diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b228bc43..413b1064 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,18 +7,18 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.7.1
+      rev: v1.8.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 23.11.0
+      rev: 24.1.1
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.4
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -56,7 +56,7 @@ repos:
           - id: blacken-docs
     - repo: https://github.com/astral-sh/ruff-pre-commit
       # Ruff version.
-      rev: v0.1.7
+      rev: v0.1.14
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]
diff --git a/src/squidpy/_constants/_constants.py b/src/squidpy/_constants/_constants.py
index 9c9f0f5d..2bdcbb6f 100644
--- a/src/squidpy/_constants/_constants.py
+++ b/src/squidpy/_constants/_constants.py
@@ -1,4 +1,5 @@
 """Constants that user deals with."""
+
 from enum import unique
 
 from squidpy._constants._utils import ModeEnum
diff --git a/src/squidpy/_constants/_pkg_constants.py b/src/squidpy/_constants/_pkg_constants.py
index 9540c8ce..5ef73ff6 100644
--- a/src/squidpy/_constants/_pkg_constants.py
+++ b/src/squidpy/_constants/_pkg_constants.py
@@ -1,4 +1,5 @@
 """Internal constants not exposed to the user."""
+
 from __future__ import annotations
 
 from typing import Any, Callable, Mapping, Optional, Sequence, Union
diff --git a/src/squidpy/_utils.py b/src/squidpy/_utils.py
index 0669c1f7..f1ad295a 100644
--- a/src/squidpy/_utils.py
+++ b/src/squidpy/_utils.py
@@ -1,4 +1,5 @@
 """Spatial tools general utility functions."""
+
 from __future__ import annotations
 
 import functools
diff --git a/src/squidpy/gr/__init__.py b/src/squidpy/gr/__init__.py
index 41449166..0a370f2e 100644
--- a/src/squidpy/gr/__init__.py
+++ b/src/squidpy/gr/__init__.py
@@ -1,4 +1,5 @@
 """The graph module."""
+
 from squidpy.gr._build import spatial_neighbors
 from squidpy.gr._ligrec import ligrec
 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment
diff --git a/src/squidpy/gr/_build.py b/src/squidpy/gr/_build.py
index 88f02aeb..46be0b88 100644
--- a/src/squidpy/gr/_build.py
+++ b/src/squidpy/gr/_build.py
@@ -1,4 +1,5 @@
 """Functions for building graphs from spatial coordinates."""
+
 from __future__ import annotations
 
 import warnings
diff --git a/src/squidpy/gr/_ligrec.py b/src/squidpy/gr/_ligrec.py
index 9007b962..d4a60448 100644
--- a/src/squidpy/gr/_ligrec.py
+++ b/src/squidpy/gr/_ligrec.py
@@ -1,4 +1,5 @@
 """Permutation test function as described in CellPhoneDB 2.0."""
+
 from __future__ import annotations
 
 from abc import ABC
diff --git a/src/squidpy/gr/_nhood.py b/src/squidpy/gr/_nhood.py
index 593c8309..a1e44519 100644
--- a/src/squidpy/gr/_nhood.py
+++ b/src/squidpy/gr/_nhood.py
@@ -1,4 +1,5 @@
 """Functions for neighborhood enrichment analysis (permutation test, centralities measures etc.)."""
+
 from __future__ import annotations
 
 from functools import partial
diff --git a/src/squidpy/gr/_ppatterns.py b/src/squidpy/gr/_ppatterns.py
index 868767d9..d23be9a0 100644
--- a/src/squidpy/gr/_ppatterns.py
+++ b/src/squidpy/gr/_ppatterns.py
@@ -1,4 +1,5 @@
 """Functions for point patterns spatial statistics."""
+
 from __future__ import annotations
 
 from itertools import chain
diff --git a/src/squidpy/gr/_ripley.py b/src/squidpy/gr/_ripley.py
index 73b79299..a26eaec1 100644
--- a/src/squidpy/gr/_ripley.py
+++ b/src/squidpy/gr/_ripley.py
@@ -1,4 +1,5 @@
 """Functions for point patterns spatial statistics."""
+
 from __future__ import annotations
 
 from typing import (
diff --git a/src/squidpy/gr/_utils.py b/src/squidpy/gr/_utils.py
index 53a9a5d1..745beaa0 100644
--- a/src/squidpy/gr/_utils.py
+++ b/src/squidpy/gr/_utils.py
@@ -1,4 +1,5 @@
 """Graph utilities."""
+
 from __future__ import annotations
 
 from contextlib import contextmanager
diff --git a/src/squidpy/im/__init__.py b/src/squidpy/im/__init__.py
index f834ae70..f400dba7 100644
--- a/src/squidpy/im/__init__.py
+++ b/src/squidpy/im/__init__.py
@@ -1,4 +1,5 @@
 """The image module."""
+
 from squidpy.im._container import ImageContainer
 from squidpy.im._feature import calculate_image_features
 from squidpy.im._process import process
diff --git a/src/squidpy/im/_feature_mixin.py b/src/squidpy/im/_feature_mixin.py
index 8bd922bf..40b3c086 100644
--- a/src/squidpy/im/_feature_mixin.py
+++ b/src/squidpy/im/_feature_mixin.py
@@ -74,18 +74,15 @@ def _get_channels(xr_img: NDArrayA | xr.DataArray, channels: Channel_t | None) -
 class HasGetItemProtocol(Protocol):
     """Protocol for FeatureMixin to have correct definition of ImageContainer."""
 
-    def __getitem__(self, key: str) -> xr.DataArray:
-        ...
+    def __getitem__(self, key: str) -> xr.DataArray: ...
 
     @property
     def data(self) -> xr.Dataset:  # noqa: D102
         ...
 
-    def _get_layer(self, layer: str | None) -> str:
-        ...
+    def _get_layer(self, layer: str | None) -> str: ...
 
-    def _get_library_id(self, library_id: str | None) -> str:
-        ...
+    def _get_library_id(self, library_id: str | None) -> str: ...
 
 
 class FeatureMixin:
diff --git a/src/squidpy/pl/__init__.py b/src/squidpy/pl/__init__.py
index a2660442..b1e39798 100644
--- a/src/squidpy/pl/__init__.py
+++ b/src/squidpy/pl/__init__.py
@@ -1,4 +1,5 @@
 """The plotting module."""
+
 from squidpy.pl._graph import (
     centrality_scores,
     co_occurrence,
diff --git a/src/squidpy/pl/_color_utils.py b/src/squidpy/pl/_color_utils.py
index d9390565..10987d01 100644
--- a/src/squidpy/pl/_color_utils.py
+++ b/src/squidpy/pl/_color_utils.py
@@ -1,4 +1,5 @@
 """Utils for plotting functions."""
+
 from __future__ import annotations
 
 from typing import Any, Mapping, Optional, Sequence, Union
diff --git a/src/squidpy/pl/_graph.py b/src/squidpy/pl/_graph.py
index 1b65b81c..afad656d 100644
--- a/src/squidpy/pl/_graph.py
+++ b/src/squidpy/pl/_graph.py
@@ -1,4 +1,5 @@
 """Plotting for graph functions."""
+
 from __future__ import annotations
 
 from pathlib import Path
diff --git a/src/squidpy/tl/__init__.py b/src/squidpy/tl/__init__.py
index 243e36f0..a7db3dcb 100644
--- a/src/squidpy/tl/__init__.py
+++ b/src/squidpy/tl/__init__.py
@@ -1,2 +1,3 @@
 """The design matrix module."""
+
 from squidpy.tl._var_by_distance import var_by_distance