Alternatives and similar repositories for sopa

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

• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆108Updated last month
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆39Updated last year
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆95Updated 2 years ago
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆84Updated 3 weeks ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆135Updated 3 months ago
• yuqiyuqitan / SPACEc
  ☆59Updated 2 months ago
• SydneyBioX / BIDCell
  Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
  ☆46Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆150Updated 3 weeks ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆51Updated last week
• scverse / spatialdata
  An open and interoperable data framework for spatial omics data
  ☆348Updated this week
• angelolab / ark-analysis
  Integrated pipeline for multiplexed image analysis
  ☆102Updated last month
• fish-quant / ComSeg
  comseg
  ☆24Updated last year
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆35Updated last year
• BodenmillerGroup / napari-imc
  Imaging Mass Cytometry (IMC) file type support for napari
  ☆12Updated 2 years ago
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆73Updated 2 years ago
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆71Updated last year
• azizilab / starfysh
  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
  ☆128Updated 8 months ago
• BiomedicalMachineLearning / stLearn
  A novel machine learning pipeline to analyse spatial transcriptomics data
  ☆239Updated last month
• kharchenkolab / Baysor
  Bayesian Segmentation of Spatial Transcriptomics Data
  ☆202Updated last year
• BodenmillerGroup / ImcSegmentationPipeline
  A pixel classification based multiplexed image segmentation pipeline
  ☆106Updated 2 years ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆149Updated last month
• rajewsky-lab / openst
  Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
  ☆110Updated 7 months ago
• BodenmillerGroup / steinbock
  A toolkit for processing multiplexed tissue images
  ☆67Updated 3 weeks ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆75Updated last year
• seqscope / ficture
  ☆44Updated 3 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Updated 2 months ago
• labsyspharm / mcmicro
  Multiple-choice microscopy pipeline
  ☆145Updated 2 weeks ago
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆105Updated this week
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆54Updated 3 years ago
• rendeirolab / LazySlide
  Accessible and interoperable whole slide image analysis
  ☆181Updated last week