Open source tools for computational pathology - Nature BME

QuPath - Open-source bioimage analysis for research

A Python toolkit for pathology image analysis algorithms.

Vision-Language Pathology Foundation Model - Nature Medicine

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

CellOrganizer for Docker

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

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.

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.

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.

cialab/DeepSlides fork to make it work with newer Python libraries.

🐳 Script to build a Singularity image for CellOrganizer