diff --git a/.flake8 b/.flake8
new file mode 100644
index 00000000..ee7178fb
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,20 @@
+[flake8]
+max-line-length = 100
+ignore =
+    # line break before a binary operator -> black does not adhere to PEP8
+    W503
+    # line break occured after a binary operator -> black does not adhere to PEP8
+    W504
+    # line too long -> we accept long comment lines; black gets rid of long code lines
+    E501
+    # whitespace before : -> black does not adhere to PEP8
+    E203
+    # leading '#' are fine if not used too often
+    E266
+    # it can be more convenient to use a bare 'except'
+    E722
+exclude = .git,__pycache__
+per-file-ignores =
+    tests/*: D
+    */__init__.py: F401
+    sopa/main.py: F401
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..3c877354
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,30 @@
+fail_fast: false
+default_language_version:
+    python: python3
+default_stages:
+    - commit
+    - push
+minimum_pre_commit_version: 2.16.0
+repos:
+    - repo: https://github.com/psf/black
+      rev: 24.1.1
+      hooks:
+          - id: black
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.13.2
+      hooks:
+          - id: isort
+    - repo: https://github.com/PyCQA/flake8
+      rev: 7.0.0
+      hooks:
+          - id: flake8
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.5.0
+      hooks:
+          - id: trailing-whitespace
+          - id: end-of-file-fixer
+          - id: check-yaml
+          - id: debug-statements
+          - id: double-quote-string-fixer
+          - id: name-tests-test
+          - id: requirements-txt-fixer
diff --git a/poetry.lock b/poetry.lock
index d35aedfd..e1c6ef3a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1200,6 +1200,23 @@ calc = ["shapely"]
 s3 = ["boto3 (>=1.3.1)"]
 test = ["Fiona[s3]", "pytest (>=7)", "pytest-cov", "pytz"]
 
+[[package]]
+name = "flake8"
+version = "7.0.0"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "main"
+optional = false
+python-versions = ">=3.8.1"
+files = [
+    {file = "flake8-7.0.0-py2.py3-none-any.whl", hash = "sha256:a6dfbb75e03252917f2473ea9653f7cd799c3064e54d4c8140044c5c065f53c3"},
+    {file = "flake8-7.0.0.tar.gz", hash = "sha256:33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132"},
+]
+
+[package.dependencies]
+mccabe = ">=0.7.0,<0.8.0"
+pycodestyle = ">=2.11.0,<2.12.0"
+pyflakes = ">=3.2.0,<3.3.0"
+
 [[package]]
 name = "fonttools"
 version = "4.47.2"
@@ -2308,6 +2325,18 @@ files = [
 [package.dependencies]
 traitlets = "*"
 
+[[package]]
+name = "mccabe"
+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"},
+    {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"},
+]
+
 [[package]]
 name = "mdit-py-plugins"
 version = "0.4.0"
@@ -3714,6 +3743,18 @@ files = [
 [package.dependencies]
 numpy = ">=1.16.6"
 
+[[package]]
+name = "pycodestyle"
+version = "2.11.1"
+description = "Python style guide checker"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pycodestyle-2.11.1-py2.py3-none-any.whl", hash = "sha256:44fe31000b2d866f2e41841b18528a505fbd7fef9017b04eff4e2648a0fadc67"},
+    {file = "pycodestyle-2.11.1.tar.gz", hash = "sha256:41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f"},
+]
+
 [[package]]
 name = "pycparser"
 version = "2.21"
@@ -3747,6 +3788,18 @@ cmd = ["pyyaml", "requests"]
 doc = ["nbsite", "sphinx-ioam-theme"]
 tests = ["flake8", "pytest"]
 
+[[package]]
+name = "pyflakes"
+version = "3.2.0"
+description = "passive checker of Python programs"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pyflakes-3.2.0-py2.py3-none-any.whl", hash = "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a"},
+    {file = "pyflakes-3.2.0.tar.gz", hash = "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f"},
+]
+
 [[package]]
 name = "pygeos"
 version = "0.14"
@@ -4018,6 +4071,7 @@ files = [
     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
     {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
     {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"},
+    {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef"},
     {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"},
     {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"},
     {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
@@ -5950,4 +6004,4 @@ tangram = ["tangram-sc"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<3.11"
-content-hash = "977234c9fae0a78884783b221a10679ce689f35298d003a6142de30e9bf38b4a"
+content-hash = "66c7434863f556e32d1f70c0d2be68d10be74014707ea1c4143c627d1c195eeb"
diff --git a/pyproject.toml b/pyproject.toml
index a84b1695..0e816cda 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,6 +49,7 @@ tangram-sc = { version = "^1.0.4", optional = true }
 
 snakemake = { version = "^7.32.4,<8.1.3", optional = true }
 pulp = { version = ">=2.3.1,<2.8", optional = true }
+flake8 = {version = "^7.0.0", extras = ["dev"]}
 
