multiplexed-imaging

There are 18 repositories under multiplexed-imaging topic.

  • gustaveroussy/sopa

    Technology-invariant pipeline for spatial omics analysis (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / ...) that scales to millions of cells

    Language:Python13089915
  • ark-analysis

    angelolab/ark-analysis

    Integrated pipeline for multiplexed image analysis

    Language:Jupyter Notebook731056726

  • camlab-bioml/astir

    astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨

    Language:Python4962011

  • mahmoodlab/MAPS

    Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

    Language:Jupyter Notebook46349

  • calico/spatial_lda

    Probabilistic topic model for identifying cellular micro-environments.

    Language:Python2661412
  • HistoJS

    Mmasoud1/HistoJS

    HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

    Language:JavaScript18100

  • nf-core/mcmicro

    An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

    Language:Nextflow81462815

  • JoshuaHess12/miaaim-python

    MIAAIM: Multi-omics Image Alignment and Analysis by Information Manifolds

    Language:Jupyter Notebook5201

  • AlanRace/imc-rs

    Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.

    Language:Rust1200

  • JoshuaHess12/hdi-prep

    High-dimensional image preparation module for MIAAIM

    Language:Python12140

  • KoellenspergerLab/MeXpose

    A workflow designed to perform multiplexed image analysis, specialising in (but not limited to) analysis of metal distribution in LA-ICP-TOFMS data.

    Language:Python1100

  • jaiprakash1824/SpatialVisVR

    SpatialVisVR is a VR platform tailored for advanced visualization and analysis of medical images in immuno-oncology. It allows real-time capture and comparison of mIF and mIHC images via mobile devices. Leveraging deep learning, it matches and displays similar images, supporting up to 100 protein channels.

    Language:Python0201

  • JoshuaHess12/hdi-reg

    High-dimensional image registration workflow as part of the MIAAIM framework. Hdi-reg is written in Python, and utilizes the Elastix library for computations.

    Language:Python0210

  • JoshuaHess12/hdi-utils

    General importing and utility functions for high-dimensional image data

    Language:Python0200

  • JoshuaHess12/miaaim

    Multi-omics image alignment and analysis by information manifolds (MIAAIM)

    Language:Nextflow0210

  • larry080201/RESTORE_norm

    Perform RESTORE normalization on multiplexed imaging data.

    Language:Python0100

  • marta-seq/PENGUIN

    Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

    Language:Jupyter Notebook0101

  • deMirandaLab/PENGUIN

    Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

    Language:Jupyter Notebook00