flows

Flows for working with cell-scale agent-based models.

analyze_basic_metrics	Workflow for analyzing basic metrics.
analyze_cell_shapes	Workflow for analyzing cell shapes.
analyze_colony_dynamics	Workflow for analyzing colony dynamics.
calculate_coefficients	Workflow for calculating spherical harmonic coefficients.
calculate_image_properties	Workflow for calculating shape properties from existing images.
calculate_neighbors	Workflow for calculating neighbor connections.
calculate_positions	Workflow for calculating voxel positions.
calculate_properties	Workflow for calculating shape properties.
convert_arcade_format	Workflow for converting ARCADE simulations to other formats.
convert_physicell_format	Workflow for converting PhysiCell simulations to other formats.
demo	Demo workflow.
download_images	Workflow for downloading images from Quilt.
generate_voronoi_tessellation	Workflow for generating Voronoi tessellation images.
group_basic_metrics	Workflow for grouping basic metrics.
group_cell_shapes	Workflow for grouping cell shapes.
group_colony_dynamics	Workflow for grouping colony dynamics.
group_resource_usage	Workflow for grouping resource usage.
initialize_arcade_simulations	Workflow for initializing ARCADE simulations.
initialize_physicell_simulations	Workflow for initializing PhysiCell simulations.
make_simulation_movies	Workflow for making simulation movies.
organize_calculation_files	Workflow for organizing calculation files.
parse_arcade_simulations	Workflow for parsing ARCADE simulations into tidy data.
parse_physicell_simulations	Workflow for parsing PhysiCell simulations into tidy data.
plot_basic_metrics	Workflow for plotting basic metrics.
plot_cell_shapes	Workflow for plotting cell shapes.
plot_colony_dynamics	Workflow for plotting colony dynamics.
plot_resource_usage	Workflow for plotting resource usage.
process_sample	Workflow for processing image samples.
run_batch_simulations	Workflow for running containerized models using AWS Batch.
run_docker_simulations	Workflow for running containerized models using local Docker.
run_fargate_calculations	Workflow for running containerized calculations using Fargate.
sample_image	Workflow for sampling cell ids from an image.
summarize_manifest	Workflow for summarizing files in the manifest.