Gridding Wert Parameters used for photometric calculations Photometric calculations Save results Positioning the grid Parameters used for positioning Save results as txt or gpr files Positioning the grid Positioning the grid Configuring the analysis parameters Exporting the results table GPR
10. or Editing a query When clicking on Manage Models the Autoflag Model Edition frame opens modele4 modele2 modele Description modele3 his model tests if the signal to noise ratio is lower than 3 in both channels which may be a sign of a bad spot i EJ E Use this window to add new queries modify or delete an existing query A Note In a query the parameters used for flagging a spot are defined in the form of a model or a single query In a model you can combine several queries at a time by using the And and Or buttons NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 54 Refer to the table below for description of each command ITEM DESCRIPTION Saved Queries Displays the existing models or queries Description Displays comments of the selected query New Query Initializes the query area to create a new query Preview Accesses information on all the queries open Opens a selected moder the parameters used in the corresponding model are displayed in the query area Insert Inserts the parameters used by a model into a new query Delete Deletes a selected model ave Saves a new model or the modifications made in an existing model Parameters Chooses the quantifiers used in a query Operator Defines the operator to be applied in a query Once the selected queries ar
11. 19 Option GAL File Spot size um Fast Accurate Mean signal level Max signal level saturated pixel Note For two color images Action Select the GAL file corresponding to your slides By selecting the GAL file the required parameters will be considered only for those pixels contained in the features defined in the GAL file This excludes the pixels of regions with no spots whose intensity will be considered as background noise If you do not have a GAL file Mapix will apply the required parameters to the totality of pixels that make up the scan area However to better fit the parameters to the spots of your image background noise estimation is calculated For this you must indicate the theoretical spot size in um You can choose to get faster results by limiting the accuracy If the signal is mainly homogeneous across the slide the option Fast would be enough to get good results in the other hand if your slide shows heterogeneous signal you should choose the Accurate option To define the desired mean signal level for each of the wavelengths of the image To define the maximum signal level of the image To define the percentage of saturated pixels on the image The selected parameters will be used to set the laser power and PMT of each wavelength in parallel INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr M
12. 386 0 053 18 018 7322 0 8418 62 7322 0 1990 797 0 14 0 236 a Eg 2 mir 41230 45310 200 011 7128 42 6667 5 1434 756 0 067 20 127 102270 9648 13 10227 0 o 2033 037 0 053 0 211 2 1 3 1 43720 45310 20001 o 6827072 6536 5 1077 005 0 043 o 15 776 81900 8455 983 8190 0 o 1814 047 0 032 0 215 a 4 1 4623 0 45310 200 6s72091 6436 0 566 887 0 021 o 8626 71280 o 7569107 o 71280 1186 809 008 0S 1 5 1 4873 0 4531 0 200 01 6383 473 6309 0 318 965 0 012 4 997 6929 0 7273 752 6929 0 1028 755 0 049 0 141 pi 6 i 51220 45310 200 011 6266 335 6237 0 212193 0 0050 3 386 6681 0 6919 728 6681 0 716 513 0 035 0 1041 1 7 1 53730 45310 200 01 o 6272 578 6253 0 258 957 90030 4 128 6751 0 7465 454 6751 0 1837 864 0 1011 0 246 i 8 i 96230 45310 200 01 6226 941 6206 0 251 773 0 0030 4 043 6844 0 7728 997 6844 0 1944 366 0 122 0 252 1 9 1 58720 45310 200 01 6207 693 6190 0 208 565 0 0030 3 36 6620 0 7091 392 6620 0 1187 815 0 059 0 168 i 10 i 61230 4531 0 200 01 6130 979 6125 0 177 371 0 0010 2 893 6454 0 6778 176 6454 0 814 3864 0 049 0 12 1 11 1 63730 45310 200 01 6117 593 6114 0 180 477 0 0010 2 95 6369 0 6845 196 6369 0 1430 244 0 072 0 209 i i2 i 66220 45310 200 01 6156 23 6133 0 178 125 0 0040 2893 6217 01 650 513 6217 0 1219 496 0 043 0 188 1 I 2 38730 47810 200 01 7075 1481 6822 0 1044 461 0 036 14 762
13. 41230 5030 0 200011 6748 28 6563 0 770 806 0 028 11 422 70370 oo 7702177 7037 0 1329 012 0 09 0 173 i 3 3 43720 5030 0 200 01 6473 72 6414 0 431 723 0 0090 6 669 6729 5 7112 967 6729 5 994 597 0 055 0 14 EE 4 3 230 50300 20001 6384976 63540 251 04 0 0020 3 944 65710 6686 304 6571 0 446 781 0 017 ow 1 5 3 4873 0 5030 0 200 011 6339 395 6315 0 222 405 0 0040 3 508 6467 0 6580 375 6467 0 392 698 0 017 0 06 1 E 3 122 0 5030 0 200 01 620 374 6256 0 205 842 0 0040 3278 63970 6434 2 6397 0 279 482 00080 oo t gt cm A gama wwii As 250 ZE 2514 A HE cw A anan 3 09 EAN A ta En gara n tY oo AA anc Each column corresponds to the results of the photometric calculations performed at each wavelength see Results description section below for details The number 532 635 670 or 785 present in some column titles indicates the corresponding wavelength Data can be sorted by a chosen column in ascending or descending values by clicking on the desired column header A small arrow indicates the sort status You can define a sub sort on other columns by holding the Ctrl key down When clicking in a row the corresponding spot is selected and zoomed in the image window The data viewer menu gives access to further data analysis and result displays Refer to the table below for brief description each of the functions are detailed later in the manual IININOP SYS T Parc Activestre
14. 6 1 4 COTATI CG OM ses sence e mma osc ei mi ae a milena e eek Gemi ae 74 6 1 5 Adtoflag and normalizat ON saian ei oem yle sasi aniei selimin 75 6 1 6 POOT A YMY E nee nd gabe Senepiaa EE E MEME EK PORMO YE DEERE SEYE 76 6 1 7 IVINS ee e gey NN RE ME NN ES E MN 77 6 2 BECO QU RM E KR Y 78 6 2 1 Ee E a E E E o ola E olak 79 6 2 2 MCEI NCO E E EEE AM E E E ME 80 Scanner VAlIAAtTION cccsssssscccccceesseccccsseseccccesseeseececsseeseeceessueusseseesseuseesecsseusseeceessauasesecesauaeeesees 81 7 1 Replacing a valldation Slide ame maa kei ee ee eee 83 Bi ETE ai E lll ln E ll nn maci sale 84 8 1 Cemer SELLEM el al il yeralan er a S 85 8 2 oee GUN SS A OL N a 87 8 3 PROS CIES e E RR E E KR Y AY E YER Ye e 88 8 4 gg 2 SY ee YAR FR ee 89 8 5 FOE e E E ena nee ceased eaesndeaaecsque E R 90 License agreement ie e ae lap la ee E lale l Gl 91 I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr A A A O A A E Ce ee Can en Cae S Mapix V7 0 0 User s guide 1 Installation 1 1 Hardware requirements Please contact INNOPSYS to get the latest information about the main hardware specifications required by MAPIX 1 2 Installation Procedure Place the software installation CD in the PC s CD ROM drive and refer to the install txt file for installation details INNOPSYS Parc Activestre 31390 CARBONNE France Tel
15. ET Re 3238 32 32 o o 2 o File name Files of type XLS XLSX Choose the file containing the ID list either from an Excel file or from a tabulation separated text file txt File format The file containing the ID list must have one of the two following formats Type 1 In which the IDs are listed as in the following matrix IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 41 List format m A B Cc D 1 Block Row Column ID 2 1 1 1 genel 3 1 1 2 gene 1 1 3 gene3 5 1 1 4 gene4 6 1 1 5 genes 7 1 1 6 gene6 8 1 1 7 gene7 9 1 1 8 genes 10 1 1 9 gene9 11 1 1 10 gene10 12 1 1 11 geneli 13 1 1 12 genei2 14 1 1 13 genel13 15 1 1 14 genel 16 1 1 15 gene15 17 1 1 16 gene16 18 1 1 17 gene17 19 1 1 18 genel8 20 1 1 19 gene19 21 1 1 20 gene20 22 1 1 21 gene21 This option is available for both txt and Excel files Type 2 In which the ID matix correspond to the exact layout of the image Layout format A B c D gene 1 gene 2 gene 3 genes gene5 gene 6 gene 7 gene 8 genes gene 10 gene 11 gene 12 gene 13 gene 14 gene 15 gene 16 gene 17 gene 18 gene 19 gene 20 gene 21 gene 22 gene 23 gene 24 gene 25 gene 26 gene 27 gene 28 gene 29 gene 30 gene 31 gene 32 gene 33 gene 34 gene 35 gene 36 gene 37 gene 38 gene 39 gene 40 gene 41 gene 47 gene 43 gene 44 gene 45 gene 46 gen
16. Slide 9 Slide 10 Slide 11 Slide 12 side 13 yide 14 Slide 15 y Slide 16 iy Slide 17 F Slide 18 7 Slide 19 Slide 20 Slide 21 Slide 22 Slide 23 Slide 24 A Note To scan the slide in an auto loader scanner you have first to perform a slide detection test To do this click on the Y icon in the tools window Please refer to Slide detection in the Auto loader only for InnoScan710AL and InnoScan900AL models section for more details f a A A A A 4 A r j NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 6 1 3 Filename amp Directory w non Pi Bia gt m Open Save Saveas Add Add Close all Start Stop b berna Ee Scan Parameters Filename amp Directory Create a sub directory with the image name Export folder to all steps Comments Separated TIFF files Keep both waves Te Prefix File Name User Name Date amp Time Barcode Pixel size Suffix File Name J Counter Reset Make New Folder Analysis Miscellaneous In this step you can define the parameters to be used when saving the obtained images Please refer to Scanning an image for details Sa a a e e a e I NNOPSYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr NR O O
17. go to the File tab of the Main menu and click on Save work as In the same way click on Open a work on the File tab of the Main menu to open an existing work file AN Note Images used for analysis are automatically linked to the work file when the file is saved a link with the image is created If you change the image location when loading a work file Mapix will ask for a new pathway to access the images INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 70 6 Working in batch mode One can use the batch mode to scan several slides with similar or different scan parameters and or to automate image analysis To open the batch editor go to the batch tab of the main menu and click on Batch Editor The following window is displayed A Batch Editor Ea kw 5 m Ve R gt n Open Save Save as Add Scan Step Add Analysis Step Close all Start Stop 6 1 Batch scans ii CE F Add Scan Step Add a scan step button permits you to define edit parameters to be used in scanning and image analysis Use this option to either only scan or scan and analyze several slides using the same or different parameters This menu consists of six steps that follow the work flow from slide scan to image analysis Scan Parameters Loader slide selection only for InnoScanxxxAL models Filename amp Directory Analy
18. not reached Please wait until lasers are warmed up scan will start automatically Click on Continue to continue anyway or dick on Cancel to abort the process KD Do the measurement before the lasers have warmed up could affect data quality Scanner s temperature I x Laser 1 635nm Red w Laser 2 532nm Green y Warm up elapsed time 01 52 To decrease the scanner temperature you should ventilate the scanner and control the room temperature below 26 C At any time you can skip this message and begin the scan by selecting the option Continue however high temperatures can disturb scanner performance and image acquisition directly impacting microarray results INNOPSYS I Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr A eee eee ee A A N A A GC SR SE ae eA Ge Sn Sn Gn Ge SE O O A O A Mapix V7 0 0 User s guide 3 3 Scanner Information To display the information about the scanner you are working with click the about the scanner option situated on the scanner tab of the main menu X 2000um gt 24000um pitch 3um gt 40um Y Oum gt 74000m pitch 3m gt 40um i 192 168 0 163 local fr 00 50 c2 54 b0 f8 255 255 255 0 192 168 0 1 192 168 0 1 635 P SmW gt 10mW aser 532 P SmW gt 10mW Information on the scanner to which you are connected includi
