Ecosystem

scVIVA-Tools consolidates eight spatial transcriptomics models and tools into one package. It is itself part of the scvi-tools ecosystem.

scVIVA​

Niche-aware representation learning that jointly models a cell's own expression and its microenvironment, disentangling cell-intrinsic from environment-driven variation.

ResolVI​

Corrects segmentation errors, background contamination, and cell-size bias in cellular-resolution spatial data (Xenium, MERFISH, CosMx).

DestVI​

Multi-resolution deconvolution of spot-based data (e.g., Visium) into continuous cell-type compositions.

DiagVI​

Diagonal integration of unpaired multi-modal single-cell data using prior cross-modal feature correspondences.

Harreman​

Infers spatially-resolved metabolic gene programs and cell-cell metabolic/ligand-receptor communication, optionally integrating DestVI, ResolVI, and scVIVA outputs.

gimVI​

Joint imputation of missing genes between paired scRNA-seq and spatial datasets.

Stereoscope​

A two-stage generative model for spot-based cell-type deconvolution.

Tangram​

Maps single cells onto spatial coordinates via optimal-transport-style alignment.