Jens' ImageJ Plugins

A set of ImageJ plugins developed by Jens Eriksson.

Most plugins are written in Jython and can be copied to your FIJI/ImageJ plugins folder.

Plugin Files

1. Collective_Migration_buddy.py: Analyzes collective cell migration with options for frame projection and time-lapse analysis of cell movement.

2. Flatfield_normalizer.py: Normalizes image flatfield by converting to float, normalizing based on maximum intensity, and converting back to 16-bit.

3. FRAP_analysis_JE.py: Performs Fluorescence Recovery After Photobleaching (FRAP) analysis with channel selection, automatic/manual post-bleach frame detection, and provides normalized FRAP curves and recovery parameters.

4. PML_buddy.py: A versatile plugin for tracking PML (Promyelocytic Leukemia) bodies and other dynamic cellular components in living cells. Features include:

   • Tracking PML body dynamics over time
   • Cropping around moving objects
   • Creating still "reference frames" around dynamic cell components
   • Analyzing various dynamic cellular structures

5. Migration_buddy.py: Analyzes migration of individual cells or cellular components, likely providing tools for tracking movement, measuring distances, and analyzing migration patterns or speeds.

Usage

1. Copy the desired .py files to your FIJI/ImageJ plugins folder.
2. Restart FIJI/ImageJ or refresh the plugins folder.
3. Access the plugins from the Plugins menu in FIJI/ImageJ.
4. Follow on-screen instructions in the dialog boxes that appear.

Installation

1. Ensure FIJI/ImageJ is installed on your system.
2. Locate your FIJI/ImageJ plugins folder (typically [FIJI/ImageJ installation directory]/plugins/).
3. Copy the .py files from this repository into the plugins folder.
4. Restart FIJI/ImageJ or use the "Refresh Menus" command to make the new plugins available.

Requirements

These plugins require FIJI/ImageJ with Python support. Ensure you have the necessary dependencies installed, such as the ij module and its components (WindowManager, IJ, ImagePlus, etc.).

TODO

• Implement proper documentation for each plugin
• Add example usage and sample results
• Create user guides for complex plugins