diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index df3754aee..712db5b5e 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.11.13 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.12.2 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e6676a75d..1dbaf1606 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.13
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
diff --git a/benchmarks/annotation_store_alloc.py b/benchmarks/annotation_store_alloc.py
index f7b9b8525..b0c77e71e 100644
--- a/benchmarks/annotation_store_alloc.py
+++ b/benchmarks/annotation_store_alloc.py
@@ -141,6 +141,7 @@ def __exit__(self: memray, *args: object) -> None:
 
 import numpy as np
 import psutil
+from shapely import affinity
 from shapely.geometry import Polygon
 from tqdm import tqdm
 
@@ -188,8 +189,6 @@ def cell_polygon(
         round_coords (bool): Round coordinates to integers. Defaults to False.
 
     """
-    from shapely import affinity
-
     rand_state = np.random.default_rng().__getstate__()
     rng = np.random.default_rng(seed)
     if repeat_first:
diff --git a/pre-commit/notebook_urls.py b/pre-commit/notebook_urls.py
index c8b0f04fb..51190dcc6 100644
--- a/pre-commit/notebook_urls.py
+++ b/pre-commit/notebook_urls.py
@@ -14,7 +14,7 @@
 def git_branch_name() -> str:
     """Get the current branch name."""
     return (
-        subprocess.check_output(  # noqa: S603
+        subprocess.check_output(
             ["/usr/bin/git", "rev-parse", "--abbrev-ref", "HEAD"],
         )
         .decode()
@@ -45,7 +45,7 @@ def git_previous_commit_modified_paths() -> set[Path]:
     """Get a set of file paths modified in the previous commit."""
     return {
         Path(p)
-        for p in subprocess.check_output(  # noqa: S603
+        for p in subprocess.check_output(
             ["/usr/bin/git", "diff", "--name-only", "HEAD~"],
         )
         .decode()
diff --git a/pre-commit/requirements_consistency.py b/pre-commit/requirements_consistency.py
index 7daecd0e8..4f8d4f442 100644
--- a/pre-commit/requirements_consistency.py
+++ b/pre-commit/requirements_consistency.py
@@ -115,7 +115,7 @@ def parse_setup_py(file_path: Path) -> dict[str, Requirement]:
             pkg_resources.Requirement.
     """
     mock_setup = {}
-    import setuptools
+    import setuptools  # noqa: PLC0415
 
     setuptools.setup = lambda **kw: mock_setup.update(kw)
     spec = importlib.util.spec_from_file_location("setup", str(file_path))
diff --git a/requirements/requirements_dev.txt b/requirements/requirements_dev.txt
index cb62bc7ae..6d481c964 100644
--- a/requirements/requirements_dev.txt
+++ b/requirements/requirements_dev.txt
@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.11.13  # This will be updated by pre-commit bot to latest version
+ruff==0.12.2  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1
diff --git a/tests/conftest.py b/tests/conftest.py
index fa205c205..2b7de0fd6 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -589,9 +589,9 @@ def chdir() -> Callable:
 
     """
     try:
-        from contextlib import chdir
+        from contextlib import chdir  # noqa: PLC0415
     except ImportError:
-        from contextlib import AbstractContextManager
+        from contextlib import AbstractContextManager  # noqa: PLC0415
 
         class chdir(AbstractContextManager):  # noqa: N801
             """Non thread-safe context manager to change the current working directory.
diff --git a/tests/test_init.py b/tests/test_init.py
index 6d8ed8238..71cb8bb5e 100644
--- a/tests/test_init.py
+++ b/tests/test_init.py
@@ -16,7 +16,7 @@ def test_set_root_dir(tmp_path: Path) -> None:
     """Test for setting new root dir."""
     # skipcq
     importlib.reload(tiatoolbox)
-    from tiatoolbox import rcParam
+    from tiatoolbox import rcParam  # noqa: PLC0415
 
