Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

Vision-Language Pathology Foundation Model - Nature Medicine

A Python toolkit for pathology image analysis algorithms.

AI-based pathology predicts origins for cancers of unknown primary - Nature

The official deployment of the Digital Slide Archive and HistomicsTK.

Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.

imageC / EVAnalyzer2 - High throughput biological image processor

A user-interface used in conjunction with HistomicsUI to facilitate active learning on whole slide images

Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub in Bioconductor)

CellOrganizer for Docker

SeeVIS is a (S)egmentation-fr(ee) (VIS)ualization pipeline for time-lapse image data. It comprises three steps: 1. preprocessing, 2. feature extraction, and 3. an extended version of the space time cube with three novel color mappings adapted to cell colony growth.

ViCAR extracts and employs (Vi)sual (C)ues for an (A)daptive (R)egistration of time-lapse image data recorded in microfluidic devices.

Track single-cells and profile the cell cycle with PCNA images.

:whale: Script to build a Singularity image for CellOrganizer

CellOrganizer on Jupyter Notebook

CYCASP is a methodology for investigating and understanding (C)olon(Y) growth and (C)ell (A)ttributes at the population level. It couples (SP)atiotemporal changes by relying on two novel data abstractions and a modular algorithm.

A Head-less Python Tool for Automated Cell Counting in Cropped Hemocytometer Frames

🐚 Build cross-platform applications with Conch C++, leveraging modern C++23 features for robust, flexible software across Windows, macOS, Linux, iOS, and Android.

Analysis of single molecule localization microscopy. 'pointpattern': statistical analysis. 'image': image processing+analysis+classification