allen-cell-animated / cell-abm-pipeline Goto Github PK

• add docstrings to analyze_cell_shapes flow
• add docstrings to analyze_colony_dynamics flow
• add docstrings to calculate_coefficients flow
• add docstrings to calculate_neighbors flow
• add docstrings to calculate_positions flow
• add docstrings to calculate_properties flow
• add docstrings to convert_arcade_format flow
• add docstrings to convert_physicell_format flow
• add docstrings to download_images flow
• add docstrings to generate_voronoi_tessellation flow
• add docstrings to group_basic_metrics flow
• add docstrings to group_cell_shapes flow
• add docstrings to group_colony_dynamics flow
• add docstrings to group_resource_usage flow
• add docstrings to initialize_arcade_simulations flow
• add docstrings to initialize_physicell_simulations flow
• add docstrings to organize_analysis_files flow
• add docstrings to parse_arcade_simulations flow
• add docstrings to parse_physicell_simulations flow
• add docstrings to plot_basic_metrics flow
• add docstrings to plot_cell_shapes flow
• add docstrings to plot_colony_dynamics flow
• add docstrings to plot_resource_usage flow
• add docstrings to process_sample flow
• add docstrings to run_batch_simulations flow
• add docstrings to run_docker_simulations flow
• add docstrings to run_fargate_calculations flow
• add docstrings to sample_image flow
• add docstrings to summarize_manifest flow

Use Case

It would be nice if PhysiCell outputs could be converted to 3D tiff files so that they can be run through the same analysis pipeline as AICS microscopy data and ARCADE outputs.

Acceptance Criteria

Users can generate 3D tiffs in the correct format to be input into experimental analysis pipelines.