diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 58656d15b..2339c6766 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,10 +15,22 @@ repos:
     hooks:
       - id: isort
         files: ^python/cucim/src/.*
-        args: ["--settings-path=python/cucim/setup.cfg"]
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+        args: ["--settings-path=python/cucim/pyproject.toml"]
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
     hooks:
-      - id: flake8
-        args: ["--config=python/cucim/setup.cfg"]
-        files: ^python/cucim/.*
+      - id: black
+        files: (python|legate)/.*
+        args: ["--config", "python/cucim/pyproject.toml"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.278
+    hooks:
+      - id: ruff
+        files: python/.*$
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        args: [--toml, python/cucim/pyproject.toml]
+        additional_dependencies:
+          - tomli
diff --git a/python/cucim/pyproject.toml b/python/cucim/pyproject.toml
index 8388c4f17..c5351f058 100644
--- a/python/cucim/pyproject.toml
+++ b/python/cucim/pyproject.toml
@@ -121,7 +121,7 @@ license-files = ["LICENSE"]
 # this is only to allow you to run codespell interactively
 # e.g. via
 #   codespell --toml python/cucim/pyproject.toml . -i 3 -w
-skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,LICENSE-3rdparty,jitify_testing"
+skip = "build*,dist,.cache,html,_build,_deps,3rdparty,_static,generated,latex,.git,*.ipynb,test_data/input/LICENSE-3rdparty,jitify_testing"
 # ignore-regex = ""
 ignore-words-list = "ans,coo,boun,bui,gool,hart,lond,nd,paeth,unser,wronly"
 quiet-level = 3
diff --git a/python/cucim/src/cucim/__init__.pyi b/python/cucim/src/cucim/__init__.pyi
index 63064a411..8c7b467f9 100644
--- a/python/cucim/src/cucim/__init__.pyi
+++ b/python/cucim/src/cucim/__init__.pyi
@@ -17,17 +17,19 @@ submodules = []
 
 try:
     import cupy
+
     _is_cupy_available = True
-    submodules += ['core', 'skimage']
+    submodules += ["core", "skimage"]
     del cupy
 except ImportError:
     pass
 
 try:
     from .clara import CuImage, __version__, cli  # noqa: F401
+
     _is_clara_available = True
-    submodules += ['clara']
+    submodules += ["clara"]
 except ImportError:
     __version__ = "23.12.00"
 
-__all__ = submodules + ['__version__', 'is_available']  # noqa: F822
+__all__ = submodules + ["__version__", "is_available"]  # noqa: F822
diff --git a/python/cucim/src/cucim/skimage/__init__.pyi b/python/cucim/src/cucim/skimage/__init__.pyi
index 5af4d4926..8b608db5b 100644
--- a/python/cucim/src/cucim/skimage/__init__.pyi
+++ b/python/cucim/src/cucim/skimage/__init__.pyi
@@ -1,19 +1,19 @@
 import lazy_loader as lazy  # noqa: F401
 
 submodules = [
-    'color',
-    'data',
-    'exposure',
-    'feature',
-    'filters',
-    'measure',
-    'metrics',
-    'morphology',
-    'registration',
-    'restoration',
-    'segmentation',
-    'transform',
-    'util',
+    "color",
+    "data",
+    "exposure",
+    "feature",
+    "filters",
+    "measure",
+    "metrics",
+    "morphology",
+    "registration",
+    "restoration",
+    "segmentation",
+    "transform",
+    "util",
 ]
 
 __all__ = submodules
diff --git a/python/cucim/src/cucim/skimage/data/__init__.pyi b/python/cucim/src/cucim/skimage/data/__init__.pyi
index 88deb1e76..990729a46 100644
--- a/python/cucim/src/cucim/skimage/data/__init__.pyi
+++ b/python/cucim/src/cucim/skimage/data/__init__.pyi
@@ -1,5 +1,5 @@
 __all__ = [
-    'binary_blobs',
+    "binary_blobs",
 ]
 
 from ._binary_blobs import binary_blobs
diff --git a/python/cucim/src/cucim/skimage/feature/tests/test_corner.py b/python/cucim/src/cucim/skimage/feature/tests/test_corner.py
index a95a281a1..3554aadb8 100644
--- a/python/cucim/src/cucim/skimage/feature/tests/test_corner.py
+++ b/python/cucim/src/cucim/skimage/feature/tests/test_corner.py
@@ -224,7 +224,7 @@ def test_hessian_matrix_3d_xy(use_gaussian_derivatives):
         hessian_matrix(
             img,
             sigma=0.1,
-            order="nonexistant",
+            order="nonexistent",
             use_gaussian_derivatives=use_gaussian_derivatives,
         )
 
diff --git a/python/cucim/src/cucim/skimage/filters/__init__.pyi b/python/cucim/src/cucim/skimage/filters/__init__.pyi
index 24a2b2e64..185f24eb3 100644
--- a/python/cucim/src/cucim/skimage/filters/__init__.pyi
+++ b/python/cucim/src/cucim/skimage/filters/__init__.pyi
@@ -1,51 +1,51 @@
 __all__ = [
-'LPIFilter2D',
-'apply_hysteresis_threshold',
-'butterworth',
-'correlate_sparse',
-'difference_of_gaussians',
-'farid',
-'farid_h',
-'farid_v',
-'filter_forward',
-'filter_inverse',
-'frangi',
-'gabor',
-'gabor_kernel',
-'gaussian',
-'hessian',
-'laplace',
-'median',
-'meijering',
-'prewitt',
-'prewitt_h',
-'prewitt_v',
-'rank_order',
-'roberts',
-'roberts_neg_diag',
-'roberts_pos_diag',
-'sato',
-'scharr',
-'scharr_h',
-'scharr_v',
-'sobel',
-'sobel_h',
-'sobel_v',
-'threshold_isodata',
-'threshold_li',
-'threshold_local',
-'threshold_mean',
-'threshold_minimum',
-'threshold_multiotsu',
-'threshold_niblack',
-'threshold_otsu',
-'threshold_sauvola',
-'threshold_triangle',
-'threshold_yen',
-'try_all_threshold',
-'unsharp_mask',
-'wiener',
-'window'
+    "LPIFilter2D",
+    "apply_hysteresis_threshold",
+    "butterworth",
+    "correlate_sparse",
+    "difference_of_gaussians",
+    "farid",
+    "farid_h",
+    "farid_v",
+    "filter_forward",
+    "filter_inverse",
+    "frangi",
+    "gabor",
+    "gabor_kernel",
+    "gaussian",
+    "hessian",
+    "laplace",
+    "median",
+    "meijering",
+    "prewitt",
+    "prewitt_h",
+    "prewitt_v",
+    "rank_order",
+    "roberts",
+    "roberts_neg_diag",
+    "roberts_pos_diag",
+    "sato",
+    "scharr",
+    "scharr_h",
+    "scharr_v",
+    "sobel",
+    "sobel_h",
+    "sobel_v",
+    "threshold_isodata",
+    "threshold_li",
+    "threshold_local",
+    "threshold_mean",
+    "threshold_minimum",
+    "threshold_multiotsu",
+    "threshold_niblack",
+    "threshold_otsu",
+    "threshold_sauvola",
+    "threshold_triangle",
+    "threshold_yen",
+    "try_all_threshold",
+    "unsharp_mask",
+    "wiener",
+    "window",
 ]
 
 from ._fft_based import butterworth