ConfluentFUCCI
A suite of tools for analyzing large scale confluent FUCCI experiments
ConfluentFUCCI has now been peer-reviewed and the publication is freely available here. To cite please use:
Goldstien L, Lavi Y, Atia L (2024) ConfluentFUCCI for fully-automated analysis of cell-cycle progression in a highly dense collective of migrating cells. PLoS ONE 19(6): e0305491. https://doi.org/10.1371/journal.pone.0305491
Overview
This repo includes an integration and automation layer for running CellPose (person-in-the-loop ML driven cell segentation) and TrackMate (cell tracking). Furthermore, a set of analysis and visualization tools for studying confluent cellular dynamics using a FUCCI stain are included.
For Users
The recommended way for trying out ConfluentFUCCI is to use our prebuilt conainer image:
docker run -it --rm \
-v /var/run/docker.sock:/var/run/docker.sock \
-p 8080:8080 \
-p 9876:9876 \
leogold/confluentfucci:latest
This will start a container that will serve ConfluentFUCCI on localhost:8080 and a virtual desktop on localhost:9876. The app served using the above command does not require a GPU, which significantly affects segmentation time. Too speed up segmentation by leveraging your CUDA compatible GPU, please use:
docker run -it --rm \
-v /var/run/docker.sock:/var/run/docker.sock \
-p 8080:8080 \
-p 9876:9876 \
--gpus all \
leogold/confluentfucci:latest
Using docker-compose
To simplify deployment, please check out our docker-compose.yaml. Placing this file in the same path as your data should allow you to test the app using:
docker compose up
If a CUDA compatible GPU is availble on your system, make sure to uncomment:
# deploy:
# resources:
# reservations:
# devices:
# - driver: nvidia
# count: 1
# capabilities: [ gpu ]
For Developers
This project is set up using poetry. To install the dependencies, run poetry install from the root of the project.
poetry install
To add a new dependency, run poetry add <dependency> from the root of the project.
poetry add <dependency>
Testing
This project uses pytest for testing. To run the tests, run pytest from the root of the project in the poetry shell.
poetry run pytest
There are sensible defaults for pytest setup in the pyproject.toml file. You can override these defaults by passing in command line arguments. For example, to run the tests with debug logging enabled, run pytest --log-cli-level=DEBUG from the root of the project.
poetry run pytest --log-cli-level=DEBUG
1 maintainer
Metadata
1 maintainer
Release files for confluentfucci 1.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| confluentfucci-1.1.1.tar.gz | 20.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| confluentfucci-1.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 40.9 kB
Release files / confluentfucci-1.1.1.tar.gz
| Download URL | confluentfucci-1.1.1.tar.gz |
|---|---|
| Size | 20.7 kB |
| Tags | Source |
|
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Release files / confluentfucci-1.1.1-py3-none-any.whl
| Download URL | confluentfucci-1.1.1-py3-none-any.whl |
|---|---|
| Size | 20.3 kB |
| Tags | Python 3 |
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