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Project description
ConfluentFUCCI
A suite of tools for analyzing large scale confluent FUCCI experiments
Overview
This repo includes an integartion and automation layer for running CellPose (person-in-the-loop ML driver cell segentation) and TrackMate (cell tracking). Furthermore, the repo includes a set ofanalysis and visualization tools for studying confluent cellular dynamics using a FUCCI stain.
Usage
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>
Pre-Commit Hooks
This project uses pre-commit to run linting and formatting tools before each commit. To install the pre-commit hooks, run pre-commit install
from the root of the project.
poetry run pre-commit install
To run the pre-commit hooks manually, run pre-commit run --all-files
from the root of the project.
poetry run pre-commit run --all-files
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
Project details
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