bioimage-informatics
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Open source tools for computational pathology - Nature BME
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Apr 14, 2025 - Python
QuPath - Open-source bioimage analysis for research
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Dec 11, 2025 - Java
A Python toolkit for pathology image analysis algorithms.
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Dec 15, 2025 - Python
Vision-Language Pathology Foundation Model - Nature Medicine
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Mar 26, 2025 - Python
AI-based pathology predicts origins for cancers of unknown primary - Nature
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Nov 1, 2021 - Python
The official deployment of the Digital Slide Archive and HistomicsTK.
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Dec 17, 2025 - Python
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
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Jun 9, 2023 - Python
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
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Jun 25, 2025 - C++
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
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Sep 23, 2025 - R
A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.
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Aug 29, 2024 - Java
imageC / EVAnalyzer2 - High throughput biological image processor
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Dec 17, 2025 - C++
A user-interface used in conjunction with HistomicsUI to facilitate active learning on whole slide images
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Jun 20, 2025 - Vue
Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub in Bioconductor)
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Nov 23, 2021 - HTML
CellOrganizer for Docker
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Sep 13, 2019 - Dockerfile
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.
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Feb 5, 2019 - Python
ViCAR extracts and employs (Vi)sual (C)ues for an (A)daptive (R)egistration of time-lapse image data recorded in microfluidic devices.
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Feb 5, 2019 - Python
Track single-cells and profile the cell cycle with PCNA images.
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Jun 9, 2022 - Python
cialab/DeepSlides fork to make it work with newer Python libraries.
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Dec 12, 2021 - Python
🐳 Script to build a Singularity image for CellOrganizer
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Apr 21, 2020 - Shell
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.
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Feb 5, 2019 - Python
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