FIJI - Microscope Measurement Tools

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This plugin for FIJI allows UCSB NanoFab users to make calibrated measurements on microscope and SEM images with freely available software, after the image acquisition.


  • FIJI is an open source package, based on ImageJ, for scientific image analysis across many disciplines.
    • Download here.
  • Microscope Measurement Tools (UCSB Fork) is a plug-in with pre-configured settings that provides the scaling factors for the UCSB NanoFab microscopes and SEMs. It also contains a script for drawing line measurements onto an image.
    • This just automates the use of the `Set Scale...` built-in function.


  1. Download FIJI and the Microscope Measurement Tools packages.
  2. Install FIJI accordingly.
  3. Unzip the Microscope Measurement Tools (aka. MMT) file. Locate the `Analyze` folder inside the package.
  4. Navigate to the FIJI `Scripts` folder, in
To Do: get path
  1. Copy the `Analyze` folder from MMT into the FIJI `Scripts` folder.
    1. In the off chance that an `Analyze` folder already exists in the FIJI scripts folder, merge the two rather than overwriting. You must have placed another script in the same menu location.
  2. (Re)Launch FIJI.
    1. There should now be a new menu option in `Analyze > Microscope Measurement Tools`

Add shortcut keys

Optionally add a shortcut key to execute the scripts.

To Do: add steps

Make a Measurement on an Image

  • Download an image from one of our microscopes on Nanofiles.
    • You must know which microscope and which objective the image was saved with.
  • Open the image in FIJI
  • Run the script `Analyze > Microscope Measurement Tools > Choose Microscope Calibration...`
  • Select the appropriate microscope and objective from the list and click
To Do: Apply
    • The calibration has now been applied to the image. Any FIJI functions will now use the correct scaling.
  • Enable the Line tool. Draw anywhere on the image you want to measure.
    • While dragging, the FIJI control window will show the calibrated measurement value of your line.
  • To draw the measurement on the image, select the menu `Analyze > Microscope Measurement Tools > Draw Measurement - Line`
    • This can not be undone without reloading the image, so be sure not to Save the file.
    • You can make a new Overlay before applying the Drawing to make the line moveable or erasable.

SEM Images

Images saved from the JEOL SEM automatically save a Text file with the same name, which contains the scaling information.

As long as this text file is kept in the same location as the image file, the function `Choose Microscope Calibration >> JEOL SEM - AutoCal from TXT` will set the measurement scale appropriately.


  • The original general-use plugin can be found here: Microscope Measurement Tools on GitHub.
  • Other FIJI plug-ins available.
  • Setting the scale on any image with FIJI or ImageJ.