19. see Image Display Options section Allows user to rotate the image 90 180 270 flip the image vertically flip the image horizontally automatically register two single wavelength images and generate a negative image Show hide the navigation window INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr wu i w r a w wu u w u ES Ya Va wu kS Mapix V7 0 0 User s guide 30 4 2 Image information The About image option on the Image tab of the main menu displays the information contained in the TIFF images such as the serial number of the scanner that acquired the image acquisition parameters etc as shown below Zerin general image1 image2 property value image name FullMoon tif image path __ C Innopsys Mapix samples Comments DA Scanner mode woo Scanner revision number E barcode vale e date number of channels Scan seed sl pixel size X um 10 0 pre size Y a e position of upper left corner X um posiion of per left omer Yi foc mode focus vale Auto Settings e Scan Mode jo Image 1 and Image 2 tab contain the information of laser power and PMT gain percentage of each wavelengths image 1 corresponding to red channel image either 635nm or 670 nm according to the scanner model while image 2 to green channel image either 532nm or 785nm
20. the laser and or scanner temperature are not adequate the following message is displayed A Laser warm up is not reached Please wait until lasers are warmed up scan will start automatically Click on Continue to continue anyway or dick on Cancel to abort the process Do the measurement before the lasers have warmed up could affect data quality Scanner s temperature li x Laser 1 635nm Red X Laser 2 532nm Green XX Warm up elapsed time 00 10 After 5 to 10 minutes the lasers will reach the adeguate operating temperature One can see thatthe message display changes to the following A Laser warm up is not reached Please wait until lasers are warmed up scan will start automatically Click on Continue to continue anyway or dick on Cancel to abort the process Do the measurement before the lasers have warmed up could affect data quality Scanner s temperature f ge Laser 1 635nm Red wW Laser 2 532nm Green Y Warm up elapsed time 01 52 The scan begins automatically after laser temperature is reached and if the scanner operating temperature is between 19 C and 26 C INNOPSYS ey Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 11 A If room temperature is higher than 26 C the Laser warm up message will stay until the scanner temperature decreases A Laser warm up is
21. which will restore Software functionality 92 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 4 Sixty 60 Day Money Back Guarantee If You are the original licensee of this copy of the Software and are not completely satisfied with it for any reason please contact Innopsys Customer Service for a refund of the money You paid for the Software less shipping handling and any applicable taxes at any time during the sixty 60 day period following the date of purchase 5 Limited Warranty Innopsys warrants that the media on which the Software is distributed will be free from defects for a period of sixty 60 days from the date of delivery of the Software to You Your sole remedy in the event of a breach of this warranty will be that Innopsys will at its option replace any defective media returned to Innopsys within the warranty period or refund the money You paid for the Software Innopsys does not warrant that the Software will meet Your requirements or that operation of the Software will be uninterrupted or that the Software will be error free You acknowledge that the scientific and technical state of the art when the Software was distributed did not enable all possible uses to be tested and verified nor for the presence of possible defects to be detected You Shall be responsible for verifying by any or all means the product s s
22. xr a w a wu a u Yan Ya Va Mapix V7 0 0 User s guide 16 If you are using a slide with a scan region predefined in Mapix you can choose it directly please refer to Defining scan parameters section for details You can do a preview scan of the selected region by clicking on the preview scan area icon 3 6 Defining scan parameters Click on 4 Scan parameters to define the parameters used during image acquisition 4 Scan Configuration ee General side Misc N Barada reading Use this panel to define the scan parameters related to pixel size and Pixel size 3 0 ov acguisition mode Speed 3S Scan Mode Normal w Manual Auto XDR You can define the laser power and PMT gain manually using this panel see table below For automatic definition of scan parameters or for scanning within an extended dynamic range you can use the auto and the XDR options respectively 20 4 60 80 100 Laser power low high For more information about manual settings please refer to table below For details on auto settings and XDR scan mode please go to Scanning within scan auto settings mode and to dynamic range extension sections respectively INNOPSYS e Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 17 ITEM DESCRIPTION Barcode reading Enables barcode reading If the slide has
23. 2 Cea gi 8 gg AP E eee 38 4 6 3 ImportingSamplelDstotheGAlfile erene 40 4 6 4 PoS TONO gp RK NM RR YA NK 43 S La e eg NE EE RP MM 45 5 1 Configuring the analysis PArAMETESS ccescccccsseccccceesccccesecccseeccecceeceeseusecessuneceseeeneceeeeeas 45 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 9 5 2 Fagene SO ONS emerek mental anadal seoidetastaaebseanaeeaiaebsceiangiat es acasated a 48 5 3 TRIS SUITS FANS ys NE EN ee eee eee OE A9 5 3 1 Thescatter e ig AN ME NY N 51 5 3 2 The automatic flag WINKOW eccccccseecccccneeeccccesecccausececcuueceecausececsuececsuuaeceetsunecetseneees 52 5 3 3 NOO OU a 4 PR ME ME E KESE MEYER e RMA EEE YY EMER EEE SE MEYE UYE YA SEY 55 5 3 4 Results eg 0g MM MN MM AN NY 58 5 4 Customizing th results taDl saanen sike ini dil Mela aa dari la ezik anda alaninin 61 5 5 Exporting the results table GPRandiXTfiles eee 63 5 6 TAC PUTIN A A MN MK KE nee 67 5 7 Saving Opening a Mapix work TiC saarassesamier sanan Bulam asamasinda 69 Working 10 Datch MO ER MR E e 70 6 1 BAN CIS CAINS EE ARR NE EN ME ME ER KENE E ME AR 70 6 1 1 010 ake elke OE A een ee ee eee 71 6 1 2 Loader slide selection Only for models equipped withanouto loader 72 6 1 3 Ename Be OCHO YENE ene cnet ME PAN E YE 73
24. 4 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 90 8 5 Folders In this section you can define The default folders for image results and work file storage The folders presented by default when using grid files and configuration files IIN INOP SYS T Parc Activestre 31390 CARBONNE France Yy Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 9 License agreement IMPORTANT PLEASE READ THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE USING THE SOFTWARE INNOPSYS AND OR ITS SUBSIDIARIES IS WILLING TO LICENSE THE SOFTWARE TO YOU AS THE INDIVIDUAL THE COMPANY OR THE LEGAL ENTITY THAT WILL BE UTILIZING THE SOFTWARE REFERENCED BELOW AS YOU OR YOUR ONLY ON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS OF THIS LICENSE AGREEMENT THIS IS A LEGAL AND ENFORCEABLE CONTRACT BETWEEN YOU AND INNOPSYS BY OPENING THIS PACKAGE BREAKING THE SEAL CLICKING THE ACCEPT OR YES BUTTON OR OTHERWISE INDICATING ASSENT ELECTRONICALLY OR LOADING THE SOFTWARE YOU AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT IF YOU DO NOT AGREE TO THESE TERMS AND CONDITIONS CLICK THE I DO NOT ACCEPT OR NO BUTTON OR OTHERWISE INDICATE REFUSAL MAKE NO FURTHER USE OF THE SOFTWARE AND CONTACT INNOPSYS CUSTOMER SERVICE FOR INFORMATION ON HOW TO OBTAIN A REFUND OF THE MONEY YOU PAID FOR THE SOFTWARE LESS SHIPPING HANDLING A
25. 41230 47810 20001 6651 6 a 3 2 ano 4781 0 20001 sao pa 4 2 230 47810 200 01 6340 5 a 5 2 48730 47810 20001 68387 1 6 2 51220 47810 200 01 o 6250 53 a 7 2 373 0 47810 20 01 6458 5 a a 2 5623 0 4781 0 200 01 la 1 9 2 58720 47810 200 01 o 62220 1 10 2 61230 47810 200 01 6138 2 a un 2 6373 0 4781 0 200 01 6181 4 e en 6622 00 47810 200 01 o 61378 a 1 3 3873 0 5030 0 200 01 6908 9 a eae ee ae 4123 0 5030 0 200 01 6748 a 3 3 4372 0 swo 20001 67 ie nm m mi i 5030 0 200 01 6364 9 a 5s 3 48730 030 0 20001 6339 3 pa 6 3 51220 50300 200 01 6280 3 a 7 3 373 0 5030 0 20001 62527 1 8 3 56230 50300 200 01 6178 a 9 3 5872 0 5030 0 20001 618 a o 3 620 soo 200 6139 2 pa d 3 63730 5030 0 200 01 6094 4 1 12 3 66220 5030 0 200 01 6033 4 INNOPSYS 61 Parc Activestre 31390 CARBONNE TE Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 62 Click on New button to create a new display al New data types display Name of the new display Custom display 1 Based on display lt Default display gt w You can create a new display based on an existing one Once the new display name is created you can customize the table results by selecting deselecting c
26. 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 34 pe 2 Pa Projection measurement shows the projection in X and in Y for each wavelength A projection is the addition of the number of pixels on each column X and each row Y in which the rectangular zone is built This option is only used for rectangular zones A A A a AN n eo ee am mr OEE e pme beye niye frh Preferences Progen Weis Hep 3 Histogram The histogram displays pixels on a graph Axis X represents pixel values from O to 65535 Axis Y represents the number of pixels which are equal to the value given by axis X While the histogram option in the tools window displays the pixels that compose the whole image this option shows the pixels contained in the selected area Histogram INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971974 Fax 33 561971 975 support innopsys fr SNe ae A A A E E ER San Caen S Mapix V7 0 0 User s guide 35 4 5 Crop an image al One can export a part of the images using the option extract image sample This option is useful to separate the blocks of an images Click on the icon Select the image zone that you want to export to do this click on the icon and then select the option rectangle then draw a rectangle corresponding to the image you want to export Once the rectangle is drawn the next message will be displayed NNOPSYS
27. 7329 0 8206 3711 7329 0 1722 489 0 113 0 21 i 2 2 41230 47810 200 01 6651 64 64730 844 636 0 027 oo 12 698 9080 00 9103 088 9060 0 1772 581 0 0050 0 195 1 3 2 43720 47810 200 01 6400 01 6391 0 197 051 0 0010 3 079 7250 0 7799 934 7250 0 1454 646 0 073 0 183 i 5 2 4230 47810 200 01 6340 592 6343 0 199 346 0 0010 3 14 6928 0 6895 935 6928 0 444 676 0 0050 0 064 i 5 2 4873 0 47810 200 01 6433 713 6406 0 1094 293 0 0050 16 995 6743 0 6769 876 6743 0 405 412 0 0040 0 06 i 6 2 1220 47810 200 01 6250 588 6236 0 180 797 0 0020 2 892 65200 o 6560 135 6520 0 339 978 0 0060 0 052 1 7 2 5373 0 781 0 200 01 6453 539 6227 5 1123 464 0 036 17 395 6712 0 7504 875 6712 0 1955 401 0 112 0 261 i 3 2 623 0 47810 200 01 6908 864 61930 874 15 0 034 13 64 73115 8139 161 73115 1966 028 0 107 0 242 1 9 2 872 0 4781 0 200 01 6222 058 6188 01 254 667 0 0050 4 093 7003 0 7442 648 7003 0 2068 801 0 061 0 278 1 10 N 6123 0 47810 200 03 _6138 227 6117 5 205 107 0 0030 331 6576 0 6999 417 6576 0 196 024 0 062 0 271 1 11 2 6373 0 4781 0 200 01 6181 421 6089 0 765 123 0 015 12 378 6396 0 6921 271 6396 0 1525 529 0 079 0 221 i 2 2 66220 4781 0 2001 6137819 61230 o 187 181 0 0020 305 62150 o 6545117 6215 0 _ 1370 942 oos2 0208 1 1 3 3873 0 5030 0 200 01 6908 932 6760 0 705 455 0 022 10 211 70780 7433 232 7078 0 1051 595 0 043 0 141 1 2 3
