GitHub topics: bioimage-informatics
qupath/qupath
QuPath - Open-source bioimage analysis for research
Language: Java - Size: 97.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1,149 - Forks: 298
DigitalSlideArchive/wsi-superpixel-guided-labeling
A user-interface used in conjunction with HistomicsUI to facilitate active learning on whole slide images
Language: Vue - Size: 17.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 3 - Forks: 6
mahmoodlab/CONCH
Vision-Language Pathology Foundation Model - Nature Medicine
Language: Python - Size: 1.22 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 355 - Forks: 28
mahmoodlab/CLAM
Open source tools for computational pathology - Nature BME
Language: Python - Size: 45.8 MB - Last synced at: 6 days ago - Pushed at: 27 days ago - Stars: 1,304 - Forks: 416
joda01/imagec
imageC / EVAnalyzer2 - High throughput biological image processor
Language: C++ - Size: 705 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 4 - Forks: 1
DigitalSlideArchive/HistomicsTK
A Python toolkit for pathology image analysis algorithms.
Language: Python - Size: 130 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 419 - Forks: 119
DigitalSlideArchive/digital_slide_archive
The official deployment of the Digital Slide Archive and HistomicsTK.
Language: Python - Size: 34.8 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 120 - Forks: 55
mahmoodlab/SISH
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
Language: Python - Size: 963 KB - Last synced at: 13 days ago - Pushed at: almost 2 years ago - Stars: 102 - Forks: 27
mahmoodlab/TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
Language: Python - Size: 2.79 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 172 - Forks: 49
arttumiettinen/pi2
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
Language: C++ - Size: 4.85 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 54 - Forks: 14
yu-lab-vt/SynQuant
A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.
Language: Java - Size: 21.7 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 14 - Forks: 4
Jeff-Gui/PCNAdeep
Track single-cells and profile the cell cycle with PCNA images.
Language: Python - Size: 74.5 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0
ghattab/cycasp
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.
Language: Python - Size: 49.8 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
murphygroup/singularity-cellorganizer
:whale: Script to build a Singularity image for CellOrganizer
Language: Shell - Size: 80.1 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
murphygroup/docker-cellorganizer
CellOrganizer for Docker
Language: Dockerfile - Size: 306 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1
ciccalab/SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
Language: R - Size: 45.2 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 26 - Forks: 4
ghattab/vicar
ViCAR extracts and employs (Vi)sual (C)ues for an (A)daptive (R)egistration of time-lapse image data recorded in microfluidic devices.
Language: Python - Size: 24.4 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
ghattab/seevis
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.
Language: Python - Size: 1.55 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
kumeS/BioImageDbs
Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub in Bioconductor)
Language: HTML - Size: 111 MB - Last synced at: 3 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1
junelsolis/DeepSlides Fork of cialab/DeepSlides
cialab/DeepSlides fork to make it work with newer Python libraries.
Language: Python - Size: 17 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
murphygroup/docker-cellorganizer-jupyter-notebook
CellOrganizer on Jupyter Notebook
Language: Jupyter Notebook - Size: 5.62 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1