0

I have a bunch of auto-scanned slides using a slide scanner (Hamamatsu), which I can export from the NDPview software at different magnifications. So far, I have been zooming in to where I get the best resolution of my region on interest and add a scale bar for 1mm (as 1000 um) using the native scale bar option in the NDP view software. I then export the "view" from NDPview to TIFF. This TIFF is then imported into ImageJ (Fiji) where I set the scale using the scale bar I drew. This has been working well, but with over 500 images to do it's a bit of a pain.

Since the TIFF imports to ImageJ with inchxinch dimensions, I figured I can go to Image -> Properties and just change the unit of length to um. To test this, I selected an area to measure. I then compared this to my old method... and the values are completely different. Any idea why? 1 is the old method, 2 is the new method.

results

I made certain to "remove scale" in the scale bar window between each test. The whole image dimensions are different too:

inches new method old method

quantixed
  • 287
  • 3
  • 12
DS14
  • 133
  • 9

1 Answers1

0

If the images are all the same magnification and resolution, then as long as you know a measured distance (in pixels) and the physical distance (in microns or mm), you can set it using Analyze > Set Scale...

To do this in a macro you can use

run("Set Scale...", "distance=255 known=1 pixel=1 unit=micron");

where 255 is the distance in pixels for your known unit (1 micron). This can be applied to all TIFFs in a folder if you wrap that line in a loop operating on all TIFFs and save each resulting image.

quantixed
  • 287
  • 3
  • 12