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ImageJ helper macros for calcium imaging timeseries
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ImageJ helper macros for calcium imaging timeseries

This repo contains some ImageJ macros for making a dF/F movie from an ImageJ timeseries array. Calculates the mean background image, F0 for the array then normalizes every frame Ft to F0 as: Ft - F0 / F0.

Works best if file extension is '.ijm' and saved in your ImageJ application folder under ImageJ/plugins/Macros/dFoFmovie.ijm or ImageJ/plugins/Macros/dFoFmovie-CatFullAutoSave.ijm so that it can be simply run as a plugin. Requires a lut named 'Jet' in your ImageJ/Fiji installation under Image --> Lookup Tables (though it can be changed manually in the macro file to any color mapping you'd like).

Learn more about the ImageJ macro language at

Also please see the many useful example macros that come with every ImageJ installation under ImageJ/macros. Just open these txt files in your text editor (Sublime Text, Atom, etc) and inspect what they do. These examples are invaluable for helping you learn to write your own macros. Also Fiji (ImageJ 'with batteries included') has an interactive interpreter for quick copy/paste/run of macro commands under Menu Plugins --> Scripting --> Macro Interpreter that is very useful while you trying to implement a routine.

  • TODO: Add optional gui dialog box prompt that allows user to enter a start and end frame for calculating the mean baseline image F0.
    • See ImageJ/macros/DialogDemo.ijm for dialog input examples
  • TODO: Consider merging and removing one of the existing functions (lots of redundancy right now)
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