Alternatives and similar repositories for codex-pipeline:

Users that are interested in codex-pipeline are comparing it to the libraries listed below

• TissUUmaps / TissUUmaps
  TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…
  ☆53Updated 2 months ago
• labsyspharm / palom
  Piecewise alignment for layers of mosaics
  ☆24Updated last week
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆30Updated 2 months ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆43Updated 9 months ago
• KerenLab / CellSighter
  ☆32Updated last year
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆37Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆86Updated 3 weeks ago
• mahmoodlab / MAPS
  Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
  ☆53Updated last year
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆90Updated this week
• TheJacksonLaboratory / STQ
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
  ☆18Updated 2 months ago
• MarkZaidi / Universal-StarDist-for-QuPath
  Transfer trained StarDist models across imaging modalities
  ☆3Updated 7 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆60Updated 3 weeks ago
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆14Updated this week
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆35Updated 11 months ago
• chenhcs / SCS
  Sub-cellular spatial transcriptomics Cell Segmentation
  ☆63Updated last year
• qupath / qupath-extension-align
  QuPath extension to interactively align images
  ☆23Updated last week
• huangch / qust
  QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis
  ☆22Updated 4 months ago
• nolanlab / TissueSchematics
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
  ☆10Updated 2 years ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆129Updated last month
• SchapiroLabor / histoCAT
  Histology Topography Cytometry Analysis Toolbox
  ☆67Updated last year
• fish-quant / ComSeg
  comseg
  ☆19Updated 2 months ago
• michaellee1 / CellSeg
  ☆23Updated last year
• ElementoLab / utag
  ☆34Updated last year
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 10 months ago
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆93Updated last year
• nolanlab / REDSEA
  ☆17Updated last year
• qupath / qupath-extension-stardist
  QuPath extension to run StarDist nucleus detection
  ☆39Updated last week
• wanglab-broad / ClusterMap
  ClusterMap for multi-scale clustering analysis of spatial gene expression
  ☆45Updated 9 months ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆57Updated 5 months ago
• qupath / qupath-extension-instanseg
  The official QuPath extension for InstanSeg
  ☆16Updated this week