     old_root_dir = rcParam["TIATOOLBOX_HOME"]
     test_dir_path = tmp_path / "tmp_check"
@@ -27,7 +27,7 @@ def test_set_root_dir(tmp_path: Path) -> None:
     # reimport to see if it overwrites
     # silence Deep Source because this is an intentional check
     # skipcq
-    from tiatoolbox import rcParam
+    from tiatoolbox import rcParam  # noqa: PLC0415
 
     rcParam["TIATOOLBOX_HOME"].mkdir(parents=True)
     if not Path.exists(test_dir_path):
@@ -135,9 +135,9 @@ def test_duplicate_filter(caplog: pytest.LogCaptureFixture) -> None:
 
 def test_lazy_import() -> None:
     """Test lazy import for tiatoolbox."""
-    import sys
+    import sys  # noqa: PLC0415
 
-    from tiatoolbox import _lazy_import
+    from tiatoolbox import _lazy_import  # noqa: PLC0415
 
     assert "exceptions" not in sys.modules
 
@@ -151,7 +151,7 @@ def test_lazy_import() -> None:
 
 def test_lazy_import_module_not_found() -> None:
     """'Test lazy import for ModuleNotFoundError."""
-    from tiatoolbox import _lazy_import
+    from tiatoolbox import _lazy_import  # noqa: PLC0415
 
     with pytest.raises(ModuleNotFoundError):
         _lazy_import(
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 3cfeefbb2..f8908f434 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import hashlib
+import json
 import shutil
 from pathlib import Path
 from typing import TYPE_CHECKING, NoReturn
@@ -27,7 +28,10 @@
 from tiatoolbox.annotation.storage import DictionaryStore, SQLiteStore
 from tiatoolbox.enums import GeometryType
 from tiatoolbox.models.architecture import fetch_pretrained_weights
-from tiatoolbox.models.architecture.utils import compile_model
+from tiatoolbox.models.architecture.utils import (
+    compile_model,
+    is_torch_compile_compatible,
+)
 from tiatoolbox.utils import misc
 from tiatoolbox.utils.exceptions import FileNotSupportedError
 from tiatoolbox.utils.transforms import locsize2bounds
@@ -1348,8 +1352,6 @@ def test_select_device() -> None:
 def test_save_as_json(tmp_path: Path) -> None:
     """Test save data to json."""
     # This should be broken up into separate tests!
-    import json
-
     # dict with nested dict, list, and np.array
     key_dict = {
         "a1": {"name": "John", "age": 23, "sex": "male"},
@@ -1860,8 +1862,6 @@ def test_torch_compile_disable() -> None:
 
 def test_torch_compile_compatibility(caplog: pytest.LogCaptureFixture) -> None:
     """Test if torch-compile compatibility is checked correctly."""
-    from tiatoolbox.models.architecture.utils import is_torch_compile_compatible
-
     is_torch_compile_compatible()
     assert "torch.compile" in caplog.text
 
diff --git a/tiatoolbox/annotation/dsl.py b/tiatoolbox/annotation/dsl.py
index 9e3820630..cbf9bf7d5 100644
--- a/tiatoolbox/annotation/dsl.py
+++ b/tiatoolbox/annotation/dsl.py
@@ -217,7 +217,7 @@ class SQLTriplet(SQLExpression):
 
     def __init__(
         self: SQLExpression,
-        lhs: SQLTriplet | str | SQLExpression | Number | bool | object,
+        lhs: SQLTriplet | str | SQLExpression | Number | bool | object,  # noqa: FBT001
         op: Callable | str | None = None,
         rhs: SQLTriplet | str | SQLExpression | Number | SQLNone | object | None = None,
     ) -> None:
@@ -373,7 +373,7 @@ def json_contains(json_str: str, x: object) -> bool:
     return x in json.loads(json_str)
 
 
-def sql_is_none(x: SQLExpression | Number | str | bool) -> SQLTriplet:
+def sql_is_none(x: SQLExpression | Number | str | bool) -> SQLTriplet:  # noqa: FBT001
     """Check if x is None.
 
