README.md

Abstract:

physicell data loader (pcdl) provides a platform-independent (Windows, MacOSX, Linux), python3 based, pip-installable set of commands, to load output, generated with the PhysiCell agent-based modeling and diffusion solver framework, into python3 or transform PhysiCell output into more widely used data formats, straight on the command line.

Software Specification:

• Language: python >= 3.11
• Library core dependencies: matplotlib, numpy, pandas, scipy
• Library optional dependencies: anndata, bioio, geopandas, networkx, neuroglancer, requests, scikit-image, shapely, simulariumio, spatialdata, vtk
• Date of origin original PhysiCell-Tools python-loader: 2019-09-02
• Date of origin pcdl fork: 2022-08-30
• Doi: https://doi.org/10.5281/ZENODO.8176399
• License: BSD-3-Clause
• User manual: this README.md file
• Source code: https://github.com/elmbeech/physicelldataloader

✨ HowTo Guide:

• installation and troubleshooting

✨ Tutorial:

Basics Tutorials:

1. pcdl background
2. pcdl processing mcds time steps in python3
3. pcdl processing mcds time series in python3
4. pcdl from the command line

Extras tutorials python3 language:

• pcdl and python3 and graphs
• pcdl and python3 and json
• pcdl and python3 and matplotlib
• pcdl and python3 and muspan
• pcdl and python3 and napari
• pcdl and python3 and ome.tiff, tiff, png, and jpeg
• pcdl and python3 and pandas
• pcdl and python3 and scanpy and squidpy
• pcdl and python3 and vtk

Extras tutorials for other languages than python3:

• pcdl and julia
• pcdl and matlab
• pcdl and R

Extras tutorials for GUI software:

• pcdl and paraview

• pcdl and blender

• pcdl and fiji imagej, icy, qupath

• pcdl and galaxy

• pcdl and napari

• pcdl and neuroglancer

• pcdl and simularium

✨ Reference Manual:

• API application interface

Discussion:

• presentations given

Cite:

@Misc{bucher2023,
  author    = {Bucher, Elmar and Wall, Patrick and Rocha, Heber and Kurtoglu, Furkan and Eng, Jennifer and Sundus, Aneequa, and Metzcar, John and Arroya, Raquel and Heiland, Randy and Macklin, Paul},
  title     = {elmbeech/physicelldataloader: pcdl platform-independent, pip-installable interface to load PhysiCell agent-based modeling framework output into python3.},
  year      = {2023},
  copyright = {Open Access},
  doi       = {10.5281/ZENODO.8176399},
  publisher = {Zenodo},
}

Contributions:

• original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin
• fork pcdl implementation: Elmar Bucher
• fork pcdl co-programmer: Furkan Kurtoglu, Heber Rocha, Jennifer Eng
• fork pcdl continuous testing and feedbacks: Aneequa Sundus (python), John Metzcar (python), Raquel Arroya (matlab)
• student prj on pcdl: Benjamin Jacobs (make_graph_gml), Jason Lu (render_neuroglancer), Katie Pletz (beta testing), Leena Sohail (beta testing), Marshal Gress (plot_scatter), Nick Oldfather (unit test model), Thierry-Pascal Fleurant (plot_timeseries), Viviana Kwong (render_neuroglancer)

Develoment:

• Road Map
• Release Notes

Developers, please make pull requests to the https://github.com/elmbeech/physicelldataloader/tree/development branch. Thanks!