phenotypic 0.9.2

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, focused on arrayed colony phenotyping on solid media.

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Overview

PhenoTypic provides a modular toolkit designed to simplify and accelerate the development of reusable bio-image analysis pipelines. PhenoTypic provides bio-image analysis tools built-in, but has a streamlined development method to integrate new tools.

Installation

uv (recommended)

To download the base package (recommended if running on a cluster)

uv add phenotypic

To download the base package plus prototyping environment (recommended for pipeline development)

uv add phenotypic --groups jupyter

Pip

pip install phenotypic

Note: may not always be the latest version. Install from repo when latest update is needed

Manual Installation (For latest updates)

git clone https://github.com/exfab/PhenoTypic.git
cd PhenoTypic
uv pip install -e .

Dev Installation

git clone https://github.com/exfab/PhenoTypic.git
cd PhenoTypic
uv sync --group dev

Optional Installation

To extract metadata from images, PhenoTypic uses the PyExifTool module. This requires an external software called ExifTool. You can install ExifTool here: https://exiftool.org/install.html. If you don't use it, some metadata from raw files may not be able to be imported. Read more here: https://pypi.org/project/PyExifTool/#pyexiftool-dependencies

Module Overview

Module	Description
phenotypic.analysis	Tools for downstream analysis of the data from phenotypic in various ways such as growth modeling or statistical filtering
phenotypic.correction	Different methods to improve the data quality of an image such as rotation to improve grid finding
phenotypic.data	Sample images to experiment your workflow with
phenotypic.detect	A suite of operations to automatically detect objects in your images
phenotypic.enhance	Preprocessing tools that alter a copy of your image and can improve the results of the detection algorithms
phenotypic.grid	Modules that rely on grid and object information to function
phenotypic.measure	The various measurements PhenoTypic is capable of extracting from objects
phenotypic.objedit	Different tools to edit the detected objects such as morphology, relabeling, joining, or removing
phenotypic.prefab	Various premade image processing pipelines that are in use at ExFAB

Sponsors

ExFAB NSF BioFoundry

National Science Foundation