     Returns:
@@ -384,7 +384,7 @@ def sql_is_none(x: SQLExpression | Number | str | bool) -> SQLTriplet:
     return SQLTriplet(x, "is_none")
 
 
-def sql_is_not_none(x: SQLExpression | Number | str | bool) -> SQLTriplet:
+def sql_is_not_none(x: SQLExpression | Number | str | bool) -> SQLTriplet:  # noqa: FBT001
     """Check if x is not None.
 
     Returns:
diff --git a/tiatoolbox/annotation/storage.py b/tiatoolbox/annotation/storage.py
index eed3ee05a..de386f3a1 100644
--- a/tiatoolbox/annotation/storage.py
+++ b/tiatoolbox/annotation/storage.py
@@ -4047,7 +4047,6 @@ def __len__(self: DictionaryStore) -> int:
         """Return the length of the instance attributes."""
         return len(self._rows)
 
-    # flake8: noqa: A003
     @classmethod
     def open(cls: type[AnnotationStore], fp: Path | str | IO) -> AnnotationStore:
         """Opens :class:`DictionaryStore` from file pointer or path."""
diff --git a/tiatoolbox/cli/common.py b/tiatoolbox/cli/common.py
index 26f85625e..c663170c9 100644
--- a/tiatoolbox/cli/common.py
+++ b/tiatoolbox/cli/common.py
@@ -13,6 +13,7 @@
 
 def add_default_to_usage_help(
     usage_help: str,
+    *,
     default: str | float | bool | None,
 ) -> str:
     """Adds default value to usage help string.
@@ -36,6 +37,7 @@ def add_default_to_usage_help(
 
 def cli_img_input(
     usage_help: str = "Path to WSI or directory containing WSIs.",
+    *,
     multiple: bool | None = None,
 ) -> Callable:
     """Enables --img-input option for cli."""
@@ -49,6 +51,7 @@ def cli_img_input(
 
 def cli_name(
     usage_help: str = "User defined name to be used as an identifier.",
+    *,
     multiple: bool | None = None,
 ) -> Callable:
     """Enable --name option for cli."""
@@ -67,7 +70,7 @@ def cli_output_path(
     """Enables --output-path option for cli."""
     return click.option(
         "--output-path",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         type=str,
         default=default,
     )
@@ -80,7 +83,7 @@ def cli_file_type(
     """Enables --file-types option for cli."""
     return click.option(
         "--file-types",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
         type=str,
     )
@@ -96,7 +99,7 @@ def cli_mode(
         input_type = click.Choice(["show", "save"], case_sensitive=False)
     return click.option(
         "--mode",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
         type=input_type,
     )
@@ -130,7 +133,7 @@ def cli_units(
         "--units",
         default=default,
         type=input_type,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
     )
 
 
@@ -143,7 +146,7 @@ def cli_resolution(
         "--resolution",
         type=float,
         default=default,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
     )
 
 
@@ -156,7 +159,7 @@ def cli_tile_objective(
         "--tile-objective-value",
         type=int,
         default=default,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
     )
 
 
@@ -197,7 +200,7 @@ def cli_method(
         "--method",
         type=input_type,
         default=default,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
     )
 
 
@@ -216,7 +219,7 @@ def cli_pretrained_model(
     """Enables --pretrained-model option for cli."""
     return click.option(
         "--pretrained-model",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -229,7 +232,7 @@ def cli_pretrained_weights(
     """Enables --pretrained-weights option for cli."""
     return click.option(
         "--pretrained-weights",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -241,7 +244,7 @@ def cli_device(
     """Enables --pretrained-weights option for cli."""
     return click.option(
         "--device",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -255,7 +258,7 @@ def cli_return_probabilities(
     return click.option(
         "--return-probabilities",
         type=bool,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -270,7 +273,7 @@ def cli_merge_predictions(
         "--merge-predictions",
         type=bool,
         default=default,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
     )
 
