FIJI - Microscope Measurement Tools
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.
- Download FIJI and the Microscope Measurement Tools packages.
- Install FIJI accordingly.
- Unzip the Microscope Measurement Tools (aka. MMT) file. Locate the `Analyze` folder inside the package.
- Navigate to the FIJI `Scripts` folder, in
|To Do: get path|
- Copy the `Analyze` folder from MMT into the FIJI `Scripts` folder.
- 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.
- (Re)Launch FIJI.
- 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.
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.