VS200 Running ASW v3.3 (Draft & incomplete)
To be replaced with VS200 Running ASW v3.4.1

Note instructions in green are for fluorescence and can be skipped for transmitted light imaging

Power Up:

• VS200 (green button),
• Xylis (green box) - fluorescence light source,
• Orca-Fusion Camera (do gently and do not rotate camera) - B/W camera for fluorescence
• Note: Even if just transmitted light (brightfield, chromogenic) imaging is being carried out the fluorescence lamp and b/w camera must be turned on otherwise the software will not permit any scanning.

Check Antivibration table - should be 3 to 7 mm between top of metal ring and bottom to rubber ring at each leg.  Adjust red knobs 1/8th of a turn and wait ~30 seconds and then recheck gap.

Start VS200 software

'Yes' to continue with trays already loaded
'No' to swap trays now or clean immersion oil

• 'No' - swap trays then 'Lock Door'
  • Insert trays gently to back and push to left.  Also should see white slide bars where there are slides in the tray
  • Hit 'Lock Door'

Pre Scan Screen

• Single Scan
• Batch Scan
• Exchange Trays
• Clean Objectives

Batch Scan

• Select Tray(s) & Slides for scanning
• Choose Brightfield  |  Fluorescence  |  Special
  • Brightfield
  • Special
  • Fluorescence
    • Tray View (Can skip to 'Gallery View')
      • Choose trays to scan with 'Define Batch Content'
        • Optionally use 'Include All in Scan' if all trays are yours  |  'Exclude All from Scan'
        • Toggle trays on/off by holding control-key and left mouse clicking on tray
        • 'Confirm' (on bottom right)
    • Gallery View
      • Choose slides to scan:
        • 'Define Batch Content'
        • 'Select All' (if all trays are yours) or
        • Choose slides to exclude or include with 'Define Batch Content' - hold control-key + left click with mouse  -
        • 'Confirm'  (on bottom right)
        • Selected slide appear white or blue for the currently loaded slide
        • Can scroll to other trays with the mouse wheel
      • Apply projects by
        • Select slide with left-mouse click and hit a project
        • &/or Select multiple slides with control-key + left-mouse-click, select ranges with left mouse click, hold-shift, click on last slide on desired range
        • Once selected click on "Brightfield" or "Fluorescence" or "Special" as required
        • Choose a 'Project'
    • (Note - selecting, deselecting is just like doing file selections in Windows  "My Computer" or "Explorer" using left mouse clicks and combinations of the 'control-key' & 'shit-key')

• Edit Scan Settings
  • +Overview (suggested setting - In this example Fluorescence is chosen.  Adapt settings as appropriate ):
    • 'Identical Settings' (for this example all slides will assigned with same parameters from selected 'Project' initially)
    • Overview mode - 'Expert' (customized scan settings)
    • 'Scan Label'
    • 'Fluorescence' (Note can do overview with transmitted for fluorescent samples)
    • 'Observation method' choose one with a percentage (Do not use ones with no percentage since will give irreproducible exposures)
    • 'Objective' 4x is more robust for fluorescence than the dimmer 2x
    • 'Focus Mode' - suggest 'No Focusing' or 'Quick Focus'
    • 'Exposure Mode:'
      • 'Manual Exposure'
      • 'Start Live'
      • 'Histogram'
        • 'Auto Contrast'  (really display brightness)
        • Suggest 'Right' 1 (1%) - hit enter (Displays image brighter so that can see cells and ignore bright spots. If no bright spots 0.1 or even 0.01 may be OK)
      • 'Manual Exposure'  
      • 'Start Live'
        • Set focus manually or try 'AF autofocus'
        • Check that 'Max:' is very roughly ~5000 to ~30,000 counts.
        • Adjust 'Exposure Time'  (avoid having spurious bright spots in the field of view)
  • +Detail
    • Choose objective
    • Z-planes - 'normal'
    • Channels
      • First channel is used for focusing
      • Select 'Channel Name' with a percentage only
      • 'Exposure mode:' manual
      • Do 'Start live' and check exposures in 'Histogram'
        • Choose channel #1
          • Adjust 'Exposure time:' so that 'Max:' is ~5000 to ~30,000 counts
          • Focus  - reduce exposure if intensity is >30,000
        • Repeat for other channels ~2000 to ~30,000 counts
        • Find region on slide with brightest intensity and repeat adjustment of exposure time if too bright
      • 'Stop live'
  • +Focusing
    • 'Prefocus'
    • 'Focus position density' - try 'Normal'
    • 'Non-sample region'
      • Try off (works well if tissue is well detected)
      • or 'Include in Scan' on if tissue is not completely detected (below after Overview scans)
      • Don't use 'Include in focusing' since trying to focus on nothing will generally fail
  • +Naming and Saving
    • 'Image name:' choose 'Image_<Slide Name>'  or '<Slide Name>'
    • 'Save to Disk'
    • 'Directory:' choose your directory on the D: drive
  • +Slide Properties'
    • 'Slide Name' - enter descriptive name which will be use to create file name for each slide
    • (Hint - take a smart phone shot of tray before loading into hotel)
    • Do this in order of first slide of tray to last slide of last tray (There seems to be a bug in the software where not following this order causes the entered 'Slide Name' to not be assigned with the correct slide)

• 'Start Scan'
  • Overview at 2x (or 4x or 10x if available) is made

• On each slide do
  • Image - brightens image for user view (does not change data)
    • 'Display limits'  adjust
  • Scan Areas
    • 'Sample Detection' - greenish is detected tissue
      • 'Sample Detection sensitivity:' - adjust 1 step at a time. Allow ~3 seconds (or ~12 seconds if 'Non-colored sample detection weight' is non zero)
      • 'Non-colored sample detection weight' - trial and error although 0% is often good
    • If tissue is not fully detected then turn on
  • Focus Map
    • Focus squares ideally contain >50% tissue
• Run
• It is OK to zoom into images while scans are in progress. Double click on the image.  Hit the "Scan" tab to go back to scanning screen.

• When done hit the 'Home' button on lower right