 
@@ -283,7 +286,7 @@ def cli_return_labels(
     return click.option(
         "--return-labels",
         type=bool,
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -295,7 +298,7 @@ def cli_batch_size(
     """Enables --batch-size option for cli."""
     return click.option(
         "--batch-size",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -312,7 +315,7 @@ def cli_masks(
     """Enables --masks option for cli."""
     return click.option(
         "--masks",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -325,7 +328,7 @@ def cli_auto_generate_mask(
     """Enables --auto-generate-mask option for cli."""
     return click.option(
         "--auto-generate-mask",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         type=bool,
         default=default,
     )
@@ -340,7 +343,7 @@ def cli_yaml_config_path(
     """Enables --yaml-config-path option for cli."""
     return click.option(
         "--yaml-config-path",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         default=default,
     )
 
@@ -353,7 +356,7 @@ def cli_num_loader_workers(
     """Enables --num-loader-workers option for cli."""
     return click.option(
         "--num-loader-workers",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         type=int,
         default=default,
     )
@@ -366,7 +369,7 @@ def cli_num_postproc_workers(
     """Enables --num-postproc-workers option for cli."""
     return click.option(
         "--num-postproc-workers",
-        help=add_default_to_usage_help(usage_help, default),
+        help=add_default_to_usage_help(usage_help, default=default),
         type=int,
         default=default,
     )
@@ -381,7 +384,7 @@ def cli_verbose(
     return click.option(
         "--verbose",
         type=bool,
-        help=add_default_to_usage_help(usage_help, str(default)),
+        help=add_default_to_usage_help(usage_help, default=str(default)),
         default=default,
     )
 
@@ -451,7 +454,10 @@ def prepare_file_dir_cli(
         pathlib.Path: updated output path.
 
     """
-    from tiatoolbox.utils.misc import grab_files_from_dir, string_to_tuple
+    from tiatoolbox.utils.misc import (  # noqa: PLC0415
+        grab_files_from_dir,
+        string_to_tuple,
+    )
 
     img_input = no_input_message(input_file=img_input)
     file_types_tuple = string_to_tuple(in_str=file_types)
@@ -512,7 +518,10 @@ def prepare_model_cli(
             Output path.
 
     """
-    from tiatoolbox.utils.misc import grab_files_from_dir, string_to_tuple
+    from tiatoolbox.utils.misc import (  # noqa: PLC0415
+        grab_files_from_dir,
+        string_to_tuple,
+    )
 
     img_input = no_input_message(input_file=img_input)
     output_path = Path(output_path)
@@ -558,7 +567,7 @@ def prepare_ioconfig_seg(
     yaml_config_path: str | Path,
 ) -> IOConfigABC | None:
     """Prepare ioconfig for segmentation."""
-    import yaml
+    import yaml  # noqa: PLC0415
 
     if pretrained_weights is not None:
         with Path(yaml_config_path).open() as registry_handle:
diff --git a/tiatoolbox/cli/nucleus_instance_segment.py b/tiatoolbox/cli/nucleus_instance_segment.py
index fdb4b95ca..ab5ad8548 100644
--- a/tiatoolbox/cli/nucleus_instance_segment.py
+++ b/tiatoolbox/cli/nucleus_instance_segment.py
@@ -67,8 +67,11 @@ def nucleus_instance_segment(
     verbose: bool,
 ) -> None:
     """Process an image/directory of input images with a patch classification CNN."""
-    from tiatoolbox.models import IOSegmentorConfig, NucleusInstanceSegmentor
-    from tiatoolbox.utils import save_as_json
+    from tiatoolbox.models import (  # noqa: PLC0415
+        IOSegmentorConfig,
+        NucleusInstanceSegmentor,
+    )
+    from tiatoolbox.utils import save_as_json  # noqa: PLC0415
 
     files_all, masks_all, output_path = prepare_model_cli(
         img_input=img_input,
diff --git a/tiatoolbox/cli/patch_predictor.py b/tiatoolbox/cli/patch_predictor.py
index 069b6c367..fdb85e3ea 100644
--- a/tiatoolbox/cli/patch_predictor.py
+++ b/tiatoolbox/cli/patch_predictor.py
@@ -72,8 +72,8 @@ def patch_predictor(
     verbose: bool,
 ) -> None:
     """Process an image/directory of input images with a patch classification CNN."""
-    from tiatoolbox.models import PatchPredictor
-    from tiatoolbox.utils import save_as_json
+    from tiatoolbox.models import PatchPredictor  # noqa: PLC0415
+    from tiatoolbox.utils import save_as_json  # noqa: PLC0415
 
