View source for 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.

== Software ==
* 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. 

== Installation ==
# 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
## FIJI.app/etc. {{todo|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. 

{{todo|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 {{todo|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. 

== References ==
* 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.