scverse · ori-kron-wis · Jul 9, 2026 · Jul 9, 2026 · Jul 9, 2026 · Jul 12, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,11 @@ to [Semantic Versioning]. The full commit history is available in the [commit lo
 
 #### Removed
 
+- Remove {class}`scvi.external.DestVI`, {class}`scvi.external.GimVI`, {class}`scvi.external.ResolVI`,
+    {class}`scvi.external.SCVIVA`, {class}`scvi.external.DiagVI`, {class}`scvi.external.Stereoscope`,
+    and {class}`scvi.external.Tangram` spatial models, along with their associated tutorials and
+    documentation, {pr}`3908`.
+
 ### 1.5.0 (2026-07-08)
 
 #### Added

diff --git a/docs/api/developer.md b/docs/api/developer.md
@@ -154,7 +154,6 @@ Existing module classes with respective generative and inference procedures.
    module.AutoZIVAE
    module.Classifier
    module.LDVAE
-   module.MRDeconv
    module.PEAKVAE
    module.MULTIVAE
    module.SCANVAE
@@ -178,25 +177,18 @@ Module classes in the external API with respective generative and inference proc
    :template: class_no_inherited.rst
    :nosignatures:
 
-   external.gimvi.JVAE
    external.cytovi.CytoVAE
    external.cellassign.CellAssignModule
    external.contrastivevi.ContrastiveDataSplitter
-   external.stereoscope.RNADeconv
-   external.stereoscope.SpatialDeconv
    external.scbasset.ScBassetModule
    external.contrastivevi.ContrastiveVAE
    external.velovi.VELOVAE
    external.mrvi.MRVAE
    external.methylvi.METHYLVAE
    external.methylvi.METHYLANVAE
    external.decipher.DecipherPyroModule
-   external.resolvi.RESOLVAE
    external.totalanvi.TOTALANVAE
-   external.scviva.nicheVAE
-   external.scviva.NicheLossOutput
    external.sysvi.SysVAE
-   external.diagvi.DIAGVAE
    external.drvi.DRVIModule
    external.JointEmbeddingVAE
 ```

diff --git a/docs/api/user.md b/docs/api/user.md
@@ -25,7 +25,6 @@ import scvi
 
    model.AUTOZI
    model.CondSCVI
-   model.DestVI
    model.LinearSCVI
    model.PEAKVI
    model.SCANVI
@@ -49,9 +48,6 @@ import scvi
 
    external.CellAssign
    external.CYTOVI
-   external.GIMVI
-   external.RNAStereoscope
-   external.SpatialStereoscope
    external.SOLO
    external.SCAR
    external.SCBASSET
@@ -63,13 +59,9 @@ import scvi
    external.METHYLANVI
    external.Decipher
    external.TOTALANVI
-   external.RESOLVI
    external.SysVI
-   external.SCVIVA
-   external.DIAGVI
    external.DRVI
    external.JointEmbeddingSCVI
-   external.Tangram
 ```
 
 ## Data loading

diff --git a/docs/installation.md b/docs/installation.md
@@ -90,7 +90,6 @@ It has many optional dependencies which expand its capabilities:
 - _parallel_ - for parallelization engine
 - _interpretability_ - for supervised models interpretability
 - _dataloaders_ - for custom dataloaders use
-- _diagvi_ - for DiagVI model (requires torch_geometric and geomloss)
 - _mlflow_ - for MLflow support
 - _tests_ - in order to be able to perform tests
 - _editing_ - for code editing

diff --git a/docs/tutorials/index.md b/docs/tutorials/index.md
@@ -19,7 +19,6 @@ index_atac
 index_cytometry
 index_scbs
 index_multimodal
-index_spatial
 index_hub
 index_use_cases
 index_custom_dl

diff --git a/docs/tutorials/index_multimodal.md b/docs/tutorials/index_multimodal.md
@@ -9,8 +9,6 @@ notebooks/multimodal/totalVI_reference_mapping
 notebooks/multimodal/cite_scrna_integration_w_totalVI
 notebooks/multimodal/MultiVI_tutorial
 notebooks/multimodal/totalanvi
-notebooks/multimodal/DiagVI_spatial_proteomics.ipynb
-notebooks/multimodal/DiagVI_spatial_transcriptomics.ipynb
 ```
 
 ```{customcard}
@@ -54,17 +52,3 @@ Go through the MultiVI workflow to perform joint analysis of paired and unpaired
 
 Use TotalANVI to perform semi-supervised analysis of CITE-seq data, leveraging partial cell type annotations for label prediction, protein imputation, and differential abundance
 ```
-
-```{customcard}
-:path: notebooks/multimodal/DiagVI_spatial_proteomics
-:tags: Analysis, Integration, Modality-imputation, Dimensionality-reduction
-
-Perform integration of spatial proteomics and single-cell transcriptomics data with DiagVI
-```
-
-```{customcard}
-:path: notebooks/multimodal/DiagVI_spatial_transcriptomics
-:tags: Analysis, Integration, Modality-imputation, Dimensionality-reduction
-
-Perform integration of spatial and single-cell transcriptomics data with DiagVI
-```
diff --git a/docs/tutorials/index_spatial.md b/docs/tutorials/index_spatial.md
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
@@ -149,42 +149,9 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In
    * - :doc:`/user_guide/models/multivi`
      - Integration of paired/unpaired multiome data, missing modality imputation, normalization of other cell- and sample-level confounding factors
      - :cite:p:`AshuachGabitto21`
-   * - :doc:`/user_guide/models/diagvi`
-     - Diagonal integration of unpaired multiome data, dimensionality reduction, cross-modality imputation, cell label transfer
-     - []
 
 ```
 
-## Spatial transcriptomics analysis
-
-```{eval-rst}
-.. list-table::
-   :widths: 15 100 25
-   :header-rows: 1
-
-   * - Model
-     - Tasks
-     - Reference
-   * - :doc:`/user_guide/models/destvi`
-     - Multi-resolution deconvolution, cell-type-specific gene expression imputation, comparative analysis
-     - :cite:p:`Lopez22`
-   * - :doc:`/user_guide/models/stereoscope`
-     - Deconvolution
-     - :cite:p:`Andersson20`
-   * - :doc:`/user_guide/models/gimvi`
-     - Imputation of missing spatial genes
-     - :cite:p:`Lopez19`
-   * - :doc:`/user_guide/models/tangram`
-     - Deconvolution, single cell spatial mapping
-     - :cite:p:`Biancalani21`
-   * - :doc:`/user_guide/models/resolvi`
-     - Generative model of single-cell resolved spatial transcriptomics
-     - :cite:p:`Ergen25`
-   * - :doc:`/user_guide/models/scviva`
-     - Representation of cells and their environments in spatial transcriptomics
-     - :cite:p:`Levy25`
-```
-
 ## General purpose analysis
 
 ```{eval-rst}