https://github.com/qupath/qupath

QuPath - Open-source bioimage analysis for research

bioimage-analysis bioimage-informatics cell-analysis cell-segmentation computational-pathology digital-pathology groovy histology image-processing imagej javafx machine-learning opencv pathology tissue-microarray-analysis whole-slide-imaging

Last synced: 14 May 2025

https://github.com/stardist/stardist

StarDist - Object Detection with Star-convex Shapes

bioimage-analysis cell-segmentation deep-learning nuclei-segmentation object-detection python

Last synced: 21 Oct 2025

https://github.com/mahmoodlab/conch

Vision-Language Pathology Foundation Model - Nature Medicine

bioimage-analysis bioimage-informatics computational-pathology conch digital-pathology foundation-model health-informatics histopathology mahmoodlab medical-imaging nature-medicine nlp-machine-learning pathology quantitative-pathology vision-language-pathology

Last synced: 16 May 2025

https://github.com/mahmoodlab/CONCH

Vision-Language Pathology Foundation Model - Nature Medicine

bioimage-analysis bioimage-informatics computational-pathology conch digital-pathology foundation-model health-informatics histopathology mahmoodlab medical-imaging nature-medicine nlp-machine-learning pathology quantitative-pathology vision-language-pathology

Last synced: 06 May 2025

https://github.com/clesperanto/pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

bioimage-analysis gpu-acceleration microscopy

Last synced: 21 Oct 2025

https://github.com/clEsperanto/pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

bioimage-analysis gpu-acceleration microscopy

Last synced: 21 Mar 2025

https://github.com/mahmoodlab/TOAD

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

bioimage-analysis bioimage-informatics cancer-detection cancer-imaging-research cancer-research cup deep deep-learning histology histopathology mahmoodlab pathology toad unknown-primary wsi-images

Last synced: 09 May 2026

https://github.com/mahmoodlab/toad

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

bioimage-analysis bioimage-informatics cancer-detection cancer-imaging-research cancer-research cup deep deep-learning histology histopathology mahmoodlab pathology toad unknown-primary wsi-images

Last synced: 09 Jan 2026

https://github.com/kreshuklab/plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

bioimage-analysis bioinformatics deep-learning image-segmentation neural-network segmentation unet

Last synced: 24 Dec 2025

https://github.com/mahmoodlab/sish

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

bioimage-analysis bioimage-informatics deep-learning fish histology histopathology image-retrieval image-search-engine mahmoodlab pathology vqvae wsi-images

Last synced: 17 Oct 2025

https://github.com/multi-template-matching/multitemplatematching-fiji

Fiji plugin for object(s) detection using template(s) matching

bioimage-analysis fiji jython object-detection object-recognition opencv template-matching

Last synced: 09 Apr 2025

https://github.com/bioimage-io/core-bioimage-io-python

Python libraries for loading, running and packaging bioimage.io models

bioimage-analysis bioimage-infomatics bioimaging deep-learning

Last synced: 12 Dec 2025

https://github.com/4DNucleome/PartSeg

Tool for segmentation in bioimaging

bioimage-analysis napari

Last synced: 07 May 2025

https://github.com/haesleinhuepf/human-eval-bia

Benchmarking Large Language Models for Bio-Image Analysis Code Generation

benchmarking bioimage-analysis llm python

Last synced: 30 Apr 2025

https://github.com/kreshuklab/go-nuclear

Guides and code for 3D nuclear instance segmentation

bioimage-analysis instance-segmentation

Last synced: 14 Dec 2025

https://github.com/sanderslab/magellanmapper

MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification

3d-reconstruction atlas bioimage-analysis cell-detection gui image-processing image-registration microscopy-image-analysis python

Last synced: 14 Jan 2026

https://github.com/joda01/imagec

imageC / EVAnalyzer2 - High throughput biological image processor

bioimage-analysis bioimage-informatics biology cell-segmentation evanalyzer image-processing opencv science

Last synced: 01 Feb 2026

https://github.com/psobolewskiphd/napari_scripts

Collection of useful (to me) python scripts for interacting with napari

bioimage-analysis napari python

Last synced: 16 Sep 2025

https://github.com/miura/yodosha-biasbook2025

『型で実践する生物画像解析　ImageJ・Python・napari』サポートサイト

bioimage-analysis fiji imagej japanese-language napari

Last synced: 22 Nov 2025

https://github.com/jhnnsrs/faser

A python based toolkit for psf estimation using a vectorial model of the electromagnetic field

bioimage-analysis napari-plugin psf vectorial-model

Last synced: 14 Oct 2025

https://github.com/fabriziomusacchio/napari_bioimage_analysis

Image data and Python scripts for the course on Bioimage analysis with Napari

bioimage-analysis image-analysis image-processing napari neuroscience neuroscience-data sample-images

Last synced: 11 Oct 2025

https://github.com/carpentries-incubator/bioimage-analysis-python

Bioimage Analysis with Python

bioimage-analysis carpentries-incubator english lesson napari-visualization pre-alpha python scikit-image

Last synced: 10 Apr 2025

https://github.com/montpellierressourcesimagerie/image-analysis-notebooks

bioimage-analysis image-analysis imagej jupyter-notebook python

Last synced: 17 May 2026

https://github.com/uw-loci/qupath-extension-image-export-toolkit

QuIET - QuPath Image Export Toolkit: batch export images for ML training and analysis

bioimage-analysis image-export machine-learning microscopy publication-figures quarep-limi qupath qupath-extension

Last synced: 02 May 2026

https://github.com/danilexn/camos

CaMOS, a GUI for analysis of multimodal neuroscience datasets.

bioimage-analysis biology gui neuroscience

Last synced: 26 May 2026

https://github.com/josegcpa/wbs-prediction

Code repository for project focusing on blood cell detection and diagnostic prediction from peripheral blood slides

bioimage-analysis deep-learning image-analysis machine-learning morphometrics

Last synced: 05 Mar 2026

https://github.com/alphonsg/bimana

Package for performing automated bio-image analysis tasks.

bioimage-analysis bioinformatics data-analysis deep-learning edge-detection image-analysis image-processing

Last synced: 10 Jul 2026

https://github.com/fabriziomusacchio/zarr_tests

Python code that I used in my blog posts on the Zarr file format.

bioimage-analysis bioimaging microscopy-data microscopy-images ome ome-zarr omero python zarr

Last synced: 17 May 2026

https://github.com/vinit-source/csl7382-medical-image-clustering-assignment.py

The IPython notebook contains the questions as well as the related code. Only numpy has been used.

bioimage-analysis kmeans-clustering numpy slic spectral-clustering

Last synced: 22 May 2026

https://github.com/oftatkofta/oftatkofta.github.io

Landing page for my consulting compant

bioimage-analysis consulting deep-learning experimental-design microscopy procurement

Last synced: 10 Mar 2026