diff --git a/README.md b/README.md index 78d449d..e773fd4 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,42 @@ -# coSMicQC + -coSMicQC is a software tool for single-cell quality control of morphology datasets. +# Single cell Morphology Quality Control + +[![Build Status](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/WayScience/coSMicQC/actions/workflows/run-tests.yml?query=branch%3Amain) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/) +![PyPI - Version](https://img.shields.io/pypi/v/cosmicqc) + +> :stars: Navigate the cosmos of single-cell morphology with confidence — coSMicQC keeps your data on course! + +coSMicQC is a Python package to evaluate converted single-cell morphology outputs from CytoTable. + +It can be challenging to get "perfect" single-cell compartment segmentation across large high-throughput screens when performing object detection in CellProfiler (or similar software). +Technical artifacts can arise during segmentation, leading to issues such as under-segmentation, over-segmentation, or the erroneous segmentation of background noise, smudges, or bright artifacts. + +In single-cell analysis, intriguing phenotypes often emerge by examining morphological differences. +However, technical outliers in the data can obscure these biological insights, compromising the validity of the findings. + +By utilizing specific morphological features extracted with CellProfiler, particularly AreaShape features, you can identify technically incorrect segmentations. +These can then be labeled or removed before further preprocessing steps, such as those performed with pycytominer. + +## Installation + +Install coSMicQC from [PyPI](https://pypi.org/project/coSMicQC/) or from source: + +```shell +# install from pypi +pip install coSMicQC + +# install directly from source +pip install git+https://github.com/WayScience/coSMicQC.git +``` + +## Contributing, Development, and Testing + +Please see [CONTRIBUTING.md](CONTRIBUTING.md) for more details on contributions, development, and testing. +## References + +- [pycytominer](https://github.com/cytomining/pycytominer) +- [CellProfiler](https://github.com/CellProfiler/CellProfiler) +- [CytoTable](https://github.com/cytomining/CytoTable)