https://github.com/allencellmodeling/workflow_colony_formation
Model of colony formation informed by timelapse video of replated cells.
https://github.com/allencellmodeling/workflow_colony_formation
Last synced: 4 months ago
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Model of colony formation informed by timelapse video of replated cells.
- Host: GitHub
- URL: https://github.com/allencellmodeling/workflow_colony_formation
- Owner: AllenCellModeling
- License: other
- Created: 2020-03-24T21:56:00.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2020-05-27T00:17:21.000Z (about 5 years ago)
- Last Synced: 2025-01-02T23:14:21.650Z (5 months ago)
- Language: Jupyter Notebook
- Size: 7.53 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: docs/contributing.rst
- License: LICENSE
Awesome Lists containing this project
README
# Workflow Colony Formation
[](https://github.com/AllenCellModeling/workflow_colony_formation/actions)
[](https://codecov.io/gh/AllenCellModeling/workflow_colony_formation)
Model of colony formation informed by timelapse video of replated cells.
---
## Features
- [ ] Load raw image from network storage
- [ ] Segment and track raw file
- [ ] Store segmentations in `exp_tracks`
- [ ] Create set of starting conditions for runs based on first image frame
- [ ] Store starting conditions on disk in `steps/sim_init`
- [ ] Load starting conditions into model and run
- [ ] Store model output in `steps/sim_tracks`
- [ ] ...
## Workflow
The steps and their dependencies or flow is described by the graph:
- [`null2mov`] copies the timelapse data from on-premises storage and uploads it to quilt
- [`mov2img`] writes out readable frames from the complicated mosaic CZI
- [`img2seg`] segments the DNA channel from each frame using [Cellpose](http://cellpose.org)
- [`seg2cen`] takes the centroids of every segmented cell, does some post processing, and saves them as a simplified CSV
- [`mod2cen`] takes the centroid inputs and runs a parameter sweep, outputting simulated centroid locations
- [`cen2met`] computes summary metrics for the experimental and simulated traces
- `met2rep` produces output images summarizing the computed metrics
[`null2mov`]:https://github.com/AllenCellModeling/workflow_colony_formation/tree/master/workflow_colony_formation/steps/null2mov
[`mov2img`]:https://github.com/AllenCellModeling/workflow_colony_formation/tree/master/workflow_colony_formation/steps/mov2img
[`img2seg`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/img2seg/img2seg.ipynb
[`seg2cen`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/seg2cen/seg2cen.ipynb
[`mod2cen`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/mod2cen/mod2cen.ipynb
[`cen2met`]:https://github.com/AllenCellModeling/workflow_colony_formation/blob/master/workflow_colony_formation/steps/cen2met/cen2met.ipynb
## Installation and running
Locally clone and run:
```
git clone https://github.com/AllenCellModeling/workflow_colony_formation.git
cd workflow_colony_formation
./run.py
```
## Documentation
For full package documentation please visit [AllenCellModeling.github.io/workflow_colony_formation](https://AllenCellModeling.github.io/workflow_colony_formation).
Available under the Allen Institute Software License