28. D MAFIE LMEN home a gon e ha fad bawane len ha Be Sig Hari doe pon 0 Shak Serko FI Ie reweakn Ey ae l Image display area Navigation window Presents all the Display the loaded available plugins image allowing a better and sim ple localzaton of the actual view regarding the slide INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 3 Displaying images in real time In this first step you will learn how to display a microarray image in real time and how to set the image acquisition parameters before the scan 3 1 Connecting the scanner MAPIX software controls any all InnoScan scanners via a TCP IP protocol over the network Each scanner has an IP address 192 168 0 254 is the default To search for an available scanner click on the Te search icon situated either on the Tools window or in the scanner tab of the Main menu A window containing the available scanners is opened search scanner 4 scanners found simulateur is 700 available innoscan is900 available innoscan is710 busy innoscan is710 busy IP Address MAC Address Serial Number IP Address MAC Address Serial Number IP Address MAC Address Serial Number IF Address MAC Address Serial Number 192 168 0 21 00 02 04 06 08 0A i 001 001 192 168 0
29. ND ANY APPLICABLE TAXES AT ANY TIME DURING THE SIXTY 60 DAY PERIOD FOLLOWING THE DATE OF PURCHASE 1 License The software and documentation that accompanies this license collectively the Software is the property of Innopsys or its licensors and is protected by copyright law While Innopsys continues to own the Software You will have certain rights to use the Software after Your acceptance of this license This license governs any releases revisions or enhancements to the Software that Innopsys may furnish to You Except as may be modified by an Innopsys license certificate license coupon or license key that accompanies precedes or follows this license Your rights and obligations with respect to the use of this Software are as follows You may A use one copy of the Software on or in conjunction with a single computer that is owned or leased by You If a License Module accompanies precedes or follows this license You may make the number of copies of the Software licensed to You by Innopsys as provided in Your License Module Your License Module shall constitute proof of Your right to make such copies B make one copy of the Software for archival purposes or copy the Software onto the hard disk of Your computer and retain the original for archival purposes C use the Software for internal business purposes only and may not use the Software on behalf of a client or customer D after written notice to Innopsys trans
30. NOPSYS I Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr L e E C O EE a aaa a E ES A A E E A A A GG E GR O A O GE A A GG A GS Mapix V7 0 0 User s guide 47 Figure1 Spot signal and background calculations Each spot is framed in a gridding circle white circles overlaid on the images This circle defines the border between spots and background Because the pixels around this gridding circle are uncertain by definition no processing is performed on the pixels located in the immediate vicinity of the gridding circle The spot background transition zone is defined in pixels by an adjustable parameter set at 2 pixels in this figure A Feature pixels B Background pixels C 2 pixel exclusion region A Note To visualize the local segmentation around the spot click the spot modification button then select and click on the show local segmentation option Once the grid is in place spots can be flagged To do this select a spot or group of spots be sure that the spot selection modification tool is selected and right click within the selection A menu appears under the cursor allowing you to flag the selected spots INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 48 5 2 Flagging spots Flag
31. Or jilename bx gpr where x corresponds to the block number in the slide The results file will contain the results corresponding to the selected spots You can save an image containing the analyzed spots When the Each block in a separate file option is selected an image of each block is saved in separate files one file for each of the wavelength images and one file for the ratio image If All blocks in a file or Selected spots in a file options were selected then an image of the complete slide is saved To choose the desired number format either decimal or integer number To choose the desired decimal separator Two options are available Mapix txt file txt Gene pix results file gpr Note The quantification data contained in the results files are the same regardless of the file extension results file If the data is sorted the results file will keep the sorted result 64 INNOPSYS I Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 65 The results file is made in an ATF Axon Text File format with the following information Headers Optional lines Item ATF 1 0 XX YY Checksum_ImageFile Checksum_ResultFile Type DateTime ConfigFile GalFile PixelSize Wavelengths Image Files Jpeg Image Ratio Formulations Description Indicates the file format ATF Axon Tex
32. ULAR PURPOSE AND NONINFRINGEMENT OF INTELLECTUAL PROPERTY RIGHTS THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS YOU MAY HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE AND COUNTRY TO COUNTRY 6 Disclaimer of Damages SOME STATES AND COUNTRIES INCLUDING MEMBER COUNTRIES OF THE EUROPEAN ECONOMIC AREA DO NOT ALLOW THE LIMITATION OR EXCLUSION OF 93 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SO THE BELOW LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW AND REGARDLESS OF WHETHER ANY REMEDY SET FORTH HEREIN FAILS OF ITS ESSENTIAL PURPOSE IN NO EVENT WILL INNOPSYS OR ITS LICENSORS BE LIABLE TO YOU FOR ANY SPECIAL CONSEQUENTIAL INDIRECT OR SIMILAR DAMAGES INCLUDING ANY LOST PROFITS OR LOST DATA ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE EVEN IF INNOPSYS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES IN NO CASE SHALL INNOPSYS S OR ITS LICENSORS LIABILITY EXCEED THE PURCHASE PRICE FOR THE SOFTWARE The disclaimers and limitations set forth above will apply regardless of whether You accept the Software 7 General This Agreement and any related License Module is the entire agreement between You and Innopsys relating to the Software and i supersedes all prior or contemporaneous oral or written communication
33. User s guide 14 Side 1 Slide 2 Slide 3 V Slide 4 Sau Click on the read the barcode icon to ask Mapix to detect the slide s barcode The barcode will be shown under the slide position number Slide 1 Side 2 Slide 3 V Slide 4 BC00246816 IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 15 3 5 Preview Scan A preview gives you a fast comprehensive image of the microarray Use preview to adjust laser output and PMT gain to prevent saturation and to define the region of interest before initiating slide scanning Click on Preview icon to begin the preview scan of the whole slide Preview scan uses the following default parameters Pixel size 40um Speed 35 lines s Scan area whole slide 22mm x 74mm To change preview parameters click on Scan parameters in the Main menu and then on the Misc tab You can define a region of interest directly in the preview image by using the mouse Click on ull F the Select area mode icon on the tools window or directly in the image by using the right click menu preview 47 Scan Area Properties 4 Zoom mode Walk mode is Scan area mode I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr wu i w
34. Yj Mapix V7 0 0 User s guide Version 7 0 0 User s guide IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide MAPIX USER S GUIDE Welcome to MAPIX your high performance easy to use microarray image analysis software With MAPIX you will be able to e Control Innopsys Innoscan scanners e Display images in real time during acquisition e Control display parameters zoom image properties contrast balance etc e Save acquired images in 16 bit or 20 bit TIFF format together with all acquisition parameters pixel size laser output etc and JPEG format e Save settings scan and analysis parameters e Perform fast image analysis using a GAL file e Display results and save them in a GPR format e Display any 16 20 bit TIFF image e Manage multiple users account This guide will help you discover all MAPIX features and enable you to perform easy image analysis INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Table of Contents PSU GIN ION ys ee lama yaa al d e alama DUL Mu amacla eee ado E N 5 1 1 meleke e ge eh gz hep e YS A E ARNE DARE YER M 5 1 2 Installation PFOCCOUME A A e E EEE 5 2 a T aaa O E E nal O E E A ag rl ada di mal OA 6 2 1 User W OI KSC meralar aamir bean a a E 6 2 2 Th
35. according to the scanner model This option is also accessible by passing the cursor over the image and typing i Note If you have scanned using auto settings use this to obtain the optimal scan settings in terms of PMT gain and laser power for future manual scans assuming that the slides are homogeneous INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 31 4 3 Image Display Options Opens a menu by which you can choose the image display options Displayed values are those used in the last Mapix session Display options ezim General Advanced brightness contrast Brightness 40 Contrast 20 Balance 50 l Auto adjust _ pallets Rainbow Grey scale Color These options can be used to adjust image brightness contrast and the proportion of red or green in the ratio image by using balance control Notes Changing these options only affects the way an image is displayed Display options have no effect on results or image data When the balance control cursor is located in the extremes values completely to the left or right only one color channel is displayed Red or green channels are displayed respectively and saturation in the invisible channel is no longer displayed Click on Auto to allow Mapix for defining the best display parameters for your image To be able of mo
36. and TXT files INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr ARS ABA gt ba p lt E aes A Dea gt Mapix V7 0 0 User s guide 75 6 1 5 Autoflag and normalization Autoflag and Normalization A Use Autoflag Normalization Factor Definition Normalization Factor Calculation Normalize quantification data with following criteria Considered Parameter Median of Ratios Selected Features All Features v Expected Mean 1 0 In this section you can choose to perform an autoflag step by using pre defined models and or to normalize your data When Perform Normalization is selected both raw data and normalized results files are automatically saved For details on each of these options please go to the automatic flag window and normalization sections NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 76 6 1 6 Plugin Plugin A Use Plugins Example of Plugin E Quality Control A A A A J A A j This step contains the different available plugins You can select the plugins to be used during the analysis You can define the order in which the plugins will be launched by using arrows If a plugin does not have access to the data it needs it will not be able to start thu
