Analyze|Set Scale...calibration from image data for particle size determination


Please classify/relocate to issue if it is determined to meet these requirements more closely.

I am currently analyzing nano-particle data I recorded. The magnification level of 300k was chosen as a standard prior to data collection. I used this as much as possible yet, some of the collections of particles were simply too large, and too interesting to view, to rigorously implement this as a constraint and potentially lose useful sample data. Is it possible for me to utilize all images with the desire of creating a particle size histogram representing publishable results? I would like to collect at least 250 measurements yet, prefer 250-500.

Additionally, I find use of the straight line tool to configure “Set Scale” somewhat cumbersome in that obtaining the exact scale from the image data is not trivial when doing so by a mouse. I consider this to be exacerbated by the angle parameter tracked by the straight line tool. Is there a better alternative than the straight line tool for this purpose?


If I understand correctly, you want to measure particle size in images with different scales (microns/pixel), and you want an easier way to set the scale factor in your images.

Yes, you can certainly combine results from images with different scales, as long as the scale is set correctly on each one.

The easiest way to get the scale factor is to use the original data from the microscope. Most microscopes record pixel size as part of the image metadata. Try opening the original image (using Bio-Formats, included in the Fiji package of ImageJ). Then your measurements will automatically be in the correct units.

For setting the scale manually, it helps to:

  • zoom up the display (press +)
  • hold down Shift while using the straight line tool, to make the line snap to horizontal or vertical
  • take the average of a few measurements of your scale reference

Hope this helps.