Alternatives and similar repositories for InSituPy

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

• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆106Updated last week
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆82Updated last month
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆19Updated last year
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆41Updated 10 months ago
• azizilab / amici
  Cross-attention-based cell-cell interaction inference from ST data.
  ☆15Updated this week
• yuqiyuqitan / SPACEc
  ☆58Updated last month
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆22Updated 9 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Updated last month
• broadinstitute / celldega
  Spatial omics analysis and visualization library
  ☆22Updated last week
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆48Updated 2 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆25Updated last year
• scverse / spatialdata-io
  ☆86Updated this week
• haniffalab / webatlas-pipeline
  A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
  ☆65Updated 6 months ago
• JEFworks-Lab / STalign
  Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping
  ☆93Updated 2 years ago
• HiDiHlabs / ssam
  ☆27Updated last year
• 10XGenomics / janesick_nature_comms_2023_companion
  Code companion to the publication "High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spat…
  ☆29Updated 2 years ago
• 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
• nolanlab / NeighborhoodCoordination
  Code accompanying our manuscript "Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive f…
  ☆70Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆147Updated last month
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆73Updated last year
• AI4SCR / ATHENA
  ☆35Updated this week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆49Updated this week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆33Updated 3 weeks ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆132Updated 2 months ago
• sggao / celllens
  CellLENS: Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data
  ☆34Updated 5 months ago
• p-gueguen / Spatial_transcriptomics_tools
  List of Spatial Transcriptomics related Tools organized per category
  ☆101Updated last week
• plevritis-lab / CELESTA
  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …
  ☆38Updated last year
• theislab / troutpy
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆24Updated this week
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆145Updated 3 weeks ago
• shuxiaoc / maxfuse
  ☆57Updated last year