multiplexed-imaging

There are 0 repository under multiplexed-imaging topic.

• gustaveroussy / sopa

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

  generalizationmemory-managementmultiplexed-imagingpipelinesnakemakespatial-omicsspatial-transcriptomicsspatialdata
  Language:Python 175
• ark-analysis

  angelolab / ark-analysis

  Integrated pipeline for multiplexed image analysis

  multiplexed-imagingpython
  Language:Jupyter Notebook 84

• camlab-bioml / astir

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

  imaging-mass-cytometrymachine-learningmultiplexed-imaging
  Language:Python 52

• mahmoodlab / MAPS

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

  cell-annotationmpifmultiplexed-imaging
  Language:Jupyter Notebook 50

• calico / spatial_lda

  Probabilistic topic model for identifying cellular micro-environments.

  cancer-imagingcancer-imaging-researchmultiplexed-imaging
  Language:Python 28
• HistoJS

  Mmasoud1 / HistoJS

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

  cell-cell-interactioncell-segmentationmibiscopemultiplexed-imagingmultiplexed-imaging-analysisome-tiffphenotypingproteomicsproteomics-data-analysissingle-cellwhole-slide-imagingdigital-slide-archiveimage-processingmultichannelspatial-biologyspatial-data-analysis
  Language:JavaScript 19

• nf-core / mcmicro

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

  nextflownf-corepipelineworkflowmicroscopymultiplexed-imagingspatialtmabioformatsome-tiffregistrationsegmentationstitchingimage-analysisimage-processingsingle-cell
  Language:Nextflow 13

• JoshuaHess12 / miaaim-python

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

  cobordism-learningcobordismmanifold-learningimage-processingimage-registrationmultiplexed-imagingmanifold-alignment
  Language:Jupyter Notebook 5

• deMirandaLab / PENGUIN

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

  denoising-imagesmass-cytometrymultiplexed-imagingmultiplexed-imaging-analysisspatial-analysisspatial-data-analysisspatial-proteomics
  Language:Jupyter Notebook 3

• deMirandaLab / PENGUIN_fork

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

  denoising-imagesmass-cytometrymultiplexed-imagingmultiplexed-imaging-analysisspatial-proteomics
  Language:Jupyter Notebook 3

• AlanRace / imc-rs

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

  imaging-mass-cytometryrustbioimagingmultiplexed-imaging
  Language:Rust 1

• JoshuaHess12 / hdi-prep

  High-dimensional image preparation module for MIAAIM

  image-processingmanifold-learningdimensionality-reductionmultiplexed-imaging
  Language:Python 1

• 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.

  clusteringmultiplexed-imagingquantificationsegmentation
  Language:Python 1

• 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.

  deep-learningdigital-pathologyimage-retrievalmultiplexed-imagingobject-detectionsimilarity-searchvirtual-realityvisualization
  Language:Python 0

• 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.

  image-registrationimage-processingmanifold-alignmentelastixmultiplexed-imaging
  Language:Python 0

• JoshuaHess12 / hdi-utils

  General importing and utility functions for high-dimensional image data

  image-processingmultiplexed-imaging
  Language:Python 0

• JoshuaHess12 / miaaim

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

  image-processingmultiplexed-imagingmanifold-learningmachine-learningimage-registrationmanifold-alignmentcobordism-learningcobordism
  Language:Nextflow 0

• larry080201 / RESTORE_norm

  Perform RESTORE normalization on multiplexed imaging data.

  multiplexed-imagingnormalizationtissue-microarray-analysisspatial-omics
  Language:Python 0

• marta-seq / PENGUIN

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

  denoising-imagesmass-cytometrymultiplexed-imagingspatial-proteomicsmultiplexed-imaging-analysis
  Language:Jupyter Notebook 0