confluentfucci 1.0.2

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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