bioimage-informatics

There are 21 repositories under bioimage-informatics topic.

  • CLAM

    mahmoodlab/CLAM

    Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

    Language:Python1.1k21250350

  • qupath/qupath

    QuPath - Bioimage analysis & digital pathology

    Language:Java1k57806278

  • DigitalSlideArchive/HistomicsTK

    A Python toolkit for pathology image analysis algorithms.

    Language:Python39022302117

  • mahmoodlab/CONCH

    A vision-language foundation model for computational pathology - Nature Medicine

    Language:Python24031819

  • mahmoodlab/TOAD

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

    Language:Python17051245

  • DigitalSlideArchive/digital_slide_archive

    The official deployment of the Digital Slide Archive and HistomicsTK.

    Language:Python108169049

  • mahmoodlab/SISH

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

    Language:Python954726

  • 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++4971113

  • ciccalab/SIMPLI

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

    Language:R34654

  • yu-lab-vt/SynQuant

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

    Language:Java14254

  • joda01/imagec

    imageC / EVAnalyzer2 - High throughput biological image processor

    Language:C++51221

  • kumeS/BioImageDbs

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

    Language:HTML2101

  • murphygroup/docker-cellorganizer

    CellOrganizer for Docker

    Language:Dockerfile24131

  • 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:Python1200

  • 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:Python111

  • Jeff-Gui/PCNAdeep

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

    Language:Python1100

  • albagranados/cellviewer

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

    Language:Python0000

  • murphygroup/docker-cellorganizer-jupyter-notebook

    CellOrganizer on Jupyter Notebook

    Language:Jupyter Notebook07401

  • murphygroup/singularity-cellorganizer

    :whale: Script to build a Singularity image for CellOrganizer

    Language:Shell05110

  • 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:Python21

  • junelsolis/DeepSlides

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

    Language:Python10