REQUIREMENTS:

OrganoID was run with the following software configuration:

• Windows 10 64-bit
• Python 3.8

The compiled executable can be downloaded here.

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SOURCE CODE INSTALLATION:

To set up OrganoID source dependencies, you could set up a venv environment first via

pip install virtualenv virtualenv OrganoIDVenv cd OrganoIDVenv/Scripts/ activate.bat

Then, you could run one of the following commands in your Python environment, depending on your use case.

OrganoID standard:

pip install -r [\path\to\OrganoID]requirements.txt

OrganoID with support for reproducing figures and statistics from publication:

pip install -r [\path\to\OrganoID]requirementsFiguresAndData.txt

OrganoID with support for model training and data augmentation:

pip install -r [\path\to\OrganoID]requirementsTrainingSuite.txt

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INSTRUCTIONS:

OrganoID is currently only available as a command line tool. To see instructions for use, run:

python OrganoID.py -h

A PySide6 graphical interface for OrganoID and an ImageJ plugin are in development with expected release mid-2022.