ASIDE: Fiji Startup Macros

A quick pro-tip to follow up on the last post.

I use the Bio-Formats plugins all the time, so I like to have the shortcut window open automatically whenever I open Fiji. To do this, make a text file containing the line:

run("Bio-Formats Plugins Shortcut Window");

Save this file (it can have any name as long as the extension is .ijm) to:


This macro will now get run every time Fiji starts and the Bio-Formats shortcut window will appear. You can add anything you like to the startup macro. Mine includes a few other things and looks like this:

run("Options...", "iterations=1 black count=1"); // set black background
run("Colors...", "foreground=white background=black selection=yellow"); // set colors
run("Appearance...", " "); // do not use Inverting LUT
run("Bio-Formats Plugins Shortcut Window");
run("Channels Tool...");

//run("ROI Manager...");
//run("Control Panel...");

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