     files_all, masks_all, output_path = prepare_model_cli(
         img_input=img_input,
diff --git a/tiatoolbox/cli/read_bounds.py b/tiatoolbox/cli/read_bounds.py
index a0460cc01..98bd62d4f 100644
--- a/tiatoolbox/cli/read_bounds.py
+++ b/tiatoolbox/cli/read_bounds.py
@@ -36,10 +36,10 @@ def read_bounds(
     mode: str,
 ) -> None:
     """Read a region in a whole slide image as specified."""
-    from PIL import Image
+    from PIL import Image  # noqa: PLC0415
 
-    from tiatoolbox.utils import imwrite
-    from tiatoolbox.wsicore.wsireader import WSIReader
+    from tiatoolbox.utils import imwrite  # noqa: PLC0415
+    from tiatoolbox.wsicore.wsireader import WSIReader  # noqa: PLC0415
 
     no_input_message(input_file=img_input)
 
diff --git a/tiatoolbox/cli/save_tiles.py b/tiatoolbox/cli/save_tiles.py
index f3211b5fe..7a5b4f4e8 100644
--- a/tiatoolbox/cli/save_tiles.py
+++ b/tiatoolbox/cli/save_tiles.py
@@ -38,7 +38,7 @@ def save_tiles(
     verbose: bool,
 ) -> None:
     """Display or save WSI metadata."""
-    from tiatoolbox.wsicore.wsireader import WSIReader
+    from tiatoolbox.wsicore.wsireader import WSIReader  # noqa: PLC0415
 
     files_all, output_path = prepare_file_dir_cli(
         img_input,
diff --git a/tiatoolbox/cli/semantic_segment.py b/tiatoolbox/cli/semantic_segment.py
index cbfe18e58..ec59ca311 100644
--- a/tiatoolbox/cli/semantic_segment.py
+++ b/tiatoolbox/cli/semantic_segment.py
@@ -61,8 +61,8 @@ def semantic_segment(
     verbose: bool,
 ) -> None:
     """Process an image/directory of input images with a patch classification CNN."""
-    from tiatoolbox.models import IOSegmentorConfig, SemanticSegmentor
-    from tiatoolbox.utils import save_as_json
+    from tiatoolbox.models import IOSegmentorConfig, SemanticSegmentor  # noqa: PLC0415
+    from tiatoolbox.utils import save_as_json  # noqa: PLC0415
 
     files_all, masks_all, output_path = prepare_model_cli(
         img_input=img_input,
diff --git a/tiatoolbox/cli/show_wsi.py b/tiatoolbox/cli/show_wsi.py
index 6a95dec13..6ac5856af 100644
--- a/tiatoolbox/cli/show_wsi.py
+++ b/tiatoolbox/cli/show_wsi.py
@@ -31,8 +31,8 @@ def show_wsi(
     colour_map: str,
 ) -> None:  # pragma: no cover
     """Show a slide together with any overlays."""
-    from tiatoolbox.utils.visualization import AnnotationRenderer
-    from tiatoolbox.visualization.tileserver import TileServer
+    from tiatoolbox.utils.visualization import AnnotationRenderer  # noqa: PLC0415
+    from tiatoolbox.visualization.tileserver import TileServer  # noqa: PLC0415
 
     renderer = AnnotationRenderer()
     if colour_by is not None:
diff --git a/tiatoolbox/cli/slide_info.py b/tiatoolbox/cli/slide_info.py
index 8733c309e..22bcd120c 100644
--- a/tiatoolbox/cli/slide_info.py
+++ b/tiatoolbox/cli/slide_info.py
@@ -33,7 +33,7 @@ def slide_info(
     verbose: bool,
 ) -> None:
     """Displays or saves WSI metadata depending on the mode argument."""
-    from tiatoolbox import utils, wsicore
+    from tiatoolbox import utils, wsicore  # noqa: PLC0415
 