37. apix V7 0 0 User s guide 20 3 6 2 Extended Dynamic Range XDR When samples have a wide dynamic rage it is useful to use the dynamic range extension to avoid saturation This option will make 20 bit images with a dynamic range of gt 10 To scan within an extended dynamic range select the XDR option on the scan configuration window Scan Configuration sim General Side Misc v Automatic scrolling vi Barcode reading Pixel size 3 0 v Fast Accurate 635 Laser power low high 532 Laser power low high Defaut vales Set the laser excitation power to be used during the XDR scan For 532nm 635nm and 670nm excitation laser the Low laser power corresponds to 5mW while High laser power defines 10mW for the 785nm excitation laser the Low laser power corresponds to 5mW while High laser power defines 20mW One can choose between Fast or Accurate mode To choose between both options you should first make a preview scan to know the approximate signal in the slide if the slide has strong signals getting a lot of saturated spots during the preview scan we recommend to use the accurate option In the other hand if the slide has moderate signals you can use the fast option INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr wu i w kos a w wu u w u Na Ya Va w M
38. apix V7 0 0 User s guide 21 3 7 Defining the Scan Area You can define the desired scan area by either defining a known type of slide or directly in the image display area of the main menu by using the mouse Click on the ia using the mouse scan area icon to draw a scan area directly in the preview image by To define a known type of slide with known scan area click on the slide tab on the configuration window a Scan Configuration General Slide Misc Select the slide type you are working on When the selected slide has known scan area a dotted area appears on the slide scheme If your slide is labeled you can define the height of the label Click on set scan area to import this defined area as the new scan area Click on to do a preview scan of the selected area INNOPSYS ey Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 22 3 8 Focus setup InnoScan scanners work with a dynamic auto focusing system which greatly reduces background noise and gives uniform images You may also manually set the focus To change focus setup go to the Misc tab on the scanner configuration window a Configuration General Slide Misc Preview setup pixel size 40 0 Mh speed 35 Pe Focus setup Auto focus Manual focus Position um 2 9 Default values Select the manual
39. as Good Flag as Bad Flag as Not found Flag as Absent Clear flags except Absent Clear flags l Flagging lets you sort these spots when analyzing the results The results file includes a Flag column containing values to identify each flag FLAG VALUE 100 Good ad Bad S Not found E 75 Notes Absent spots cannot be modified by Mapix These spots are a bse n t defined in the GAL file or designed with an empty ID Absent Absent spots are not handled by the user interface and are ignored by the automatic search algorithms Not flagged spot O I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 49 5 3 Theresults table Use Photometric Calculations icon located either in the tools menu or in the Analyse tab of the Main Menu to begin the image quantification process The resulting table is displayed in a spreadsheet Display Flags Selected spots lt Defauit display gt Configure Notfound w 0 flags NotFound out of 7392 spots gt 0 0 0 Selected spots Save results ScatterPlot Automatic Flag Normalization Block Column Row x Y Da Flags F635Mean F635Medan F635S50 F635 jlog Mean Medan F635CV 68635 O B63SMean O B8635Medan 6863550 B635 jlog Mean Medan B635CY 1 1 1 3873 0 4531 0 200 01 7239 183 6855 5 1304
40. aser powers are available For 532nm 635nm and 670nm IR model excitation lasers Low stands for 5mW while high stands for 10mW while for 785nm excitation laser IR model Low stands for 5mW while high stands for 20mW Default values Sets the parameters to their default values These values are given by the scanner itself Scan parameters can only be adjusted during or after the preview scan INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 3 6 1 Scanning within auto settings mode 18 Using the scan auto settings mode Mapix searches automatically for the laser power and PMT gain that best fit your specifications i e saturated pixels mean signal level or maximal signal level To work within scan auto settings mode choose the Auto option on the general tab of the configuration window the following menu appears Genera sie nc T Scan Configuration Genera V Automatic scrolling V Barcode reading Pixel size 3 0 v Speed 35 gt Scan Mode Normal Y Spot size um 200 gt U 1 0 100 0 200 0 300 0 400 0 500 0 Fast Accurate Mean signal level 22 000 lt Max signal level 60 000 saturated pixel 0 2 INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide
41. bout each parameter please refer to section Scanning an image IININOPSYS 4 T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr h ES x DDA AD Mapix V7 0 0 User s guide 88 8 3 Results Files In this section you can define your preferences to be applied when saving the results table Please refer to Customizing the results table and Exporting the results table GPR and TXT files sections for details Save a JPEG image containing analyzed spots Decimal separator Point Comma INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 89 8 4 Gridding In this section you can define the actions associated with those buttons related to the grid You can define default gridding and photometric calculation parameters A A A A A A A 4 Fixed Diameter Dth Pa Find Selected Blocks Max position offset pitch A Find All Blocks and Spots Min diameter Dth Find Selected Blocks and Spots Max diameter 2 Dth Find Spots in All Blocks S B border width pixels Find Spots in Selected Blocks Background diameter pitch Find Selected Spots Please refer to Positioning the grid section for details eee rL NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 97
42. color images default To do this keep the separate files box unchecked Separate TIFF files the default name will have the suffix _ xxx i h Separated TIFF files where xxx is the relevant wavelengt You can also choose to keep either one or both colors Note a single TIFF file containing both color images is easier to manage and guarantees image correspondence You can compress your TIFF image using LZW compression LZW Use TIFF LZW leads to a lossless image compression which guarantees no quality loss due to compression see Preferences section es Select the prefix file name options that you want to be Prefix File Name l automatically set on the file name see Preferences section For similar file names you can add the file number by clicking on Suffix File Name the suffix file name box Counter can be reset Text area Use this area to manually write the file name Images are saved on Tagged Image File Format TIFF As a format TIFF offers specific features such as lossless image restitution and the ability to save one or more images together with related information called tags File Type Click on save to start the scan Click on Stop icon to stop the current image acquisition sequence INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 27 4 Working with images Once images are acquired you ca
43. ctivestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971975 support innopsys fr Mapix V7 0 0 User s guide Fxxx Median Bxxx Fxxx Mean Bxxx Fxxx Total Intensity Bxxx Mean Bxxx Median Bxxx SD Bxxx log Mean Median Bxxx CV gt Bxxx 1 SD gt Bxxx 2 SD SNRXxxx F Pixels B Pixels Circularity Ratio of Medians w1 w2 59 wavelength Saturation is defined at an intensity value of 65535 The median spot pixel intensity with the background subtracted at the referenced wavelength The mean spot pixel intensity with the background subtracted at the referenced wavelength Sum of intensity values of spot pixels at the referenced wavelength Background noise pixel mean at the referenced wavelength Background noise pixel median at the referenced wavelength Background noise pixel standard deviation at the referenced wavelength absolute value of the logarithm of the background noise Mean Median ratio Background noise coefficient of variation at the referenced wavelength which corresponds to the background standard deviation mean ratio Percentage of background pixels at the referenced wavelength with an intensity values greater than 1 or 2 SD above the median background intensity value signal to noise ratio at the referenced wavelength defined by spot mean noise mean standard deviation noise spot area in pixels pixel area used to compute background noise
44. d for normalization calculations Corresponds to the expected ratio mean Lowess normalization is performed ina R software based algorithm You must install R software to use this option To download R software please go to the R project website hitp cran r project org For the first use of lowess normalization you have to define the complete Path to R software either in 56 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide A Note Smoothing parameter the preferences menu see preferences section or directly by using the Set R Path option Gives the proportions of points of the curve which influence the smoothness at each value Smaller smoothing factor values give a better fit When the smoothing factor is 1 all points influence the regression at each value of the X axis You can modify this value to adjust the flexibility of the regression function used during lowess normalization A smoothing parameter between 0 25 and 0 5 is recommended Once the normalization is performed the title of the data viewer indicates that the data has been normalized together with the normalization parameters Also the Normalization icon becomes disabled indicating that the data has been normalized When using lowess normalization a PDF file containing the graphs MA plot and RG densities before and after no
45. defines the maximum distance tolerated between the mean position and the observed position this distance is expressed as a percentage of average spot pitch Note This value should never exceed 50 and 30 is generally about right Defines the minimal spot diameter as a percentage of the theoretical diameter DTH given by the gal file that will be used to find a spot If one spot is smaller than this value it will be flagged as Not found Defines the maximimum spot diameter as a percentage of the theoretical diameter DTH given by the gal file that will be used to find a spot If one spot is larger than this value it will be flagged as Not found Each spot is framed in a gridding circle overlaid above the images This circle defines the border between spots and background The pixels in the immediate vicinity of this circle have an indeterminate status because they are located at the border between spot and background The width of the exclusion area is defined by this parameter An average value of 2 pixels is generally acceptable the first circle 1 pixel thick inside and 1 pixel thick outside the gridding circle are ignored Figure 1 Background value is calculated as a local value estimated within a circular area centered on the spot excluding all the spots located within this circle This parameter defines the diameter of this circular area It is expressed by the number of pitch units between spots Figure 1 IN
46. difying the display parameters you should deselect this option Click on advanced tab to modify the saturation value and to select the parameters used for image conversion INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561971 975 support innopsys fr Mapix V7 0 0 User s guide ITEM Saturation 8 Bits translate Equalization of histogram 8 less significant bits LSB 8 most significant bits MSB Square root A Note 8 bits translate 32 Display options General Advanced Saturation Saturation 65 535 equalization of histogram 8 least significant bits 8 most significant bits square root DESCRIPTION The maximum saturation value is 65535 This means that the white color used to show saturation on images will appear as soon as this new value will be reached The images displayed are 8 bit images converted from 16 bit images 16 bit images can be converted to 8 bit images Adjust optimum 8 bit conversion using histogram equalization to display all the 16 bit values It shows saturation on the most luminous pixels while the least luminous pixels are visible Displays only the 8 least significant bits showing the least luminous pixels while saturating all pixels with a value exceeding 255 Displays only the 8 most significant bits showing up the most luminous pixels Converts the 16 bit image using the square root method which co