 [tool.poetry.extras]
 cellpose = ["cellpose", "opencv-python", "torch"]
diff --git a/sopa/annotation/tangram/run.py b/sopa/annotation/tangram/run.py
index d1df98f6..c96414f6 100644
--- a/sopa/annotation/tangram/run.py
+++ b/sopa/annotation/tangram/run.py
@@ -166,7 +166,7 @@ def pp_adata(self, ad_sp_: AnnData, ad_sc_: AnnData, split: np.ndarray) -> AnnDa
 
         assert len(
             selection
-        ), f"No gene in common between the reference and the spatial adata object. Have you run transcript aggregation?"
+        ), "No gene in common between the reference and the spatial adata object. Have you run transcript aggregation?"
         log.info(f"Keeping {len(selection)} shared genes")
 
         for ad_ in [ad_sp_split, ad_sc_]:
diff --git a/sopa/cli/annotate.py b/sopa/cli/annotate.py
index 9733fbfe..8774e02a 100644
--- a/sopa/cli/annotate.py
+++ b/sopa/cli/annotate.py
@@ -26,7 +26,7 @@ def fluorescence(
 
     sdata = read_zarr_standardized(sdata_path)
 
-    assert sdata.table is not None, f"Annotation requires `sdata.table` to be not None"
+    assert sdata.table is not None, "Annotation requires `sdata.table` to be not None"
 
     higher_z_score(sdata.table, marker_cell_dict, cell_type_key)
     sdata.table.write_zarr(Path(sdata_path) / "table" / "table")
diff --git a/sopa/cli/check.py b/sopa/cli/check.py
index 2442e38b..35ac084e 100644
--- a/sopa/cli/check.py
+++ b/sopa/cli/check.py
@@ -77,7 +77,7 @@ def reference(
 
 def _get(config, *args):
     for arg in args:
-        if not arg in config:
+        if arg not in config:
             return False
         config = config[arg]
     return config
@@ -85,7 +85,7 @@ def _get(config, *args):
 
 def _check_dict(config: dict, d: dict, log, prefix: str = "config"):
     for key, values in d.items():
-        if not key in config:
+        if key not in config:
             log.warn(f"Required config key {prefix}['{key}'] not found")
         elif isinstance(values, dict):
             _check_dict(config[key], values, log, f"{prefix}['{key}']")
diff --git a/sopa/cli/patchify.py b/sopa/cli/patchify.py
index 3f2ff4b2..54523e8c 100644
--- a/sopa/cli/patchify.py
+++ b/sopa/cli/patchify.py
@@ -69,8 +69,6 @@ def baysor(
     ),
 ):
     """Prepare the patches for Baysor segmentation"""
-    from pathlib import Path
-
     from sopa._constants import SopaFiles, SopaKeys
     from sopa._sdata import get_key
     from sopa.io.standardize import read_zarr_standardized, sanity_check
diff --git a/sopa/cli/utils.py b/sopa/cli/utils.py
index d84bfd5a..523696f0 100644
--- a/sopa/cli/utils.py
+++ b/sopa/cli/utils.py
@@ -1,7 +1,7 @@
 def _check_zip(names: list[str]):
     for name in names:
         if isinstance(name, str):
-            assert name.endswith(".zip"), f"Intermediate files names must end with .zip"
+            assert name.endswith(".zip"), "Intermediate files names must end with .zip"
 