     all_files, output_path = prepare_file_dir_cli(
         img_input,
diff --git a/tiatoolbox/cli/slide_thumbnail.py b/tiatoolbox/cli/slide_thumbnail.py
index a2029b8dc..854ac35a6 100644
--- a/tiatoolbox/cli/slide_thumbnail.py
+++ b/tiatoolbox/cli/slide_thumbnail.py
@@ -34,10 +34,10 @@ def slide_thumbnail(
     file-types="*.ndpi, *.svs, *.mrxs, *.jp2".
 
     """
-    from PIL import Image
+    from PIL import Image  # noqa: PLC0415
 
-    from tiatoolbox.utils import imwrite
-    from tiatoolbox.wsicore.wsireader import WSIReader
+    from tiatoolbox.utils import imwrite  # noqa: PLC0415
+    from tiatoolbox.wsicore.wsireader import WSIReader  # noqa: PLC0415
 
     files_all, output_path = prepare_file_dir_cli(
         img_input,
diff --git a/tiatoolbox/cli/stain_norm.py b/tiatoolbox/cli/stain_norm.py
index e2fdcbac1..068c342dd 100644
--- a/tiatoolbox/cli/stain_norm.py
+++ b/tiatoolbox/cli/stain_norm.py
@@ -48,8 +48,8 @@ def stain_norm(
     file_types: str,
 ) -> None:
     """Stain normalize an input image/directory of input images."""
-    from tiatoolbox.tools import stainnorm as sn
-    from tiatoolbox.utils import imread, imwrite
+    from tiatoolbox.tools import stainnorm as sn  # noqa: PLC0415
+    from tiatoolbox.utils import imread, imwrite  # noqa: PLC0415
 
     files_all, output_path = prepare_file_dir_cli(
         img_input,
diff --git a/tiatoolbox/cli/tissue_mask.py b/tiatoolbox/cli/tissue_mask.py
index a73dd2f30..bb5bfe3af 100644
--- a/tiatoolbox/cli/tissue_mask.py
+++ b/tiatoolbox/cli/tissue_mask.py
@@ -30,7 +30,7 @@ def get_masker(
     resolution: float,
 ) -> TissueMasker:
     """Get Tissue Masker."""
-    from tiatoolbox.tools import tissuemask
+    from tiatoolbox.tools import tissuemask  # noqa: PLC0415
 
     if method == "Otsu":
         return tissuemask.OtsuTissueMasker()
@@ -73,11 +73,11 @@ def tissue_mask(
     file_types: str,
 ) -> None:
     """Generate tissue mask for a WSI."""
-    import numpy as np
-    from PIL import Image
+    import numpy as np  # noqa: PLC0415
+    from PIL import Image  # noqa: PLC0415
 
-    from tiatoolbox.utils import imwrite
-    from tiatoolbox.wsicore.wsireader import WSIReader
+    from tiatoolbox.utils import imwrite  # noqa: PLC0415
+    from tiatoolbox.wsicore.wsireader import WSIReader  # noqa: PLC0415
 
     files_all, output_path = prepare_file_dir_cli(
         img_input,
diff --git a/tiatoolbox/cli/visualize.py b/tiatoolbox/cli/visualize.py
index f1edbb318..30627dcf2 100644
--- a/tiatoolbox/cli/visualize.py
+++ b/tiatoolbox/cli/visualize.py
@@ -19,7 +19,7 @@ def run_tileserver() -> None:
 
     def run_app() -> None:
         """Run the tileserver app."""
-        from tiatoolbox.visualization.tileserver import TileServer
+        from tiatoolbox.visualization.tileserver import TileServer  # noqa: PLC0415
 
         app = TileServer(
             title="Tiatoolbox TileServer",
diff --git a/tiatoolbox/data/__init__.py b/tiatoolbox/data/__init__.py
index ba922df4c..9379f2740 100644
--- a/tiatoolbox/data/__init__.py
+++ b/tiatoolbox/data/__init__.py
@@ -12,6 +12,7 @@
 from urllib.parse import urlparse
 
