Alternatives and similar repositories for histoCAT

Users that are interested in histoCAT are comparing it to the libraries listed below

• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆92Updated last week
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆96Updated last year
• nolanlab / CODEX
  Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation
  ☆47Updated 3 years ago
• nf-core / imcyto
  Image Mass Cytometry analysis pipeline
  ☆26Updated last month
• ElementoLab / utag
  ☆36Updated last year
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆91Updated 3 months ago
• nolanlab / SpatialScore
  R script for calculating the SpatialScore as described in our manuscript: "Immune cell topography predicts response to PD-1 blockade in c…
  ☆14Updated 3 years ago
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆38Updated 2 years ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆81Updated last year
• BodenmillerGroup / cytomapper
  R package for visualization of highly multiplexed imaging data
  ☆32Updated last month
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆64Updated 8 months ago
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆35Updated last year
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆53Updated 2 weeks ago
• TheJacksonLaboratory / STQ
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
  ☆20Updated 2 months ago
• BodenmillerGroup / readimc
  Python package for reading imaging mass cytometry (IMC) files
  ☆15Updated this week
• nolanlab / TissueSchematics
  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"
  ☆10Updated 2 years ago
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆133Updated 4 months ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆43Updated 11 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆80Updated 3 weeks ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆27Updated 9 months ago
• wollmanlab / JSTA
  ☆14Updated 3 years ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆61Updated 2 weeks ago
• akoyabio / phenoptr
  Helper functions for working with inForm data.
  ☆18Updated 3 years ago
• scverse / spatialdata-io
  ☆63Updated last week
• qupath / qupath-extension-stardist
  QuPath extension to run StarDist nucleus detection
  ☆41Updated last week
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆23Updated 11 months ago
• AllenInstitute / cell_type_mapper
  Repository for storing prototype functionality implementations for the BKP
  ☆29Updated last week
• HiDiHlabs / ssam
  ☆27Updated 9 months ago
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆63Updated last week