ybajaj-29 / stardist_cmd

Command-line based, automatic image analysis pipeline to evaluate the bactericidal efficacy of polymer surface coatings against E. coli.

Downloads:

1. Download Fiji (ImageJ) from: https://downloads.imagej.net/fiji/archive/20230710-2317/
   

   • Do not update beyond this version! You should be running v1.54f.
     
   • v1.54i (the 03/2024 update) is buggy and not yet fully headless compatible.
     
   • If you are having trouble downloading the older version, let me know and I will email you a zip file of the installation.

2. Download StarDist, following the instructions from this link exactly: https://imagej.net/plugins/stardist#installation

3. Check this link for more info on the plugin and what each parameter means: https://imagej.net/plugins/stardist#usage

Usage:

python StarDist_cmd.py "path\to\ImageJ.exe" "path\to\unprocessed\images"
"path\to\preprocessing\script" "path\to\preprocessed\images"
"model_folder_or_pretrained_name" "path\to\postprocessed\images" -v

Note: You may need to run the ImageJ executable differently depending on your system.
The current script is configured for win64. More information can be found at: https://imagej.net/scripting/headless