Workflow to convert a PhysiCell model's results (/output
) to a Simularium file that can be uploaded and viewed at https://simularium.allencell.org/viewer
You will need to pip install simulariumio[physicell]
(we assume you've already installed the Anaconda Python 3.x distribution).
Finally, from the directory of your model's output files:
python convert_to_simularium.py # you want to customize this script for your data
This will generate a Simularium file which you can upload from https://simularium.allencell.org/viewer