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.
- Locate your ImageJ dir
- Put the FISH_Join directory in the
plugins
directory of ImageJ - Put the fish_join_modules in the
jars/Lib
directory if ImageJ. Note: you may need to create theLib
directory underjars
. - Restart ImageJ
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