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Consolidated spatial transcriptomics analysis toolkit built on scvi-tools

scVIVA-Tools unifies scVIVA, ResolVI, DestVI, DiagVI, Harreman, gimVI, Stereoscope, and Tangram behind one AnnData-first API, built on scvi-tools.

pip install scviva-tools
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Eight spatial models, one package

scVIVA-Tools packages scVIVA, ResolVI, DestVI, DiagVI, Harreman, gimVI, Stereoscope, and Tangram — deconvolution, denoising, niche-aware differential expression, gene imputation, and cell-cell communication — behind a single, consistent API.

Unified AnnData-first API

Every model follows the same setup/train/extract pattern, so switching from deconvolution with DestVI to niche-aware modeling with scVIVA means changing the class name, not relearning an API.

One install, shared infrastructure

A single pip install scviva-tools replaces juggling separate packages, docs, and release cadences for each spatial method, with optional SpatialData/squidpy interop via the spatial extra.

GPU-accelerated where it counts

Neighbor-graph-heavy steps (e.g. ResolVI, scVIVA) can use GPU acceleration via the optional rapids extra (cuML/cuPy/cuGraph), so analyses scale with dataset size.