https://github.com/allencellmodeling/c6
Circular center-based cell colony creation and clustering
https://github.com/allencellmodeling/c6
Last synced: 4 months ago
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Circular center-based cell colony creation and clustering
- Host: GitHub
- URL: https://github.com/allencellmodeling/c6
- Owner: AllenCellModeling
- License: other
- Created: 2020-01-29T00:47:33.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-05-21T19:12:39.000Z (about 5 years ago)
- Last Synced: 2025-02-03T22:36:07.924Z (4 months ago)
- Language: Python
- Size: 6.12 MB
- Stars: 0
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# c6 (Circular Center-based Cell Colony Creation and Clustering) 
[](https://github.com/AllenCellModeling/c6/actions)
[](https://AllenCellModeling.github.io/c6)
[](https://codecov.io/gh/AllenCellModeling/c6)
C6 is a toy center-based model of the initial clustering that occurs as a cells aggregate after replating.
---
## Features
- [x] Represents cells as non-overlapping circles
- [x] Cells exclude each other
- [x] Cells sense each other with tunable strength and distances
- [x] Cells grow at tunable rates
- [x] Cells divide at tunable sizes
- [x] Cells' growth is contact inhibited
- [x] Runs are launched from stored initial conditions
- [x] Runs are selectable as deterministic or stochastic
- [x] Runs are logged to tidy data file
- [x] Run state is visualized
- [x] You can save run states out to pretty MP4s
- [ ] Summary statistics are available for probing run logs
- [ ] Easy run profiling
## Quick Start
```python
import c6
import numpy as np
import matplotlib.pyplot as plt
space = c6.Space()
cell_locs = 20*np.random.random((10,2))
cells = [c6.Cell(space, loc) for loc in cell_locs]
fig, ax = plt.subplots(1,1, figsize=(10,10))
ax.set(xlim=(-10, 20), ylim=(-10, 20))
animation = c6.plot.animate(fig, ax, space, 500)
animation.save('example.mp4', fps=20)
```
## Installation
Clone and install or `pip install git+https://github.com/AllenCellModeling/c6.git`
## Creating initial conditions and logging runs
Both initial conditions and run logs are stored as JSON in this form:
```json
{
"seed": 123,
"universal": {"sensing": 12.3,
"influence_max": 12,
"influence_decay": 0.3,
"adhesion": 0.5
},
"cells": [{"time": 0,
"id": [0, 1, ..., 100],
"loc": [[1, 2], [3, 4], ..., [0.5, 2]],
"radius": [0.3, 0.5, ..., 2.0]
}]
}
```
Any property that can be passed to `c6.Cell` as a parameter can be serialized either as a key/value pair in `'universal'`, in which case it applies to all cells at all time points, or to `"cells"`, in which case it is parsed on a per cell per time point basis. Starting conditions are this file, but with only the first entry in `"cells"` specified. The first entry in `"cells"` is always applied before later entries and so per-cell values that do not change (e.g. ids) can be set there.
## Documentation
For full package documentation please visit [AllenCellModeling.github.io/c6](https://AllenCellModeling.github.io/c6).
Available under the Allen Institute Software License