 
 def _default_boundary_dir(sdata_path: str, directory_name: str):
diff --git a/sopa/io/explorer/_constants.py b/sopa/io/explorer/_constants.py
index 91fd77f6..5c5d421f 100644
--- a/sopa/io/explorer/_constants.py
+++ b/sopa/io/explorer/_constants.py
@@ -97,7 +97,6 @@ def experiment_dict(run_name: str, region_name: str, num_cells: int, pixel_size:
         "instrument_sn": "N/A",
         "instrument_sw_version": "N/A",
         "analysis_sw_version": "xenium-1.3.0.5",
-        "experiment_uuid": "",
         "cassette_uuid": "",
         "roi_uuid": "",
         "z_step_size": 3.0,
diff --git a/sopa/io/explorer/converter.py b/sopa/io/explorer/converter.py
index faf216f1..5555563b 100644
--- a/sopa/io/explorer/converter.py
+++ b/sopa/io/explorer/converter.py
@@ -22,7 +22,7 @@
 def _check_explorer_directory(path: Path):
     assert (
         not path.exists() or path.is_dir()
-    ), f"A path to an existing file was provided. It should be a path to a directory."
+    ), "A path to an existing file was provided. It should be a path to a directory."
     path.mkdir(parents=True, exist_ok=True)
 
 
@@ -33,7 +33,7 @@ def _should_save(mode: str | None, character: str):
     assert len(mode) and mode[0] in [
         "-",
         "+",
-    ], f"Mode should be a string that starts with '+' or '-'"
+    ], "Mode should be a string that starts with '+' or '-'"
 
     return character in mode if mode[0] == "+" else character not in mode
 
diff --git a/sopa/io/explorer/images.py b/sopa/io/explorer/images.py
index 269b8089..bc6c12ca 100644
--- a/sopa/io/explorer/images.py
+++ b/sopa/io/explorer/images.py
@@ -144,7 +144,7 @@ def _set_colors(channel_names: list[str]) -> list[str]:
     ]
     valid_colors = [c for c in ExplorerConstants.COLORS if c != ExplorerConstants.NUCLEUS_COLOR]
     n_missing = sum(
-        not is_wavelength and not c in ExplorerConstants.KNOWN_CHANNELS
+        not is_wavelength and c not in ExplorerConstants.KNOWN_CHANNELS
         for c, is_wavelength in zip(channel_names, existing_wavelength)
     )
     colors_iterator: list = np.repeat(valid_colors, ceil(n_missing / len(valid_colors))).tolist()
diff --git a/sopa/io/explorer/shapes.py b/sopa/io/explorer/shapes.py
index 26f803cd..26fb7273 100644
--- a/sopa/io/explorer/shapes.py
+++ b/sopa/io/explorer/shapes.py
@@ -7,7 +7,7 @@
 import zarr
 from shapely.geometry import Polygon
 
-from ._constants import ExplorerConstants, FileNames, cell_summary_attrs, group_attrs
+from ._constants import FileNames, cell_summary_attrs, group_attrs
 from .utils import explorer_file_path
 
 log = logging.getLogger(__name__)
diff --git a/sopa/io/imaging.py b/sopa/io/imaging.py
index c9f232e2..88a8839a 100644
--- a/sopa/io/imaging.py
+++ b/sopa/io/imaging.py
@@ -272,7 +272,7 @@ def ome_tif(path: Path, as_image: bool = False) -> SpatialImage | SpatialData:
     image: da.Array = imread(path)
 
     if image.ndim == 4:
-        assert image.shape[0] == 1, f"4D images not supported"
+        assert image.shape[0] == 1, "4D images not supported"
         image = da.moveaxis(image[0], 2, 0)
         log.info(f"Transformed 4D image into a 3D image of shape (c, y, x) = {image.shape}")
     elif image.ndim != 3:
diff --git a/sopa/io/report/generate.py b/sopa/io/report/generate.py
index 2d65a07b..b43e57a1 100644
--- a/sopa/io/report/generate.py
+++ b/sopa/io/report/generate.py
@@ -56,7 +56,7 @@ def __init__(self, sdata: SpatialData):
         self.sdata = sdata
 
     def _table_has(self, key, default=False):
-        if not SopaKeys.UNS_KEY in self.sdata.table.uns:
+        if SopaKeys.UNS_KEY not in self.sdata.table.uns:
             return default
         return self.sdata.table.uns[SopaKeys.UNS_KEY].get(key, default)
 
