README.md

ImageJ Macros

A collection of random ImageJ/FIJI macros I use at the lab for analysis of microscopy images.

How to use

1. Click on the ImageJ/FIJI script (".ijm" file) you want to download.
2. Click on "Raw"
3. Save page as .ijm file
4. Drag and drop the ijm file onto FIJI (or install macro in ImageJ)

How to cite

Please acknowledge these scripts if you use them in your publication (just cite the repository).

Macros currently listed (as of Jun 2023)

• Autosegment_coloc A script to segment and calculate colocalization in multichannel images.
• DoG Filter A simple Difference-of-gaussians filter for fluorescence images.
• Draw_Trajectory Draws a trajectory of a single molecule on top of its video file based on coordinates previously calculated in TrackMate.
• Puncta_Quant A script to quantify lysosomal puncta (Legacy Version).
• Puncta_Quant_MultiSlice A script to quantify colocalization and number, size and fluorescence intensity of lysosomal puncta in a cell-defined ROI (uses predefined slices within z-stacks).
• Lesion_Profiler A script to draw and quantify linear profiles according to a circular-ish ROI (e.g. a lesion, a tumour).
• Organoids_analyzer A script to segment brightfield images of brain organoids (or other objects) and obtain the shape descriptors.