47. e 47 gene 48 gene 49 gene 50 gene 51 gene 52 gene 53 gene 54 gene 55 gene 56 gene 57 gene 58 gene 59 gene 60 gene 61 gene 62 gene 63 gene 64 gene 65 gene 66 gene 67 gene 68 gene 69 gene 70 gene 71 gene 72 gene 73 gene 74 gene 75 gene 76 gene 77 gene 78 gene 79 gene 80 gene 81 gene 82 gene 83 gene g4 Please note that the ID matrix mustn t contain empty lines or columns This option is only available for Excel files Reading orientation Choose the orientation in which the matrix IDs should be read according to the image First choose the block orientation and then the spot orientation Image orientation in Mapix should be read as follows V Blocs Spots 7 re Ba 3 and z INNOPSYS ey Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr wu Na wu N xr Va o w u Sa a Na Mapix V7 0 0 User s guide 42 Once you have selected the format of the file containing the IDs click on Import ID to continue The following window is displayed a Please check that the file format corresponds to the image layout Select the first line that should be read as the first ID in the image by clicking on the first ID of your list Select the folder in which you want to save the GAL file D avneori x a Save in de ID imports a F ete tess gal zy j test_tex
48. e software applicationmainwindoW ere 7 gt Displaying IMAGES 1 Fea Spam ama eA E A KAE EEEN ieee 8 3l Connecting the SCANNEL csccccssccceesececenececenecccencceesececeneceseneeeeesceeseuecessueceeecessenceeeeneceneness 8 3 2 Sea VY e E E EE E AE A E E 10 3 3 Scanner Norna O Neren a EET 12 3 4 Slide detection in the Auto loader onlyforInnoScanXXXALmodels 13 3 5 PI ON SC a ers EE PE ERE e e e 15 3 6 Denning scan Dal ANC LENS urno a anama l le ailesinde dada dale iamiiekina lid ledemi 16 3 6 1 SCANNING withinauto settingsmode eee 18 3 6 2 Extended Dynamic Range XDR eee 20 3 7 Bene ME SC aU E aan a la E di ai an al amda ee 21 3 8 e e a Me en e e 22 3 9 Background g8 eg e A A RaRa 23 a EN go 0 a e 9c A ER YE YMM e 24 3 11 Scanning an Mage ea beda e ee lom sail alama ali adale saa imi e dansa 25 AV e di e ge A A A ran 27 4 1 Open AN existing IM ABE cccceccseccsccescceccsccaeceseceecceeessecsecseeeeeeseeeaeeseeesseeeeeseceeeeseesaeseaeenseees 27 4 2 MRS n e gp e eg A EN EZ ME EZE 30 4 3 mesa e NM EN EMRE ME E EYE 31 4 4 Measurement tools essssensssssesnersssserresssserrssssrreresssrerressserressserreressssereessseeressseerrreesseereessene 33 4 5 COD ONIA aa ale A A at dali E EA 35 4 6 TACE e T E E E E E EE 37 4 6 1 Open an existing grid file GAL file seans syn ei akin end siyan r 37 4 6
49. e submitted a flagging report is displayed describing each performed query and the number of spots selected by them Fr sM Autoflag Process Report So Model choice for query 1 modele4 Flag Selection Good Normalisation choice Include Number of selected spots 12533 out of 45220 spots gt 27 72 lmi le When multiple queries are combined the number of spots flagged by several queries is shown Click on see details for detailed information of these spots Click on the Quit button to submit the query A confirmation dialog is then displayed INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr e w w gt a r r i wu Nan Nin Mapix V7 0 0 User s guide 55 When validated the query is then performed You can see the results in both the image and the results table In the Flags column of the results table the symbol of the last designated flag is displayed In the AutoFlag column the legend indicates the query in the automatic flag function by which the flag was performed The normalization column indicates whether the flagged spot will be used Include or not Exclude for normalization calculations 5 3 3 Normalization You can normalize your data by either a fixed factor or using a global method seli Click on the normalization icon to o
50. e whole grid will be charged independently of the blocs present in the image Finally the option Cancel will stop the grid opening process INNOPSYS a Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 4 6 2 Creating a grid 38 A grid is a set of evenly spaced blocks a block is a set of evenly laid out spots forming an array grid 79 00000 66856 000000 000000 spot se 00 6000 00 0000 ee 6000 ee 6000 ee 6000 ee 6000 ee 0000 ee 6000 ee 0000 ee 6000 ee 0000 ee 0000 block To create a grid use the grid drawing tool either in the tools window or in the Analyse tab of the Main Menu You can then specify the grid parameters in the following window X coordinate of top left corner Y coordinate of top left corner Use the spiicon to establish the X Y coordinates of the top left spot of the grid by clicking the center of the spot in the top left corner of the top left block of the microarray IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 39 In the blocks panel the column spacing corresponds to the distance between the first spot of the first block and the first soot of the second block along the X axis In the same way the row spacing co
51. ect it to Mapix as described in the Connecting the scanner section Insert the validation slide into the scanner Select the check scanner option on the scanner Tab of the Main menu Image Analyse Batch Pre 8 Connect FS Disconnect F5 A Scan parameters F6 gt Preview whole slide F7 gt Previewscanarea Ctri F7 gt Scan F8 M Stop Ctrl F8 Barcode reading Search Ctrl F IP configuration Check scanner About the scanner Send Scanner s Logs During this operation the scanner runs several scans in which its main functions are tested At the end of the check scanner process a results report is displayed EE revs Ck Se es mm er S Seles BAA m 635 532 635 532 S S e S Sa Please note that for the InnoScan 710 IR scanner model the CrossTalk function is not evaluated within the check scanner process You can export the check scanner report as a pdf file NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr SNe eee O A E E A GR a GS en a oe Mapix V7 0 0 User s guide 82 If check scanner results don t conform to the expected results the following message is displayed An issue has been detected during the verification process Please select a folder in order to create an analysis file that you will be able to provide to your supplier Select a directory to save the analy
52. ened Tap Save N m m Sn k Savein k ID imports Pedia Prefix results filename with image filename Recent Items o All blocks in a file Desktop Each block in a separate file Selected spots in a file Save a JPEG image containing analyzed spots f jmber format Decimal value Integer value A Se Computer Decimal value Point Comma a File name results_file gpr Files of type GenePix Results files gpr Refer to the following table for details Item Description Prefix results filename with Fix the image name as a prefix of the results file image filename name If the slide contains several blocks this option will All blocks in a file keep the results for all blocks in the same results file INNOPSYS a Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Each block in a separate file Selected spots in a file Save a JPEG image containing analyzed spots Number format Decimal separator File type The results file contains the data displayed in the data viewer table together with the information on the origin of the results This information is displayed in the first lines of the If the slide contains several blocks this option generates as many resulting files as the number of blocks present in the slide The files are named filenaqme_bx txt
53. esents the number of pixels which are egual to the value given by Axis X At the left hand side of the graphic area scale parameter may be manually adjusted To retrieve automatic scale just check the box at the left of the scale Log scale is available for each axis You can also display the Y ordinate axis in percentage Bin size may also be manually set The lower the bin size is the larger the number of dots will be displayed Thus it is better to work with high bin size to speed up display The saturation percentage is indicated for each of the wavelengths the red value corresponds to the percentage of saturated pixels on the first channel either 635nm or 670nm according to the scanner model while the green value indicates the percentage of saturated pixels on the second channel either 532nm or 785nm according to the scanner model The histogram helps you visualize the number of saturated pixels in each channel You can modify laser intensity and PMT gain in the general tab of the configuration window INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 25 3 11 Scanning an image Scan reads the slide within the area of interest using the current acquisition parameters Images are saved automatically after the scan Before the scan begins you have to choose where to save your image s
54. etween executing each step You can define the order of batch step by using this option INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 78 6 2 Batch analysis ut Add Analysis Step Add an analysis step icon opens the options for defining editing the parameters to be used during the analysis of images Use this option when you want to analyze several images at once using the same or different parameters By clicking on this option a menu consisting of four sections for image analysis is opened Quantification Autoflag and normalization Plugin Files Miscellaneous The Quantification Autoflag and normalization and Plugin steps are the same as those of the Batch scans menu Please refer to these sections for details INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 79 6 2 1 Files Files A amp Remove All Files amp Folders Files amp Folders A J 4 A In this section you can add the files for the analysis Notes when opening a folder If the E recursive check box is selected all the files contained in this folder and sub folders will be included during the analysis If it is not selected only this folder will be considered in the study If
55. fer the Software on a permanent basis to another person or entity provided that You retain no copies of the Software and the transferee agrees to the terms of this license and 91 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide E use the Software in accordance with any additional permitted uses set forth below You may not A copy the printed documentation that accompanies the Software B sublicense rent or lease any portion of the Software reverse engineer decompile disassemble modify translate make any attempt to discover the source code of the Software or create derivative works from the Software C use a previous version or copy of the Software after You have received and installed a disk replacement set or an upgraded version Upon upgrading the Software all copies of the prior version must be destroyed D use a later version of the Software than is provided herewith unless You have purchased upgrade insurance or have otherwise separately acquired the right to use such later version E use the Software in any manner not authorized by this license nor F use the Software in any manner that contradicts any additional restrictions set forth below 2 Content Updates You shall have the right to obtain Content Updates for any period for which You have purchased maintenance except for those Content Update
