SpindleLengthPlugin

This FIJI plugin tracks the spindle length of S.pombe cells dividing. It works on TIFF stacks. You can try it out on the files in the input folder in this repository.

Please note that to use this plugin, you'll need to have FIJI (obviously) and anaconda installed (to run Python). You can download these here:

https://imagej.net/Fiji/Downloads

https://www.anaconda.com/distribution/

Mac Installation Instructions

• Download a ZIP of the repository.

- Unpack the zip and open the folder. All of the files you will need for installation are in the "Installation" folder.

- In your file system, go to "Applications", right-click on "FIJI", select "Show package contents".

- enter the "plugins" folder and copy/paste or drag the .jar file from "Installation" folder here.

- copy/paste or drag the "Python" folder here in the "Show package contents" folder

- the FIJI "Show package contents" folder should look like this:

- restart FIJI and you should see "Spindle Length" in your "Plugins" menu.

To run:

• open your desired TIFF stack in FIJI (you can use one from the "input" folder of the repository if you like)
• select "Spindle Length" from the plugins menu
• follow the directions from the popup menus to choose where to save the output file and scale the image
• after the program is done running, the output file, called "lengths.csv" will be saved in the folder you chose.

Windows Installation Instructions

• Configure python executable For the plugin to work correctly, there's an additional step to take on Windows. You must be able to run Python scripts in the command prompt using the command "python", i.e. running "python test.py" will run the file. This site has instructions on how to do it: https://www.pythoncentral.io/add-python-to-path-python-is-not-recognized-as-an-internal-or-external-command/. You'll just need to add a new environment variable pointing to where the Python executable file is. I'd suggest you test this out with a test script; just run "python test.py" or whatever your file is called in the Windows command prompt to make sure that it runs.

• Download a ZIP of the repository.

• Open the folder. Click "SpindleLengthPlugin-master", then "SpindleLengthPlugin". All of the files you'll need are in the "Installation" folder.

• Right-click on the FIJI icon and select "open file location" to access the contents of FIJI.

• Drag (or copy/paste) the .jar file from the "Installation" folder of the download to the "plugins" folder of FIJI.

• Drag (or copy/paste) the "python" folder from "Installation" into "Fiji.app".

• Now, the "Fiji.app" folder should look like this:

• Restart FIJI and you should see "Spindle Length" in your "Plugins" menu.

To run:

• open your desired TIFF stack in FIJI (you can use one from the "input" folder of the repository if you like)
• select "Spindle Length" from the plugins menu
• follow the directions from the popup menus to choose where to save the output file and scale the image
• after the program is done running, the output file, called "lengths.csv" will be saved in the folder you chose.

Thank you for using the Spindle Length plugin!