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Getting started

  • Installation
  • Quickstart

Guides

  • How-to guides
  • Tutorials
    • Basic

      • Intro to SpatialData
      • Transformations and coordinate systems
      • Spatial query/subsampling
      • Annotating regions of interest with napari
      • Use landmark annotations to align multiple -omics layers
    • Intermediate

      • Create SpatialData objects from scratch
      • Working with annotations in SpatialData
      • Filtering SpatialData elements with Table Queries
      • I. Use SpatialData with your data: the SpatialData object.
      • II. Use SpatialData with your data: SpatialElements and tables
      • Integrate/aggregate signals across spatial layers
      • Interchangeability between raster and vector representations
      • Squidpy integration
      • Deep learning example on image tiles
    • Technology-specific

      • Technology focus: 10x Genomics Visium
      • Technology focus: MIBI-TOF
      • Technology focus: MERFISH
      • Technology focus: Visium HD
      • Technology focus: Visium HD (SpaceRanger 4.0)
      • Technology focus: Xenium
      • Technology focus: SpaceM
    • Advanced

      • Implicit performance improvements when plotting raster data
      • Raster data and translations (technical topic)

Reference

  • API
    • SpatialData object
    • Input/Output
    • Operations
    • Transformations
    • Transformations utils
    • Datasets
    • Data Loaders
    • Models
    • Models utils
    • Testing utilities
    • Data formats (advanced)
  • Spatial omics datasets
  • Glossary
  • SpatialData specifications
  • Design document for SpatialData
  • Interoperability

Project

  • Changelog
  • Contributing guide
  • Citation
  • Bibliography
  • GitHub
  • Discourse
  • API
  • GitHub
  • Discourse
  • scverse.org
  • Core
  • AnnData
  • decoupler
  • MuData
  • Muon
  • Pertpy
  • rapids-singlecell
  • Scanpy
  • Scirpy
  • scvi-tools
  • SnapATAC2
  • SpatialData
  • Squidpy
  • Ecosystem
  • AESTETIK
  • AlphaPeptTools
  • AmbiDose
  • annbatch
  • anndata for R
  • anndataR
  • annsel
  • AnnZarro
  • ATLAS
  • benGRN
  • bento-tools
  • biolord
  • cell2location
  • Cell_BLAST
  • CellAnnotator
  • CellCharter
  • CellMapper
  • CellOracle
  • CellphoneDB
  • CellRank
  • cellxgene
  • Cirrocumulus
  • clone2vec
  • cuspa
  • dandelion
  • delnx
  • DOTools_py
  • DoubletDetection
  • DRVI
  • dvp-io
  • dynamo-release
  • epiScanpy
  • eschr
  • fava
  • flashdeconv
  • flowsom
  • GATAC
  • GPTBioInsightor
  • grassp
  • GRnnData
  • gssnng
  • harpy
  • hotspot
  • illico
  • infercnvpy
  • kompot
  • LazySlide
  • liana
  • mantispy
  • Marsilea
  • maxspin
  • moscot
  • Mowgli
  • Multivelo
  • ncountr
  • NicheNetPy
  • nichepca
  • novae
  • omicverse
  • Palantir
  • Panpipes
  • ParTIpy
  • PathML
  • pcdl
  • PEAKQC
  • pegasus
  • PILOT
  • popV
  • pycea
  • pychromVAR
  • pyCrossTalkeR
  • PyDESeq2
  • pyLemur
  • pySCENIC
  • pytximport
  • pyUCell
  • Rectangle
  • SC2Spa
  • SCALEX
  • scanpro
  • scATrans
  • scCellFie
  • scDataLoader
  • scFair
  • scFates
  • scGen
  • schist
  • scib
  • scib-metrics
  • scib-rapids
  • scmcp
  • scPRINT
  • scPRINT-2
  • scTriangulate
  • scVelo
  • scviva-tools
  • scxmatch
  • scXpand
  • scyan
  • sift-sc
  • sincei
  • Sobolev Alignment
  • sopa
  • spatial-eggplant
  • spatialdataR
  • spatialproteomics
  • spatiomic
  • STMiner
  • Symphonypy
  • tangram
  • TAU Community Detection
  • TreeData
  • vitessce
  • wsidata
  • zellkonverter

API#

  • SpatialData object
  • Input/Output
  • Operations
  • Transformations
  • Transformations utils
  • Datasets
  • Data Loaders
  • Models
  • Models utils
  • Testing utilities
  • Data formats (advanced)

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Raster data and translations (technical topic)

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SpatialData object

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