Alternatives and similar repositories for SpatialData

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

• klarman-cell-observatory / PowerAnalysisForSpatialOmics
  ☆27Updated 7 months ago
• scverse / spatialdata-io
  ☆62Updated this week
• saeyslab / harpy
  Single-cell spatial proteomics analysis that makes you happy!
  ☆28Updated this week
• Vizgen / vizgen-postprocessing
  The Vizgen Post-processing Tool (VPT) enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
  ☆27Updated 8 months ago
• camlab-bioml / starling
  Segmentation error aware clustering for multiplexed imaging
  ☆18Updated 4 months ago
• miti-consortium / MITI
  Minimum Information about Tissue Imaging
  ☆20Updated last year
• schienstockd / cecelia
  Framework for image and flow cytometry analysis
  ☆25Updated 2 weeks ago
• nf-core / mcmicro
  An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
  ☆15Updated last month
• giovp / spatialdata-sandbox
  ☆13Updated last month
• quentinblampey / spatialdata_xenium_explorer
  Interoperability between SpatialData and the Xenium Explorer
  ☆23Updated 10 months ago
• rockdeme / chrysalis
  Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.
  ☆17Updated 6 months ago
• labsyspharm / cylinter
  An Interactive Image Segmentation Filter for Multiplex Microscopy
  ☆30Updated 4 months ago
• saeyslab / napari-sparrow
  https://sparrow-pipeline.readthedocs.io/en/latest/
  ☆27Updated this week
• quadbio / cell-annotator
  Automatically annotate cell types, consistently across samples.
  ☆13Updated last month
• scverse / napari-spatialdata
  Interactive visualization of spatial omics data
  ☆58Updated this week
• sagar87 / spatialproteomics
  Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly mu…
  ☆27Updated this week
• MannLabs / scPortrait
  scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images
  ☆45Updated this week
• GuignardLab / napari-sc3D-viewer
  A plugin to visualise 3D spatial single cell omics
  ☆22Updated last year
• hubmapconsortium / spatial-transcriptomics-pipeline
  ☆29Updated last year
• scverse / spatialdata-plot
  Static plotting for spatialdata
  ☆58Updated this week
• 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
• estellad / SpatialExperimentIO
  Read in Xenium, CosMx, Vizgen, STARmap PLUS, seqFISH data as Spatial or SingleCell Experiment object.
  ☆11Updated last month
• HiDiHlabs / ssam
  ☆28Updated 7 months ago
• Feanor007 / MESA
  A python package for Multiomics and Ecological Spatial Analysis (MESA)
  ☆18Updated last month
• PreibischLab / STIM
  Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.
  ☆27Updated 3 months ago
• metaspace2020 / metaspace-converter
  Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
  ☆11Updated last year
• nf-core / molkart
  A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
  ☆12Updated last month
• scverse / conference-2024
  Slides and Notebooks for scverse 2024
  ☆17Updated 8 months ago
• haniffalab / webatlas-app
  An application to display spatial and single-cell experiment data. Built in React, on the Vitessce framework.
  ☆14Updated last year
• theislab / spapros
  Python package for Probe set selection for targeted spatial transcriptomics.
  ☆37Updated 6 months ago