Wednesday, 25 February 2015

Scanning the fields of a microscope slide

Q: Do you have a preferred method/pattern for ‘scanning’ the fields of a microscope slide?  I have seen numerous patterns listed, but (like a telescope I imagine) moving the stage is counter-intuitive to what my brain wants to do when I move the image while viewing it through the
objective.  Any tips?

Lily flower TS photographed in tiles 7 X 8
starting top left to right, row by row
A: I'm assuming you have a mechanical stage.

  • Start at a low power objective (10x)
  • Find a random subject to focus on somewhere on the slide to be scanned
  • Get your lighting set up correctly
  • Then go to the top left corner of the coverslip or area to be scanned (as seen through the microscope). If your microscope gives you an inverted image, it will initially feel strange and counterintuitive (ie. you move the slide to the left, but the image appears to move to the right). However, if you concentrate on what the image does, you soon adapt.

If just scanning by eye:

  • Scan towards the right across a predetermined width (e.g. coverslip width)
  • At the end of your first scan, go down about three quarters of a field of view
  • Scan back to the left across the slide till you reach the coverslip boundary
  • Go down about three quarters of a field of view and scan to the right again.
I tend to scan at lower powers, then when I find an object of interest, I centre on it and zoom in with the higher objectives.

Lily flower TS photo panorama created using
Panorama Maker 8 using tiles as above
If you want to create a photo panorama you need to:

  • Do one row scan from left to right, taking pictures every three quarters of the field of view
  • Once you reach the end of a scanned 'lane', go all the way back to the beginning on the left 
  • Go down three quarters of the field of view
  • Scan the next row from left to right, taking pictures every three quarters of the field of view.
  • Etc.

This ensures that your images are tiled in matching rows and columns. This makes for easier processing by a 2D panorama stitching program.

If you have a microscopy question, contact Chris at Chris@miltoncontact.com or go to www.usingthemicroscope.com


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