56. focus option and define the focus position in um INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971974 Fax 33 561971 975 support innopsys fr Mapix V7 0 0 User s guide 3 9 Background smoothing 23 During the image acquisition a background smoothing is done automatically You can remove the background smoothing option by deselecting it at the miscellaneous tab of the scan configuration window Scan Configuration General side Msc Pixel size 40 0 v Speed 35 rFocus setup Auto focus Position um Note Removing the smoothing background makes feature seeking more efficient for slides with very low signal Remove the smoothing background when your slide has very low signals INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 24 3 10 The histogram Click on the RE histogram icon to display the histogram Histogramm a Number of Pixels log A v 635 vj 532 min 0 0 Ji max log scale J min J max J log scale Percentage bin size 100 4 Saturation Percentage 0 0020 0 0028 Update e A TA 0 0 6550 0 13100 0 19650 0 39300 0 45850 0 52400 0 58950 0 65500 0 200 0 32750 0 Signal Intensity The histogram displays pixels on a graph Axis X represents pixel values from 0 to 65535 Axis Y repr
57. ge is opened you can navigate through it by using the mouse To change the mouse mode use the icons on the tools window or right click in the image display area I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide MODE ni Zoomin window Zoom mode ny Drag image Walk mode 29 ACTION Zoom into the selected area When this icon is selected click the image to zoom in You can also zoom out by holding the Ctrl key down and clicking on the image You can also use the mouse wheel to zoom in and out by holding the Ctrl key down Move through the image inside the image display window This is the equivalent of using the sliders in the window You can also change image display using the following resources ITEM Sa Zoom Unzoom t Undo 4 Redo 3 Fit to page width Full image nm 1 Real size lt r a Display options 3 Transform Image e ACTION Zooms the entire image by 20 Zooms out the entire image by 20 Returns you to the previous zoom Returns you to the zoom just canceled Fits image width to the display window Fits the entire image into the display window Displays the image with a 100 zoom factor One pixel on the screen corresponds to one image pixel Lets you change the parameters by which an image is displayed Please
58. left corner of slide in microns References of the software that produced the file References of the scanner that produced the image Temperature during scan in C Optional image comments Laser output during scan in mWatts PMT Gain during scan Note Optional lines are also defined from the GAL file INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr w x x w e Va Va w Va w L Va i han Man X a Mapix V7 0 0 User s guide 67 5 6 The plugins A plugin jar file enables you to extend the capabilities of Mapix adapting them to your own needs When Mapix version 4 0 0 and later is opened for the first time a directory named plugins is automatically created as a sub directory of the Mapix folder To make a plugin available for use in Mapix it has to be located in the plugins sub directory of the mapix folder To see the available plugins installed on Mapix go to the Plugins tab at the Main menu Plugins C Load plugins E Qpen the plugins frame m Example of Flugin e Quality Control Load plugins option allows you to search for plugins added to the plugins sub directory after Mapix was started start starts the plugin stop stops the plugin about displays information about the plugin Indicated are information needed to initiate the plugin image grid quantifica
59. lock and the position and diameter of each spot Find selected blocks and spots locates the position of selected blocks and the position and diameter of spots in selected blocks A Find spots automatically accurately locates the position of each spot and determines their diameter The following options are available Find spots in all blocks finds each spot without taking into account any block selection INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 44 Find spots in selected blocks finds each spot in selected blocks Find selected spots finds each selected spot The Global search find all automatically icon allows to perform all steps 1 3 automatically in only one step You can use this option if the blocks are correctly aligned with each other and the image matches the theoretical grid closely This can be useful when processing a large number of slides spotted simultaneously Once the grid is correctly positioned you can quantify the image INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 45 5 Image quantification 5 1 Configuring the analysis parameters Each scan starts with standard parameters however you can define some analysis parameters that better fit your image Click on
60. me Administrator Standard Restricted Imapinno A user can be stated as administrator standard or restricted user amp The administrator can access different user s accounts as well as create delete or modify the status of other user s accounts 2 A standard user has complete access to Mapix but cannot change or enter other user s accounts SS A restricted user has only restricted access to Mapix and cannot modify scan parameters or table results display The status of a user s account is displayed in the users dialog when Mapix starts INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr ARS ABA gt Yaseen A pe i Mapix V7 0 0 User s guide 87 Each user can protect their account by defining a password To define a password go to the Preference tab on the main menu and then click on Password Note The password must consist of at least 6 characters 8 2 Image Files Use this section to define the parameters to be used during image acquisition and saving Date amp Time Barcode Current counter value 0001 J Allow existing images to be overwritten F Separated TIFF files Use TIFF LZW compression lossless You can choose the parameters to be used as prefix or suffix of the image file name Those parameters in the unused box will not be present as options in the image save dialog box For details a
61. mpresses image dynamics When an image is acquired by an InnoScan scanner pixel depth is 16 bit or 20 bit meaning that pixel values range from O and 65 535 or from 0 to 1 480 575 respectively Because of the hardware limitations of standard graphics boards these images are only displayed with a 8 bit pixel depth meaning that on screen pixel values range from 0 to 255 The software also uses the 16 bit and 20 bit values for processing the images 8 bit images are only used for display purposes INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 33 4 4 Measurement tools Using the measurement tools you can measure the number of pixels and their intensities inside specific zone on the image You can choose either a line or a rectangular zone on your image by clicking on icon gt line rectangle SS Once you have drawn a line or a rectangular zone select one using the S icon Click on icon to choose a measurement tool There are three available tools 1 Profile measurement shows the intensity for each pixel inside the drawn line You can only use this option when selecting a line and not when selecting rectangular zones The intensity profile for the selected line is shown in the window INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33
62. n work on them to set the quantification parameters You can work with TIFF files created by Mapix or by any other compatible software These files may contain one or multiple images Mapix only handles files containing 1 or 2 images and 1 or 2 previews Note Previews are not displayed 4 1 Open an existing image To open an image go to the File tab on the Main Menu Click on open image and search for the images you want to open If you have saved your images in separate TIFF files you can open them either separately or in a single image Ratio metric Images Ratio metric images use 3 channels Red Green and Blue They are commonly called RGB images Each channel uses 8 bits so each channel comprises values from 0 to 255 Ratio metric images are formed using the red channel to display image1 the green channel to display image2 while the blue channel is constantly left at 0 Ratio metric images thus show red predominance when pixel values are higher in imagel than in image2 and green predominance when pixel values are higher in image2 than in image1 When parity exists between imagel and image2 pixel values the color displayed will be yellow Notes The red channel corresponds to intensities at the first wavelength channel either 635nm or 670nm according to the scanner model while the green channel represents the intensities at the second wavelength channel either 532nm or 785nm according to the scanner model F
63. ng the version of the software currently used is displayed NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr 12 Ne L L Mapix V7 0 0 User s guide 13 3 4 Slide detection in the Auto loader only for InnoScanXXXAL models If your scanner has an auto loader system you can load your slides in the autoloader s holder without having to put them in a sequential order Mapix detects the position in which the slides are loaded Once Mapix is connected to the scanner the auto loader zone in the tools window becomes visible see figure To detect the location in which slides were loaded click on the Y read loader icon Tools SIRE EFOR DEJ LA Preview il gt EL Available w A 3 moa ala FE Note To enable scanning your slides you must perform this detection step Once the slides are detected Preview and Scan icons become visible Once the slides have been detected by the scanner one can ask Mapix to read the barcode for each slide in order to know the position of each loaded slide When passing the mouse on the slide position the following scan parameters appear INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Yj Yj SSG KK WV Mapix V7 0 0
64. no barcode disable this feature so the message barcode reading error won t be displayed Automatic scrolling Scrolls the image window automatically during the scanning process pixel size Selects a scan resolution Scan resolution represents the individual pixel size in the scanned image Pixel size can be set from 3 to 40 microns for the InnoScan 700 710 and 710 R scanner models and from 1 to 40microns for the InnoScan 900 and 910 scanner models Speed Refers to scan speed Speed can be set from 10 to 35 lines second The signal intensity correlates with the time of integration longer slide exposition gives higher intensity slides Click on scan mode to choose between normal or median scan mode Scan Mode In normal mode the scan is done in the defined pixel size while in median mode the scan is done in a step equal to a half of the defined pixel size In median scan mode for each image pixel four values are considered and the pixel value is set as the median of these four values In this way scanning is done in a higher resolution but with smaller image size Note Because scanning is done in a higher resolution than set scan time is doubled in median scan mode This scan mode is only available for even resolutions Detection gain Sets a value for the gain percentage for each color channel wavelength The default value is the value used in the last scan session Changing gain one can avoid saturation Laser power Two l
