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ScantheWholeSlideSpecimensVectraPolaris.md

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4.4.5.5. Scan the Whole Slide Specimens (Vectra Polaris)

If everything checks out scan the specimens as follows for the Vectra Polaris

  1. Take exposures (create a single protocol) for all of the clinical specimen multiplex slides
    • The name of the protocol should be BatchX_MM.DD.YYYY
    • Save to the corresponding <spath> folder
  2. On the Slide Log Template
    1. Enter the Clinical_Specimen_XX study in the column Study. XX should match the next available Project Number
    2. Enter the appropriate scanning protocol for each slide in the column Protocol
    3. Select Scan Only in the Task column
    4. In box G1 enter a name to help you identify the setup
    5. Click the Save icon on the spreadsheet
  3. On the computer desktop double-click the icon Polaris_setup
  4. In the Vectra Polaris start menu, click Scan Slides
  5. Click Load Setup, select the setup that matches the information you entered in box G1, and click Load.
  6. Click Scan at the top of the screen.
  7. Watch the Polaris until you see Performing fluorescent whole slide scan using protocol XXX.
  8. Load the slide carrier with the slides
    • Clean the slides using a Kimwipe to remove dust and excess mounting medium
    • Load the carriers so that the first slide corresponds to Slot 1 on the Task list
  9. Scan the whole slide overview on the microscope
  10. Create the annotation file for the Whole Slide Overlap imagery
  11. Acquire HPFs on the microscope
  12. If using a network storage server, wait for data to backup
    • Manually check that the image files are in both the local and backup locations
      • Open two windows explorers, one for the local and one for the backup location
      • Check that the same number of im3s exist in both locations
      • Sort by ‘Size’ in the windows explorer to be sure that all of the images are the same size
        • If there is a file with 0 bytes, check for M# duplicate file. This is the only time variation in field size is allowed, see ‘Notes’ section below for details on how to handle M# files.
      • Check that the annotation.xml modified data are the same
  13. Check that the data scanned properly
    • Open the overview scans in Phenochart and check that at least 95% of the fields correctly scanned
      • Never retake single HPFs, if more than 5% of fields failed restart the entire HPF set
      • If a HPF fails in the region of interest, rescan the slide
      • By making the image files 'extra large icons' a quick visual inspection can be performed of the slides. Here check for two things:
        • sometimes the microscope gets mixed up and scans the wrong part of the tissue, usually this creates a number of empty fields but can be hard to catch
          • the AstroPath Pipeline code has been modfied to handle such cases so this is not a breaking issue but does cause a loss of data.
        • sometimes the microscope will automatic focus will fail and fields will be blurry
        • In both cases rescan the HPFs
  14. If you need to rescan a slide:
    • Go into the folder of the slide you need to rescan
    • Create a new folder
    • Name the folder ScanX where X is the number of the last scan folder plus 1
    • Go into the failed scan folder and copy everything except for the MSI folder and both annotation files
    • Copy into the new Scan folder
    • On the qptiff, change ScanX to match the folder name
    • Open the qptiff and redo the ROI
  15. If using a network server for microscope backup, delete the local copy of the data
  16. Add the BatchID.txt, described above, to the proper ‘Scan’ folder