Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.1.0] (Unreleased)#

Added#

  • Initial release of spatialvi-tools

  • Core spatial VAE model (SpatialVAE) for spatial-aware dimensionality reduction

  • External model integrations:

    • AMICI: Cross-attention cell-cell interaction model

    • VIVS: Variable importance via variance statistics

    • Starfysh: Spatial deconvolution with histology

    • Harreman: Metabolic exchange via spatial correlation

    • Nolan: Self-supervised spatial niche detection (NicheExplorer)

    • Lambda: LLM-based cell type annotation

    • PPIInference: Prediction-powered statistical inference

    • SPARL: Spatial proteomics representation learning

  • scvi-tools integrations:

    • scVIVA: Cellular microenvironment modeling

    • ResolVI: Spatial denoising for cell-resolved data

    • DestVI: Spatial deconvolution

  • Comprehensive data utilities for spatial preprocessing

  • Spatial metrics and visualization functions

  • Comprehensive test suite with 295+ tests

Dependencies#

  • Requires Python >= 3.11

  • Requires scvi-tools >= 1.1.0

  • Requires PyTorch >= 2.0

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