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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.
- Do not update beyond this version! You should be running v1.54f.
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Download StarDist, following the instructions from this link exactly: https://imagej.net/plugins/stardist#installation
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Check this link for more info on the plugin and what each parameter means: https://imagej.net/plugins/stardist#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