Alternatives and similar repositories for STIM:

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

• miti-consortium / MITI
  Minimum Information about Tissue Imaging
  ☆20Updated last year
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆27Updated 7 months ago
• scverse / spatialdata-notebooks
  ☆53Updated last week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆26Updated 7 months ago
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆23Updated last week
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• ciccalab / SIMPLI
  SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
  ☆37Updated last year
• giovp / spatialdata-sandbox
  ☆13Updated 2 weeks ago
• scverse / spatialdata-io
  ☆60Updated last week
• camlab-bioml / astir
  astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨
  ☆52Updated 11 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆30Updated 3 months ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆21Updated 9 months ago
• HiDiHlabs / ssam
  ☆28Updated 6 months ago
• TheJacksonLaboratory / STQ
  Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
  ☆18Updated 2 months ago
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆27Updated this week
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆26Updated this week
• ElementoLab / utag
  ☆35Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆36Updated 5 months ago
• YeoLab / bento-tools
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆77Updated last month
• emanuega / MERlin
  MERlin is an extensible analysis pipeline applied to decoding MERFISH data
  ☆35Updated 3 years ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆16Updated 3 weeks ago
• PreibischLab / RS-FISH
  Tool for precise, interactive, fast and scalable FISH spot detection
  ☆49Updated 3 months ago
• HelenaLC / SpatialData
  ☆17Updated 2 months ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆53Updated last week
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated last year
• 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
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆19Updated last week
• labsyspharm / scimap
  Spatial Single-Cell Analysis Toolkit
  ☆90Updated 2 weeks ago
• theislab / interactive_plotting
  ☆21Updated 4 years ago
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆17Updated 3 months ago