diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index edd142a..2fca442 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,12 +7,12 @@ ci:
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.3.5'
+    rev: 'v0.6.3'
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/fsfe/reuse-tool
-    rev: v3.0.1
+    rev: v4.0.3
     hooks:
       - id: reuse
diff --git a/scripts/searchfirst.py b/scripts/searchfirst.py
index f5bb888..6ffe3c3 100644
--- a/scripts/searchfirst.py
+++ b/scripts/searchfirst.py
@@ -5,6 +5,7 @@
 """SearchFirst script to run a simple segmentation."""
 
 import typer
+
 from faim_wako_searchfirst.main import run
 
 
diff --git a/tests/test_cellpose.py b/tests/test_cellpose.py
index a8b6091..0efcc48 100644
--- a/tests/test_cellpose.py
+++ b/tests/test_cellpose.py
@@ -9,6 +9,7 @@
 from pathlib import Path
 
 import pytest
+
 from faim_wako_searchfirst.main import run
 
 
diff --git a/tests/test_filter.py b/tests/test_filter.py
index 2e77173..6f0f412 100644
--- a/tests/test_filter.py
+++ b/tests/test_filter.py
@@ -8,9 +8,10 @@
 
 import numpy as np
 import pytest
-from faim_wako_searchfirst.filter import border, dilate, feature
 from skimage.io import imread
 
+from faim_wako_searchfirst.filter import border, dilate, feature
+
 
 @pytest.fixture
 def _label_image():
diff --git a/tests/test_main.py b/tests/test_main.py
index 910c14d..4b99c33 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -11,11 +11,12 @@
 import numpy as np
 import pandas as pd
 import pytest
+from skimage.io import imread
+
 from faim_wako_searchfirst.filter import area, bounding_box, solidity
 from faim_wako_searchfirst.main import run
 from faim_wako_searchfirst.sample import centers, dense_grid, grid_overlap
 from faim_wako_searchfirst.segment import threshold
-from skimage.io import imread
 
 
 @pytest.fixture
diff --git a/tests/test_sample.py b/tests/test_sample.py
index 74cfd36..a4d9078 100644
--- a/tests/test_sample.py
+++ b/tests/test_sample.py
@@ -8,9 +8,10 @@
 
 import pandas as pd
 import pytest
-from faim_wako_searchfirst.sample import object_centered_grid, region_centered_grid
 from skimage.io import imread
 
+from faim_wako_searchfirst.sample import object_centered_grid, region_centered_grid
+
 
 @pytest.fixture
 def _label_image():