Benchmarking cell segmentation in brain tissue

Structure of this repository

• src Function definitions
• scripts Scripts for metric calculations and segmentation algorithms
• notebooks Jupyter notebooks for development and analysis
• archive Symlink to raw MERSCOPE data on DSS
• data Symlink to processed data on DSS
• sbatch_utils Scripts for creating sbatch scripts for each method

Development

We are using ruff and the ruff pre-commit hook to check and format the code and docstrings

Installation

Install ruff and pre-commit in your environment and install the pre-commit hooks for ruff defined in .pre-commit-config.yml

pip install ruff
pip install pre-commit
pre-commit install
# (optional: run against all files & fix any errors that are in your current codebase)
pre-commit run --all-files

Basic usage

The ruff config is located in pyproject.toml. See the ruff documentation of rules for all possible rules that we can enable / disable. As we have installed the pre-commit hook, ruff formatting and liniting will run automatically for all changed files whenever you do git commit. If there are errors, you will get a detailled messaged of the offending code and the error. Fix the errors, add the changed file and try to commit again.

You can also manually run the ruff formatter and checker on all files with:

ruff format
ruff check --fix

or

pre-commit run --all-files

If necessary, you can also temporarily disable all pre-commit hooks when committing by using the --no-verify flag with git commit.