PoreSpy
PoreSpy: A Python Toolkit for Quantitative Analysis of Porous Media Images - Published in JOSS (2019)
PlatiPy
PlatiPy: Processing Library and Analysis Toolkit for Medical Imaging in Python - Published in JOSS (2023)
Pylinac
Pylinac: Image analysis for routine quality assurance in radiotherapy - Published in JOSS (2023)
SCIMAP
SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data - Published in JOSS (2024)
KALMUS
KALMUS: tools for color analysis of films - Published in JOSS (2021)
Rainbow
Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow - Published in JOSS (2022)
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves.
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves. - Published in JOSS (2020)
imaging-server-kit
Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
itk
Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
cytodataframe
An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
frc
frc is a Python package for computing the Fourier Ring Correlation (FRC) of images using DIPlib
biomero
BIOMERO - A python library for easy connecting between OMERO (jobs) and a Slurm cluster
simpleitk
SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
napari-time-series-plotter
A napari Plugin for visualisaton of pixel values over time (t+ nD) as graphs.
pyelispotanalysis
Detecting spots (IFN-Gamma positive cells) from an Elispot assay image using Deep learning
clustimage
clustimage is a python package for unsupervised clustering of images.
itkwidgets
An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
https://github.com/cellprofiler/cellprofiler-analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
https://github.com/aryashah2k/image-processing-pattern-recognition
Repository for programme elective- Image Processing & Pattern Recognition (IPPR). Contains awesome study resources, references, tutorials and lab work, code files and projects.
https://github.com/cbica/captk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://github.com/capjamesg/cv-book-svg
Turn an image of a bookshelf into an interactive SVG.
https://github.com/centre-for-humanities-computing/artful-image-analysis
CHCAA's introductory workshop on image retrieval and computer vision
lsmquant
A pipeline for processing and analysis of light-sheet microscopy images.
cactool
An easy way to collaboratively code social media posts for manual content and discourse analysis
swelling_tablet_fronts_d_k_from_mri_t2_or_img
Tool for calculating swelling tablet eroding front's diffusion rate D and the rate of the swelling k from time series of either T2-maps or MRI images in FDF or Text Image format. (Python 3)
mri_k-space-derived_details_edges
k-space based details/edges detection in MRI images with optional k-space based denoising and detail control (on the example of Agilent FID data). (Python 3)
nematode-fecundity-computer-vision-counting
Automated C. elegans counting system using deep learning (YOLO models) for fecundity assays
https://github.com/clesperanto/clic
GPU-accelerated Image Processing library for C++
3DQLayers
3DQLayers: Volumetric Layer Based Analysis for Quantitative Renal MRI - Published in JOSS (2025)
https://github.com/bodenmillergroup/imcdataanalysis
R based workflow for multiplexed imaging data