{"id":19091962,"url":"https://github.com/allencellmodeling/workflow_colony_formation","last_synced_at":"2025-08-29T16:39:56.671Z","repository":{"id":91697898,"uuid":"249826663","full_name":"AllenCellModeling/workflow_colony_formation","owner":"AllenCellModeling","description":"Model of colony formation informed by timelapse video of replated cells.","archived":false,"fork":false,"pushed_at":"2020-05-27T00:17:21.000Z","size":7892,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-22T07:31:42.084Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter 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Notebook","readme":"# Workflow Colony Formation\n\n[![Build Status](https://github.com/AllenCellModeling/workflow_colony_formation/workflows/Build%20Master/badge.svg)](https://github.com/AllenCellModeling/workflow_colony_formation/actions)\n[![Code Coverage](https://codecov.io/gh/AllenCellModeling/workflow_colony_formation/branch/master/graph/badge.svg)](https://codecov.io/gh/AllenCellModeling/workflow_colony_formation)\n\nModel of colony formation informed by timelapse video of replated cells.\n\n---\n\n## Features\n\n- [ ] Load raw image from network storage\n- [ ] Segment and track raw file\n- [ ] Store segmentations in `exp_tracks`\n- [ ] Create set of starting conditions for runs based on first image frame\n- [ ] Store starting conditions on disk in `steps/sim_init`\n- [ ] Load starting conditions into model and run\n- [ ] Store model output in `steps/sim_tracks`\n- [ ] ...\n\n## Workflow\n\nThe steps and their dependencies or flow is described by the graph:\n\n![MTI-ABM Workflow](./docs/imgs/steps.svg)\n\n- [`null2mov`] copies the timelapse data from on-premises storage and uploads it to quilt\n- [`mov2img`] writes out readable frames from the complicated mosaic CZI\n- [`img2seg`] segments the DNA channel from each frame using [Cellpose](http://cellpose.org)\n- [`seg2cen`] takes the centroids of every segmented cell, does some post processing, and saves them as a simplified CSV\n- [`mod2cen`] takes the centroid inputs and runs a parameter sweep, outputting simulated centroid locations\n- [`cen2met`] computes summary metrics for the experimental and simulated traces\n- `met2rep` produces output images summarizing the computed metrics\n\n[`null2mov`]:https://github.com/AllenCellModeling/workflow_colony_formation/tree/master/workflow_colony_formation/steps/null2mov\n[`mov2img`]:https://github.com/AllenCellModeling/workflow_colony_formation/tree/master/workflow_colony_formation/steps/mov2img\n[`img2seg`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/img2seg/img2seg.ipynb\n[`seg2cen`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/seg2cen/seg2cen.ipynb\n[`mod2cen`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/mod2cen/mod2cen.ipynb\n[`cen2met`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/cen2met/cen2met.ipynb\n\n## Installation and running\n\nLocally clone and run: \n\n```\ngit clone https://github.com/AllenCellModeling/workflow_colony_formation.git\ncd workflow_colony_formation\n./run.py\n```\n\n## Documentation\n\nFor full package documentation please visit [AllenCellModeling.github.io/workflow_colony_formation](https://AllenCellModeling.github.io/workflow_colony_formation).\n\nAvailable under the Allen Institute Software License\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fworkflow_colony_formation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fallencellmodeling%2Fworkflow_colony_formation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fallencellmodeling%2Fworkflow_colony_formation/lists"}