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spatialvi-tools

  • Installation
  • User Guide
    • Models
      • ResolVI
      • DestVI
      • scVIVA
    • Background
      • Variational Inference
      • Differential Expression
      • Spatial Transcriptomics Methods
    • Use Cases
      • Saving and Loading Models
      • Training Configuration
      • Downstream Analysis
  • API Reference
    • User API
      • spatialvi.model.SCVIVA
      • spatialvi.model.DestVI
      • spatialvi.model.ResolVI
      • spatialvi.model.GIMVI
      • spatialvi.external.RNAStereoscope
      • spatialvi.external.SpatialStereoscope
      • spatialvi.settings
    • Developer API
      • spatialvi.model.base.SpatialBaseModel
      • spatialvi.model.base.SpatialNeighborhoodMixin
      • spatialvi.model.base.SpatialDeconvolutionMixin
      • spatialvi.model.base.ResolVIPredictiveMixin
      • spatialvi.data.SpatialCoordsField
      • spatialvi.data.NeighborhoodGraphField
      • spatialvi.module.nicheVAE
      • spatialvi.module.JVAE
  • Developer Documentation
    • Contributing Code
    • Maintenance Guide
  • Tutorials
    • ResolVI to address noise and biases in spatial transcriptomics
    • Multi-resolution deconvolution of spatial transcriptomics
    • scVIVA for representing cells and their environment in spatial transcriptomics
    • Introduction to gimVI
    • Stereoscope applied to left ventricule data
    • Mapping human lymph node cell types to 10X Visium with Cell2location
    • Spatial mapping with Tangram
  • Frequently Asked Questions
  • References
  • Repository
  • Open issue

Index

_ | D | G | J | N | R | S

_

  • __init__() (spatialvi.data.NeighborhoodGraphField method)
    • (spatialvi.data.SpatialCoordsField method)
    • (spatialvi.external.RNAStereoscope method)
    • (spatialvi.external.SpatialStereoscope method)
    • (spatialvi.model.base.ResolVIPredictiveMixin method)
    • (spatialvi.model.base.SpatialBaseModel method)
    • (spatialvi.model.base.SpatialDeconvolutionMixin method)
    • (spatialvi.model.base.SpatialNeighborhoodMixin method)
    • (spatialvi.model.DestVI method)
    • (spatialvi.model.GIMVI method)
    • (spatialvi.model.ResolVI method)
    • (spatialvi.model.SCVIVA method)
    • (spatialvi.module.JVAE method)
    • (spatialvi.module.nicheVAE method)

D

  • DestVI (class in spatialvi.model)

G

  • GIMVI (class in spatialvi.model)

J

  • JVAE (class in spatialvi.module)

N

  • NeighborhoodGraphField (class in spatialvi.data)
  • nicheVAE (class in spatialvi.module)

R

  • ResolVI (class in spatialvi.model)
  • ResolVIPredictiveMixin (class in spatialvi.model.base)
  • RNAStereoscope (class in spatialvi.external)

S

  • SCVIVA (class in spatialvi.model)
  • settings (in module spatialvi)
  • SpatialBaseModel (class in spatialvi.model.base)
  • SpatialCoordsField (class in spatialvi.data)
  • SpatialDeconvolutionMixin (class in spatialvi.model.base)
  • SpatialNeighborhoodMixin (class in spatialvi.model.base)
  • SpatialStereoscope (class in spatialvi.external)

By Ori Kronfeld

© Copyright 2026, Ori Kronfeld..