65. olumns Item New Remove Rename Data type visibility and order Aly Apply Cancel Hide Export Import Description Creates a new display Removes an existing display Changes the name of an existing display Shows the available columns and their order Check Uncheck the boxes to select deselect a column Allows you to change the column order in the table Validates the modifications Returns to the last display Hides the display area Note If there are no applied modifications a window will appear to save or ignore modifications Exports the display configuration into a mapix display configuration file mdp Opens a mapix display configuration file mdp Click on Apply button to apply the desired modifications The modifications are automatically saved INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 63 Use Export button to save the results table display configuration as an independent file that can later be imported using the Import button This would be useful when different users want to use the same results table display configuration 5 5 Exporting the results table GPR and TXT files You can save your data in a Mapix text format txt or a GenePix Result format gpr YV Click on the Save Results icon to save the table results The following dialog window is op
66. or images taken at a pixel size of lum sometimes it is not possible to display both channels at once due to memory issues However this INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 28 concerns the image display only image analysis and quantification are done in both channels even when only one color is displayed To open two separated TIFF files in a single ratio image you can either Hold the Ctrl button down when selecting the images Open one image in first and then open the second one A Notes To open two separated TIFF files and generate ratio images images must have the same dimensions the same pixel size and different color channels Otherwise only one of the selected images will be displayed When opening images created by other compatible software if there is no wavelength indicated in the TIFF file Mapix will ask you to assign a wavelength value for each channel to create the ratio metric image al Assign mage The image file selected was not created by Mapix File C Documents and Settings vincent Bureau Cyanines AUBU44bocyS tit Assign an excitation wavelength to the image 635 nm 0532 nm 594 nm 1561 nm C 488 nm OL am If you do not know these values click on Cancel then the default values will be 1 and 2 for the first and second channel respectively Once the ima
67. pen the normalization process window m Normalization Process m Sm r Normalization Factor Definition r Normalization Factor Calculation Normalize quantification data with following criteria Considered Parameter Median of Ratios v Selected Features All Features X Expected Mean 1 0 Lowess ameter Set R Path INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Refer to the table below for information PANEL ITEM n Factor for Wavelength Normalization 635nm or 670nm Factor Definition e EA 532nm or 785nm Considered Parameter Normalization Factor Calculation Global method Selected Features Expected Mean Lowess Set R Path 1 2 DESCRIPTION By selecting this panel the normalization is done with a fixed factor You can define the factor for each wavelength Selects the parameter to be used for normalization you can choose among Ratio of medians Ratio of means Median of ratios Mean of Ratios Regression ratios Choose which features will be taken to calculate the normalization factor When selecting Included features the spots used for calculating the normalization factor are those selected during the automatic flag function In order to avoid the influence of extreme values only features with a ratio value between 0 1 and 100 are considere
68. rmalization is automatically created in the image directory 57 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 58 5 34 Results description Column Title Block Column Row Dia Flags Fxxx Mean Fxxx Median Fxxx SD Fxxx log Mean Median Fxxx CV Fxxx Sat Description Block number Spot column number Spot row number X coordinate of the spot center in um from the top left corner of the image Y coordinate of the spot center in um from the top left corner of the image Spot diameter in um Spot flag See Flagging spots section Spot pixels mean at the referenced wavelength Spot pixels median at the referenced wavelength Note The median is less sensitive to dust than the mean value Standard deviation of spot pixels at the referenced wavelength Absolute value of the logarithm of the spot Mean Median ratio at the referenced wavelength This parameter indicates the consistency between mean and median values normally very similar When mean and median values are very different log Mean Median value tends to differ from zero This may indicate dust effect on mean value or non homogeneity in the spot Coefficient of variation of the spot at the referenced wavelength CV corresponds to the SD mean ratio Percentage of spot saturated pixels at the referenced INNOPSYS a Parc A
69. rresponds to the distance between the first spot of the first block and the first spot of the second block along the Y axis as is shown in the following image Block column spacing Block row spacing In the case of the spots the column spacing refers to the distance between the spots on the X axis while the row spacing corresponds to the distance between the spots on the Y axis Spot column spacing N j Spot row spacing Use the js icon to directly select the corresponding spots in the image INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 40 When selecting the export option a grid file is saved in a GAL file format that can be further uploaded for other images One can import the sample IDs corresponding to the image when exporting the grid 4 6 3 Importing Sample IDs to the GAL file Once the grid parameters are defined one can import the sample IDs corresponding to the image by choosing the option Yes when exporting the GAL file Select an Option X Do you want to import ID file No Cancel The following window is displayed gt 8 POA rFie Format Type 1 listof I0 Look in ID imports plan de spotting AM xdsx a plan de spotting AM tetxlsx Recent Items Type 2 layoutofID amp Repeat IDs for al blocs a rReading orientation
70. s creating an error message in the batch report For details about plugins please refer to the plugins section KR SA lt lt O A SE a a Aa A IININOP SYS T Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 6 1 7 Miscellaneous Miscellaneous Change the slide before scanning Save image as a JPEG file C Save as a work before doing next step scan Repeat this step Change PMT gain during repeated scan C Wait For At the end of this step go to 77 before doing next action Use this section to define the steps to be done between each scan Refer to the table below for information Item Change the slide before scanning Save image as a JEPG file Save as a work before doing next step scan Repeat this step Change PMT gain during repeated scan Wait for before doing next action At the end of this step go to Description When conducting the same analysis for different slides on a one slide scanner model you may select this option This option is not available for the auto loader scanner models Saves an additional image in JEPG format Saves each step before doing the next scan Defines the number of repetitions of the same batch step Use this option when conducting the same analysis on different slides Changes the PMIT gain during repeated scans Defines wait time b
71. s proposals and representations with respect to its subject matter and ii prevails over any conflicting or additional terms of any quote order acknowledgement or similar communications between the parties This Agreement shall terminate upon Your breach of any term contained herein and You shall cease use of and destroy all copies of the Software The disclaimers of warranties and damages and limitations on liability shall survive termination Mapix software uses F2D SAFIR software F2D SAFIR software was created by INRA and INRIA IRISA Rennes 2008 Some parts of Mapix software are based on the Open source software programs listed below Each included Open source software program is displayed followed by the license he refers to Note that the terms software and program refer to the corresponding Open source software program iText Version 2 1 4 subject to Affero General Public License JAI Java Advanced Imaging Version 1 1 subject to Binary Code License Agreement Jcommon Version 1 0 10 subject to GNU LESSER GENERAL PUBLIC LICENSE JFreeChart Version 1 0 6 subject to GNU LESSER GENERAL PUBLIC LICENSE Java Help System jh jhall jhbasic jsearch Version 2 0 3 subject to GNU General Public License 2 0 94 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 95 2fprod common all Version 7 3 subject to Apache P
72. s that Innopsys elects to make available by separate paid subscription or for any period for which You have otherwise separately acquired the right to obtain Content Updates Innopsys reserves the right to designate specified Content Updates as requiring purchase of a separate subscription at any time and without notice to You provided however that if You purchase maintenance hereunder that includes particular Content Updates on the date of purchase You will not have to pay an additional fee to continue receiving such Content Updates through the term of such maintenance even if Innopsys designates such Content Updates as requiring separate purchase This License does not otherwise permit the licensee to obtain and use Content Updates 3 Product Installation and Required Activation There are technological measures in this Software that are designed to prevent unlicensed or illegal use of the Software You agree that Innopsys may use these measures to protect Innopsys against software piracy This License and the Software containing enforcement technology require activation key as further set forth in the documentation The Software will operate for an infinite period of time prior to Software activation by You During activation You will provide Your unique product key accompanying the Software and computer configuration in the form of an USB key If You do not complete the activation the Software will cease to function until activation is complete
73. sis Plugin Miscellaneous A Note Each of these steps has been previously described Please refer to the referenced sections for details I INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr eS SE SE SE SE O SE e e a Mapix V7 0 0 User s guide 6 1 1 Scan Parameters ZA RR pen Save Saveas Add Analysis Step Close al Start Stop ERE psen Area e epee 420193 ig Unlabeled she wj Top um 6 520 gt Right um 18 880 gt Bottom um 16 480 gt Set scan area This step describes the definition of the scan parameters here you can define the scan area and detection gain laser power Please refer to Defining scan parameters and Defining the Scan Area sections for details re Imports the scan area from the preview window 5 Exports the scan area to the preview window NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr 71 Mapix V7 0 0 User s guide 72 6 1 2 Loader slide selection Only for models equipped with an auto loader If the scanner is equipped with an auto loader you can select the slides to be used in the batch AS SE E SE A Loader slide selection O Asides Beste Slide 1 Slide 2 Slide 3 Slide 4 Slide 5 Slide 6 Slides Slide 7 Slide 3