 from tiatoolbox import logger, read_registry_files
+from tiatoolbox.utils import imread
 
 if TYPE_CHECKING:  # pragma: no cover
     import numpy as np
@@ -87,8 +88,6 @@ def _local_sample_path(path: str | Path) -> Path:
 
 def stain_norm_target() -> np.ndarray:
     """Target image for stain normalization."""
-    from tiatoolbox.utils import imread
-
     return imread(_local_sample_path("target_image.png"))
 
 
diff --git a/tiatoolbox/models/engine/semantic_segmentor.py b/tiatoolbox/models/engine/semantic_segmentor.py
index 80f6e57c9..f4b85e5c1 100644
--- a/tiatoolbox/models/engine/semantic_segmentor.py
+++ b/tiatoolbox/models/engine/semantic_segmentor.py
@@ -20,7 +20,10 @@
 
 from tiatoolbox import logger, rcParam
 from tiatoolbox.models.architecture import get_pretrained_model
-from tiatoolbox.models.architecture.utils import compile_model
+from tiatoolbox.models.architecture.utils import (
+    compile_model,
+    is_torch_compile_compatible,
+)
 from tiatoolbox.models.models_abc import IOConfigABC, model_to
 from tiatoolbox.tools.patchextraction import PatchExtractor
 from tiatoolbox.utils import imread
@@ -1422,7 +1425,6 @@ def predict(  # noqa: PLR0913
             logger.warning("Unable to remove %s", self._cache_dir)
 
         self._memory_cleanup()
-        from tiatoolbox.models.architecture.utils import is_torch_compile_compatible
 
         if (
             device == "cuda"
diff --git a/tiatoolbox/tools/graph.py b/tiatoolbox/tools/graph.py
index 1f812333d..0cc036b51 100644
--- a/tiatoolbox/tools/graph.py
+++ b/tiatoolbox/tools/graph.py
@@ -9,6 +9,7 @@
 import numpy as np
 import torch
 import umap
+from matplotlib import collections as mc
 from matplotlib import pyplot as plt
 from scipy.cluster import hierarchy
 from scipy.spatial import Delaunay, cKDTree
@@ -479,8 +480,6 @@ def visualise(
             >>> plt.show()
 
         """
-        from matplotlib import collections as mc
-
         # Check that the graph is valid
         if "x" not in graph:
             msg = "Graph must contain key `x`."
diff --git a/tiatoolbox/utils/env_detection.py b/tiatoolbox/utils/env_detection.py
index 8605af745..bc6f72ca4 100644
--- a/tiatoolbox/utils/env_detection.py
+++ b/tiatoolbox/utils/env_detection.py
@@ -97,7 +97,7 @@ def is_notebook() -> bool:
 
     """
     try:
-        from IPython import get_ipython
+        from IPython import get_ipython  # noqa: PLC0415
 
         shell = get_ipython().__class__.__name__
         if shell == "ZMQInteractiveShell":
@@ -250,11 +250,11 @@ def check_pixman_using_anaconda(versions: list) -> tuple[list, str]:
     """Using anaconda to check for pixman."""
     using = "conda"
     try:
-        conda_list = subprocess.Popen(  # noqa: S603
+        conda_list = subprocess.Popen(
             ("conda", "list"),
             stdout=subprocess.PIPE,
         )
-        conda_pixman = subprocess.check_output(  # noqa: S603
+        conda_pixman = subprocess.check_output(
             ("grep", "pixman"),
             stdin=conda_list.stdout,
         )
@@ -276,7 +276,7 @@ def check_pixman_using_dpkg(versions: list) -> tuple[list, str]:
     """Using dpkg to check for pixman."""
     using = "dpkg"
     try:
-        dkpg_output = subprocess.check_output(  # noqa: S603
+        dkpg_output = subprocess.check_output(
             ["/usr/bin/dpkg", "-s", "libpixman-1-0"],
         )
     except subprocess.SubprocessError:
@@ -296,11 +296,11 @@ def check_pixman_using_brew(versions: list) -> tuple[list, str]:
     """Using homebrew to check for pixman."""
     using = "brew"
     try:
-        brew_list = subprocess.Popen(  # noqa: S603
+        brew_list = subprocess.Popen(
             ("brew", "list", "--versions"),
             stdout=subprocess.PIPE,
         )
-        brew_pixman = subprocess.check_output(  # noqa: S603
+        brew_pixman = subprocess.check_output(
             ("grep", "pixman"),
             stdin=brew_list.stdout,
         )
@@ -326,11 +326,11 @@ def check_pixman_using_macports(versions: list) -> tuple[list, str]:
 
