phenotypic 0.7.0

An image processing framework created for Ex-FAB NSF BioFoundry that aims to streamline the development of image processing pipelines for images analysis of phenotypes.

PhenoTypic: A Python Framework for Bio-Image Analysis

A modular image processing framework developed at the NSF Ex-FAB BioFoundry.

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Documentation here

Overview

PhenoTypic provides a modular toolkit designed to simplify and accelerate the development of bio-image analysis pipelines. Its structured architecture allows researchers and developers to seamlessly integrate custom computer vision modules, avoiding the need to build entirely new packages from scratch. Additionally, PhenoTypic supports incorporating components from other existing image analysis tools into a cohesive, unified ecosystem.

Installation

Pip

pip install phenotypic

Note: may not always be the most up-to-date version

Manual Installation

git clone https://github.com/Wheeldon-Lab/PhenoTypic.git
cd PhenoTypic
pip install -e .

Dev Installation

git clone https://github.com/Wheeldon-Lab/PhenoTypic.git
cd PhenoTypic
pip install -e ".[dev]"

Acknowledgements

CellProfiler

PhenoTypic has drawn inspiration and foundational concepts from CellProfiler, an open-source software platform for bio-image analysis developed by the Broad Institute Imaging Platform. CellProfiler's modularity, pipeline-oriented design, and extensive documentation have significantly influenced the development approach and structure of PhenoTypic.

Reference:

• CellProfiler GitHub Repository
• CellProfiler Official Website