Segmentation of mitotic spindles - MontpellierRessourcesImagerie/imagej_macros_and_scripts GitHub Wiki

User manual

Download the script as a .py file

Open an image where a unique spindle is visible on each frame. Multiple spindles can be bundled in an image if they are assembled as a time sequence.

Open it in ImageJ and adjust the settings in the code:

• _stained_channel: (default: 2) The channel in which your microtubules are stained. (start=1)
• _rolling_ball_radius: (default: 50) Same setting as in the Subtract background
• _min_size: (default: 90) Minimal area (in number of pixels) covered by an instance of spindle.

You can now run the script, it should provide you with a results table.

When you run the script, a prompt will show up asking you to chose a folder. You should either create a new folder or give the path of an empty one. An ROI will be exported for each frame showing what was segmented. You can edit each individual ROI and press [M] again to add the fixed measurement. You can use the "T" column of the results table, matching the frame index of each spindle to determine which one you can delete.