     """
     using = "port"
-    port_list = subprocess.Popen(  # noqa: S603
+    port_list = subprocess.Popen(
         ("port", "installed"),
         stdout=subprocess.PIPE,
     )
-    port_pixman = subprocess.check_output(  # noqa: S603
+    port_pixman = subprocess.check_output(
         ("grep", "pixman"),
         stdin=port_list.stdout,
     )
diff --git a/tiatoolbox/utils/misc.py b/tiatoolbox/utils/misc.py
index 060efcaa4..6c755d04e 100644
--- a/tiatoolbox/utils/misc.py
+++ b/tiatoolbox/utils/misc.py
@@ -162,7 +162,7 @@ def imwrite(image_path: PathLike, img: np.ndarray) -> None:
         raise OSError(msg)
 
 
-def imread(image_path: PathLike, as_uint8: bool | None = None) -> np.ndarray:
+def imread(image_path: PathLike, *, as_uint8: bool | None = None) -> np.ndarray:
     """Read an image as a NumPy array.
 
     Args:
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
index 73481060c..46f10cc36 100644
--- a/tiatoolbox/wsicore/wsireader.py
+++ b/tiatoolbox/wsicore/wsireader.py
@@ -1552,7 +1552,7 @@ def tissue_mask(
                 Extra kwargs passed to the masker class.
 
         """
-        from tiatoolbox.tools import tissuemask
+        from tiatoolbox.tools import tissuemask  # noqa: PLC0415
 
         thumbnail = self.slide_thumbnail(resolution, units)
         if method not in ["otsu", "morphological"]:
@@ -2285,7 +2285,7 @@ def __init__(
     ) -> None:
         """Initialize :class:`OmnyxJP2WSIReader`."""
         super().__init__(input_img=input_img, mpp=mpp, power=power)
-        import glymur
+        import glymur  # noqa: PLC0415
 
         glymur.set_option("lib.num_threads", os.cpu_count() or 1)
         self.glymur_jp2 = glymur.Jp2k(filename=str(self.input_path))
@@ -2780,7 +2780,7 @@ def _info(self: JP2WSIReader) -> WSIMeta:
                 Metadata information.
 
         """
-        import glymur
+        import glymur  # noqa: PLC0415
 
         jp2 = self.glymur_jp2
         boxes = self._get_jp2_boxes(jp2)
@@ -4561,7 +4561,7 @@ def __init__(
         power: Number | None = None,
     ) -> None:
         """Initialize :class:`DICOMWSIReader`."""
-        from wsidicom import WsiDicom
+        from wsidicom import WsiDicom  # noqa: PLC0415
 
         super().__init__(input_img, mpp, power)
         self.wsi = WsiDicom.open(input_img)
@@ -5075,9 +5075,9 @@ class NGFFWSIReader(WSIReader):
     def __init__(self: NGFFWSIReader, path: str | Path, **kwargs: dict) -> None:
         """Initialize :class:`NGFFWSIReader`."""
         super().__init__(path, **kwargs)
-        from imagecodecs import numcodecs
+        from imagecodecs import numcodecs  # noqa: PLC0415
 
-        from tiatoolbox.wsicore.metadata import ngff
+        from tiatoolbox.wsicore.metadata import ngff  # noqa: PLC0415
 
         numcodecs.register_codecs()
         store = zarr.SQLiteStore(path) if is_sqlite3(path) else path