@@ -70,7 +70,7 @@ def general_section(self):
                     "SpatialData information",
                     [
                         Paragraph(
-                            f"Sopa is using <a href='https://spatialdata.scverse.org/en/latest/'>SpatialData</a> under the hood. This is how the object looks like:"
+                            "Sopa is using <a href='https://spatialdata.scverse.org/en/latest/'>SpatialData</a> under the hood. This is how the object looks like:"
                         ),
                         CodeBlock(str(self.sdata)),
                     ],
diff --git a/sopa/io/standardize.py b/sopa/io/standardize.py
index 12489f92..fb422598 100644
--- a/sopa/io/standardize.py
+++ b/sopa/io/standardize.py
@@ -14,7 +14,7 @@
 def sanity_check(sdata: SpatialData, delete_table: bool = False, warn: bool = False):
     assert (
         len(sdata.images) > 0
-    ), f"The spatialdata object has no image. Sopa is not designed for this."
+    ), "The spatialdata object has no image. Sopa is not designed for this."
 
     if len(sdata.images) != 1:
         message = f"The spatialdata object has {len(sdata.images)} images. We advise to run sopa on one image (which can have multiple channels and multiple scales)"
diff --git a/sopa/io/transcriptomics.py b/sopa/io/transcriptomics.py
index cb0fa9ba..60320567 100644
--- a/sopa/io/transcriptomics.py
+++ b/sopa/io/transcriptomics.py
@@ -21,8 +21,7 @@
 from spatialdata import SpatialData
 from spatialdata._logging import logger
 from spatialdata.models import Image2DModel, PointsModel, ShapesModel, TableModel
-from spatialdata.transformations import Affine, Identity
-from spatialdata.transformations.transformations import Identity, Scale
+from spatialdata.transformations import Affine, Identity, Scale
 from spatialdata_io._constants._constants import MerscopeKeys, XeniumKeys
 
 
diff --git a/sopa/segmentation/aggregate.py b/sopa/segmentation/aggregate.py
index 37dbb5a0..0c5f152b 100644
--- a/sopa/segmentation/aggregate.py
+++ b/sopa/segmentation/aggregate.py
@@ -130,7 +130,7 @@ def update_table(
 
         assert (
             average_intensities or does_count
-        ), f"You must choose at least one aggregation: transcripts or fluorescence intensities"
+        ), "You must choose at least one aggregation: transcripts or fluorescence intensities"
 
         if gene_column is not None:
             if self.table is not None:
diff --git a/sopa/segmentation/shapes.py b/sopa/segmentation/shapes.py
index 8a2b77f7..cc87724d 100644
--- a/sopa/segmentation/shapes.py
+++ b/sopa/segmentation/shapes.py
@@ -31,7 +31,7 @@ def solve_conflicts(
     n_cells = len(cells)
     resolved_indices = np.arange(n_cells)
 
-    assert n_cells > 0, f"No cells was segmented, cannot continue"
+    assert n_cells > 0, "No cells was segmented, cannot continue"
 
     tree = shapely.STRtree(cells)
     conflicts = tree.query(cells, predicate="intersects")
diff --git a/sopa/segmentation/stainings.py b/sopa/segmentation/stainings.py
index cc0259da..71af765a 100644
--- a/sopa/segmentation/stainings.py
+++ b/sopa/segmentation/stainings.py
@@ -4,7 +4,6 @@
 
 import geopandas as gpd
 import numpy as np
-import zarr
 from scipy.ndimage import gaussian_filter
 from shapely import affinity
 from shapely.geometry import Polygon, box
diff --git a/sopa/spatial/_build.py b/sopa/spatial/_build.py
index 2b0c7322..b2caf921 100644
--- a/sopa/spatial/_build.py
+++ b/sopa/spatial/_build.py
@@ -42,7 +42,7 @@ def spatial_neighbors(
 
     assert (
         radius is None or len(radius) == 2
-    ), f"Radius is expected to be a tuple (min_radius, max_radius)"
+    ), "Radius is expected to be a tuple (min_radius, max_radius)"
 
     log.info("Computing delaunay graph")
 
diff --git a/sopa/spatial/morpho.py b/sopa/spatial/morpho.py
index f8402d02..166474f2 100644
--- a/sopa/spatial/morpho.py
+++ b/sopa/spatial/morpho.py
@@ -141,7 +141,7 @@ def niches_geometry_stats(
     gdf = geometrize_niches(adata, niche_key, **geometrize_niches_kwargs)
     value_counts = gdf[niche_key].value_counts()
 
-    assert len(gdf), f"No niche geometry found, stats can't be computed"
+    assert len(gdf), "No niche geometry found, stats can't be computed"
 
     log.info(f"Computing pairwise distances between {len(gdf)} components")
     pairwise_distances: pd.DataFrame = gdf.geometry.apply(lambda g: gdf.distance(g))