74. sis file inl Once the file saved the check scanner report is displayed am EE EIAHA Linearity 635 532 635 532 W g ee E Choose to save the check scanner report Send the scanner report together with the analysis file inl to your supplier for a rapid intervention A Notes Checking the scanner verifies that its main functions are working properly It is recommended to run a check scanner at least once per month The validation slide has a lifecycle of one year at the end of which you should acquire a new validation slide To get a new validation slide please contact your supplier NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr L e S A eee a YA I ES A SD O A I A A GG E GR O is A A GS O Mapix V7 0 0 User s guide 83 7 1 Replacing a validation slide If the validation slide is expired the following error message is displayed Validation slide has expired Do you want to check the scanner anyway One can continue the check scanner with an expired slide by clicking on the Check anyway option However verification results might be influenced since the slide is no longer valid To acquire a new validation slide please contact your supplier The validation slide is then provided with an exchange code Write this code to perform the validation slide exchange
75. startup Direct connection to the Internet Manual proxy configuration item Language Look amp Feel Do not show preventive messages Scanner Update settings Description You can choose the language of Mapix between French and English versions Use this option to change the appearance of Mapix Preventive messages are displayed when a work or a configuration has been created or modified without having been saved You can choose to turn this off or on In this panel you can define some parameters on the scanner connection To receive Mapix updates keep this option active You can handle the user accounts by choosing between single access user and multi access user When Multi access user is selected each user must choose his her own session when Mapix starts on Users account control option allows an administrator account to be defined Only the administrator can add modify or delete another user s accounts INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 86 Once Users account control option has been selected the Users Account Manager is added in the preferences tab of the Main Menu Preferences Window Help 2 Users D Password ae User Account Manager Use this menu to control the access of different Mapix users User Account Manager rx N Na
76. t la k a gt Design When generating a scatter plot choose the data to be plotted on the X and Y axis in the options dialog of the scatter plot window INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 52 KIL The automatic flag window As seen in the flagging spots section spots can be flagged as good bad or not found You can perform an automatic flag by introducing flag parameters in this window When clicking on the following window opens Automatic Flag Features Saved Models modele4 Ss Dere ITEM DESCRIPTION Saved Models Shows the existing queries used for flagging a spot Flag as Defines the flag associated to a query Defines whether flagged spots will be used during the Normalization NO normalization process or not Opens the Autoflag Model Edition frame Use this window to Manage Models e 6 add new or edit existing queries Preview Shows the parameters and the description of each query Add a new query Delete a guery Submit Applies the guery to the results Close Exit the automatic flag window INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr TA TATA a a TR TRR J j J l j A j A A A A A Mapix V7 0 0 User s guide 53 Lo ee LAN Adding a new
77. t File XX Number of header lines YY Number of result columns These values are calculated when the image and the results files are created Identifies the exact results file type Date when the image was scanned Name of configuration file used Name of GAL file used Pixel size in microns List of wavelengths Name of image file two names if separate files Shows the directory where the JPEG Image was saved It is only present if a JPEG file was saved during analysis Shows the direction by which ratio values were calculated 635 532 or 532 635 for InnoScan 710 and 900 models and 670 785 or 785 670 for InnoScan 710 IR model INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide Feature Type Barcode Background subtraction Normalization Image Origin Jpeg Origin Creator Scanner Temperature Comment Laser Power PMT Gain 66 Shows the type of analyzed feature since Mapix can process only circular features this item will be always circular Barcode number if present on slide Describes whether or not the local background was substracted Defines if a normalization of data was done describing the normalization method used Position of top left corner of image in relation to top left corner of slide in microns Position of top left corner of image in relation to top
78. the e link check box is selected separate TIFF files of the same scan will be analyzed together in a single step the intensity ratio is then computed and results will be saved in a single result file DOO VO eee NNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr OA JTA VA NTA NTA A TA A A Ta m e ED e sn Ma KA A ae en Se O O A A A E O YO e Mapix V7 0 0 User s guide 80 6 2 2 Miscellaneous ii e a F Save image as a JPEG file Saveasa work before doing next step scan At the end of this step go to Step 1 v 1 times Use this option to define if you want to save an image in a JEPG file format and to save a work in a Mapix work file mwk file before launching the next batch step Once all the parameters have been defined for each batch step use the start button to start the application You can stop the application at any time by using the stop button You can save the parameters in a Mapix Batch File mbt INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr SNe A A E A A A eh ee Caen Sn Caen Mapix V7 0 0 User s guide 81 7 Scanner Validation InnoScan scanners are provided with a validation slide which allows the validation of scanner performance To run a check scanner turn on the scanner and conn
79. tion etc A Only when all the information that is needed by the plugin is available in Mapix will the start option become enabled Notes When a plugin is started start is inaccessible whereas stop is enabled INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 68 The Open the plugins frame option opens the Plugins frame displaying the available plugins in the desktop of Mapix amp Plugins Example of Plugin j Dualit Conkral start stop About This frame permits users to easily start the plugins by clicking on the appropriate icon The icons are disabled until the needed objects are created in Mapix When a plugin is started the appropriate icon is disabled since it first has to be stopped A Note Plugins can be created by the users For more information about how to create a plugin please refer to the plugins creation documentation available in our website or in the installation CD ROM INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 69 5 7 Saving Opening a Mapix work file You can save your work at any moment on a Mapix work file mwk This file will save all the Mapix settings images scan parameters grid flags and the analysis made To save a work file
80. tl_grid gal Recent Items test tet2 grid gal test xis grid gal ttl gal o jtt2 gal INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr Mapix V7 0 0 User s guide 43 4 6 4 Positioning the grid Once the grid file is opened a grid is positioned on the image To hide the grid click on the x hide the grid icon to see the grid click on the gt 9 show the grid icon 4 6 4 1 Block selection spot selection To align the grid to its correct position with respect to the features you can move the blocks b b and spots manually by using kaloro modification and S epok modification icons of the tools window or you can perform it automatically by following the next steps see sve Find grid automatically this option locates the position of the entire grid without moving blocks in relation to each other This tool does not take into account any selection of blocks or spots and then acts directly on the entire grid A Find blocks automatically this option finds the best position of each block The following options are available Find all blocks locates the position of each block without moving the spots in relation to each other Find selected blocks locates the position of selected blocks without moving the spots in relation to each other Find all blocks and spots locates the position of each b
81. transform of the ratio of the medians for wavelengths w1 and w2 INNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr a AN ER EE lt lt SE Mapix V7 0 0 User s guide You can change the results table display and select the guantifiers of interest for your work 5 4 Customizing the results table by using the Display area on the data viewer menu Click on the Configure button on the Display area to set the display configuration area A Bd Save results Refresh ScatterPlot AutomaticFlag Normalization Rs Display pe Default display gt Rename Note The lt default display gt cannot be modified To change the display settings you have to create a new display Display p Fa lt Default display gt z Configure j Block Column Row X Y Dia Flags F635 Mean 1 1 1 3873 0 4531 0 200 01 7239 li a 2 1 41230 45310 200 01 7128 a 3 1 43720 45310 20001 o 68270 4 1 46230 45310 200 01 6572 0 a s 1 4873 0 45310 200 01 6383 4 a a T 4531 0 200 01 6266 3 a 7 1 373 0 4531 0 200 01 6272 5 a a a 4531 0 200 01 6226 9 E 56720 4531 0 6207 6 1 10 1 61230 45310 200 01 6130 9 a un 1 6373 0 4531 0 200 01 a7 Pp 1 12 1 66220 453 0 20001 6156 i 1 2 3873 0 4781 0 200 011 775 1 pa 2 2
82. ublic License 2 0 I2fProd LookAndFeel subject to Apache Public License 2 0 Commons logging Version 1 0 4 subject to Apache Public License 2 0 PDFRenderer subject to GNU LESSER GENERAL PUBLIC LICENSE SwingX subject to GNU Lesser General Public License INNOPSYS Parc Activestre 31390 CARBONNE France Tel 33 561 971974 Fax 33 561971 975 support innopsys fr Uy Mapix V7 0 0 User s guide 96 Function Signature Written by Field Applications Specialist Software Development Approved by Manager NNOPSYS L Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr f Mapix V7 0 0 User s guide 97 INNOPRSYS L www innopsys fr INNOPSYS 7 Parc Activestre 31390 CARBONNE France Tel 33 561 971 974 Fax 33 561 971 975 support innopsys fr
83. uitability for its requirements its good working order and for ensuring that it shall not cause damage to either persons or properties You acknowledge that the Software is supplied as is by Innopsys without any other express or tacit warranty and in particular without any warranty as to its commercial value its secured safe innovative or relevant nature Specifically You do not warrant that the Software is free from any error that it will operate without interruption that it is compliant with its documentation that it will be compatible with the Your own equipment and software configuration nor that it will meet the Your requirements Innopsys does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent software or any other property right Therefore Innopsys disclaims any and all liability towards You arising out of any or all proceedings for infringement that may be instituted in respect of the use of the Software Innopsys disclaims any and all liability as regards Your use of the name of the Software No warranty is given as regards the existence of prior rights over the name of the Software or as regards the existence of a trademark TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW THE ABOVE WARRANTY IS EXCLUSIVE AND IN LIEU OF ALL OTHER WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTIC

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