hkariti / fish_join

FISH Join - Join FISH nuclei and spots information

This ImageJ module combines the output of nuclei segmentors (e.g. QuPath) and spot detectors (like RS-FISH). It runs both plugins, then creates a table that lists each spot and its matching nucleus. Matching nuclei and spots can also be shown visually.

Installation

1. Locate your ImageJ dir
2. Put the FISH_Join directory in the plugins directory of ImageJ
3. Put the fish_join_modules in the jars/Lib directory if ImageJ. Note: you may need to create the Lib directory under jars.
4. Restart ImageJ

Usage

The following actions are provided:

• Detect nuclei and dots: Run segmentation and joining on all images matching the given glob pattern under the given directory, including sub directories.
• Highlight nuclei: Open an image with the requested nuclei marked using an overlay. The spots inside these nuclei can be put in the ROI.
• Show results for all files: Open the final results table that lists all nuclei and spots