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scVIVA-Tools is a consolidated spatial transcriptomics analysis toolkit built on top of scvi-tools, exposing scVIVA, ResolVI, DestVI, DiagVI, Harreman, gimVI, Stereoscope, and Tangram through one AnnData-first API.

Installation​

pip install scviva-tools

Optional extras:

pip install "scviva-tools[spatial]"    # SpatialData + squidpy integration
pip install "scviva-tools[rapids]"     # GPU-accelerated neighbor graphs (cuML/cuPy/cuGraph)
pip install "scviva-tools[tutorials]"  # jupyter, matplotlib, seaborn
pip install "scviva-tools[all]"        # everything above

Quick Start​

import scviva

# ResolVI: denoising and segmentation-error correction
scviva.ResolVI.setup_anndata(adata, layer="counts")
model = scviva.ResolVI(adata)
model.train()

adata.obsm["X_resolvi"] = model.get_latent_representation()

Swapping in scviva.SCVIVA for niche-aware differential expression, or scviva.DestVI for Visium deconvolution, follows the same setup → train → extract pattern.

Resources​