Update README with logo and documentation (#61)

* update README with logo and documentation

* update documentation based on review

Author: jenna-tomkinson

README.md

@@ -1,3 +1,42 @@
-# coSMicQC
+<img height="200" src="https://raw.githubusercontent.com/WayScience/coSMicQC/main/logo/with-text-for-light-bg.png?raw=true">
 
-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)