These scripts are mainly quality-of-life improvements for my workflow using the builtin ImageJ ROI manager to define volumetric ROIs (on movies with a Z dimension).

The main improvement is a script to overlay ROIs only in the Z-plane they are defined in, rather than the promiscuous Show All function in the ROI manager.

In the ROI Manager Options menu there is an option called Associate "Show All" ROIs with slices, but then it seems the overlays are specific to the combination of the time and Z-index, and I wanted to see the ROIs as I scrolled through the time axis of the movie.

Installation

git clone https://github.com/ejhonglab/imagej_macros

Linux (and maybe Mac?)

./imagej_macros/install.sh

The above command will make symbolic links to all the *.py files in this repo under the Fiji plugins folder. Restart Fiji.

Windows

Copy:

• all of the *.py files from this repo to Fiji.app/plugins
• install_macros.ijm to Fiji.app/macros/AutoRun
• startup_macros.ijm to Fiji.app/macros/toolsets/hong.ijm (renaming to hong.ijm)

Restart Fiji.

Hotkeys

Current hotkeys:

• [f1]: plot time profile of selected ROI

• [f2]: opens raw.tif and ROI manager ROIs in a RoiSet.zip from within selected directory

• [f3]: overlays ROIs with names, only drawing them in the planes they are defined in, for movies with a Z dimension

• [f4]: same as above, but without drawing ROI labels

• [f5]: clear overlay

• [f6]: close all time profile plots open

• [f8]: overlay odor information found in trial_frames_and_odors.json in the image directory

• r: update selected overlay ROI in ROI Manager / rename if points not changed

See startup_macros.fiji.ijm for a mostly complete list of my current hotkeys.

The corresponding scripts installed above should also be available towards the bottom of the Plugins menu (not under a sub-menu), though I generally run them through the installed hotkeys.