Alternatives and similar repositories for SpatialData:

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

• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆17Updated last week
• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆25Updated 5 months ago
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆26Updated 6 months ago
• scverse / spatialdata-io
  ☆52Updated 2 weeks ago
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆51Updated this week
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆42Updated this week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆23Updated last week
• scverse / spatialdata-plot
  Static plotting for spatialdata
  ☆49Updated this week
• miti-consortium / MITI
  Minimum Information about Tissue Imaging
  ☆20Updated last year
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆26Updated 2 weeks ago
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆19Updated 7 months ago
• dcjones / proseg
  Probabilistic cell segmentation for in situ spatial transcriptomics
  ☆66Updated this week
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆15Updated 2 months ago
• rockdeme / chrysalis
  Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.
  ☆16Updated 4 months ago
• vitessce / vitessce-python
  Python API and Jupyter widget for Vitessce
  ☆44Updated last month
• HiDiHlabs / ssam
  ☆27Updated 5 months ago
• schienstockd / cecelia
  Framework for image and flow cytometry analysis
  ☆24Updated this week
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 5 months ago
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆35Updated 3 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆28Updated last month
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated 10 months ago
• EliHei2 / segger_dev
  a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…
  ☆48Updated last week
• acycliq / pciSeq
  A probabilistic cell typing algorithm for spatial transcriptomics.
  ☆23Updated this week
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated 11 months ago
• giovp / spatialdata-sandbox
  ☆12Updated this week
• VasylVaskivskyi / microaligner
  Image registration (alignment) software for large microscopy images
  ☆24Updated 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