scverse · selmanozleyen · Dec 14, 2025 · Dec 16, 2025 · Dec 16, 2025 · Dec 18, 2025
diff --git a/README.md b/README.md
@@ -36,18 +36,16 @@ conda install -c conda-forge squidpy
 
 ### Interactive visualization
 
-To get optional dependencies required for the napari-based interactive plotting APIs, install the `interactive` extra:
-
-```console
-pip install 'squidpy[interactive]'
-```
+For interactive visualization with napari, please use [napari-spatialdata](https://github.com/scverse/napari-spatialdata).
+The original napari plugin from Squidpy has been deprecated and replaced by napari-spatialdata, which offers
+improved functionality and support for the SpatialData ecosystem.
 
 ## Key capabilities
 
 - Build and analyze spatial neighbor graphs directly from Visium, Slide-seq, Xenium, and other spatial omics assays.
 - Compute spatial statistics for cell types and genes, including neighborhood enrichment, co-occurrence, and Moran's I.
 - Efficiently store, featurize, and visualize high-resolution tissue microscopy images via [scikit-image](https://scikit-image.org/).
-- Explore annotated datasets interactively with [napari](https://napari.org/) and scverse visualization tooling.
+- Explore annotated datasets interactively with [napari-spatialdata](https://github.com/scverse/napari-spatialdata).
 
 ## Contributing
 

diff --git a/docs/index.md b/docs/index.md
@@ -44,7 +44,7 @@ Please see our manuscript [Palla, Spitzer et al. (2022)](https://doi.org/10.1038
 - Build and analyze the neighborhood graph from spatial coordinates
 - Compute spatial statistics for cell-types and genes
 - Efficiently store, analyze and visualize large tissue images, leveraging [scikit-image](https://scikit-image.org/)
-- Interactively explore [anndata](https://anndata.readthedocs.io/en/stable/) and large tissue images in [napari](https://napari.org/)
+- Interactively explore spatial data with [napari-spatialdata](https://github.com/scverse/napari-spatialdata)
 
 ## Getting started with Squidpy
 

diff --git a/docs/installation.md b/docs/installation.md
@@ -8,10 +8,6 @@ Install Squidpy by running::
 
     pip install squidpy
 
-Alternatively, to include all dependencies, such as the interactive image viewer {mod}`napari`, run::
-
-    pip install 'squidpy[interactive]'
-
 ## Conda
 
 Install Squidpy via Conda as::
@@ -23,3 +19,13 @@ Install Squidpy via Conda as::
 To install Squidpy from GitHub, run::
 
     pip install git+https://github.com/scverse/squidpy@main
+
+## Interactive visualization
+
+For interactive visualization with napari, please use [napari-spatialdata](https://github.com/scverse/napari-spatialdata).
+The original napari plugin from Squidpy has been deprecated and replaced by napari-spatialdata,
+which offers improved functionality and support for the SpatialData ecosystem.
+
+Install napari-spatialdata with::
+
+    pip install napari-spatialdata
diff --git a/docs/notebooks b/docs/notebooks
diff --git a/pyproject.toml b/pyproject.toml
@@ -219,8 +219,6 @@ lint.per-file-ignores.".scripts/ci/download_data.py" = [ "B", "D" ]
 lint.per-file-ignores."docs/*" = [ "B", "D" ]
 lint.per-file-ignores."src/squidpy/_constants/_constants.py" = [ "D101" ]
 lint.per-file-ignores."src/squidpy/_constants/_pkg_constants.py" = [ "D101", "D102", "D106" ]
-lint.per-file-ignores."src/squidpy/pl/_interactive/_widgets.py" = [ "D" ]
-lint.per-file-ignores."src/squidpy/pl/_interactive/interactive.py" = [ "E", "F" ]
 lint.per-file-ignores."src/squidpy/pl/_ligrec.py" = [ "B", "D" ]
 lint.per-file-ignores."tests/*" = [ "D" ]
 lint.unfixable = [
@@ -244,7 +242,6 @@ python_files = "test_*.py"
 testpaths = [ "tests/" ]
 xfail_strict = true
 addopts = [
-  "--ignore=tests/plotting/test_interactive.py",
   "--ignore=docs",
 ]
 
@@ -255,7 +252,6 @@ source = [ "squidpy" ]
 omit = [
   "*/__init__.py",
   "*/_version.py",
-  "squidpy/pl/_interactive/*",
   "tox/*",
 ]
 

diff --git a/src/squidpy/im/_container.py b/src/squidpy/im/_container.py
@@ -7,7 +7,7 @@
 from itertools import chain
 from pathlib import Path
 from types import MappingProxyType
-from typing import TYPE_CHECKING, Any, Literal, TypeAlias, TypeVar
+from typing import TYPE_CHECKING, Any, Literal, TypeAlias
 
 import dask.array as da
 import matplotlib as mpl
@@ -51,7 +51,6 @@
 Arraylike_t: TypeAlias = NDArrayA | xr.DataArray
 InferDims_t: TypeAlias = Literal["default", "prefer_channels", "prefer_z"] | Sequence[str]
 Input_t: TypeAlias = Pathlike_t | Arraylike_t | Literal["ImageContainer"]
-Interactive = TypeVar("Interactive")  # cannot import because of cyclic dependencies
 _ERROR_NOTIMPLEMENTED_LIBID = f"It seems there are multiple `library_id` in `adata.uns[{Key.uns.spatial!r}]`.\n \
                                 Loading multiple images is not implemented (yet), please specify a `library_id`."
 

diff --git a/src/squidpy/pl/__init__.py b/src/squidpy/pl/__init__.py
@@ -9,8 +9,6 @@
     nhood_enrichment,
     ripley,
 )
-
-# from squidpy.pl._interactive import Interactive  # type: ignore[attr-defined] # deprecated
 from squidpy.pl._ligrec import ligrec
 from squidpy.pl._spatial import spatial_scatter, spatial_segment
 from squidpy.pl._utils import extract

diff --git a/src/squidpy/pl/_interactive/__init__.py b/src/squidpy/pl/_interactive/__init__.py
@@ -1,3 +1,13 @@
+"""Deprecated napari interactive visualization module.
+
+This module has been deprecated in favor of napari-spatialdata.
+Please see https://github.com/scverse/napari-spatialdata for the replacement.
+"""
+
 from __future__ import annotations
 
-# from squidpy.pl._interactive.interactive import Interactive
+raise ImportError(
+    "The squidpy napari plugin has been deprecated and removed. "
+    "Please use napari-spatialdata instead: "
+    "https://github.com/scverse/napari-spatialdata"
+)
+2 −4		README.rst
+1 −3		examples/image/compute_histogram_features.ipynb
+1 −3		examples/image/compute_summary_features.ipynb
+1 −3		examples/image/compute_texture_features.ipynb
+2 −2		tutorials/tutorial_image_container.ipynb
+3 −15		tutorials/tutorial_image_container_zstacks.ipynb
+2 −6		tutorials/tutorial_mibitof.ipynb