diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b9d1c654..6fd28d95 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,6 +16,8 @@ jobs:
       - run: python -m pip install ruff
       - run: ruff check .
       - run: ruff format --check .
+      # The code standards (spec §9) against their shrink-only baseline.
+      - run: python tools/check.py --rules
 
   test:
     runs-on: ${{ matrix.os }}
diff --git a/AGENTS.md b/AGENTS.md
index fb963ab4..312ed122 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -174,7 +174,8 @@ functions the tests use.
    PR description:
    *Summary* (by module), *Decisions*, *Notes for review* (limitations, what was not
    verified), *Tests* (exact counts, e.g. "455 passed, 2 skipped").
-5. **Done means:** `ruff check .`, `ruff format --check .` and `pytest` all pass (CI runs
+5. **Done means:** `python tools/check.py` passes (`ruff check .`, `ruff format --check .`,
+   `pytest` and the code rules of `docs/development.md` against their baseline), (CI runs
    lint on Ubuntu and tests on Ubuntu, Windows and macOS with Python 3.11 and 3.13), docs
    updated, and local changes ready for review. Open a PR only when the user requests it.
 6. **Be honest in reports.** Say what was verified and what was not (for example: "widgets
diff --git a/docs/development.md b/docs/development.md
index af0a17df..fa314cd9 100644
--- a/docs/development.md
+++ b/docs/development.md
@@ -30,10 +30,38 @@ Its environment alternatives are tested without installing packages during the t
 
 - PEP 8 naming; lines up to 100 characters.
 - `ruff format` formats the code and `ruff check` lints it; both run in CI.
-- Type hints on all public functions.
+- Type hints on all functions (see the code standards below).
 - NumPy-style docstrings on public modules, classes and functions.
 - Comments explain *why*, not *what*.
 
+## Code standards (MorphoBricks spec §9)
+
+`python tools/check.py` runs everything a pull request must pass: `ruff check`,
+`ruff format --check`, pytest and the code rules. CI runs the code rules with
+`python tools/check.py --rules`.
+
+- **Size:** files at most 600 lines; functions at most 60 executable lines, complexity 15
+  (`C901`), 8 parameters (`PLR0913`) and 50 statements (`PLR0915`).
+- **Annotations** on every function in `src` and `tools`, private and nested ones included
+  (`ANN`), with `from __future__ import annotations` in every module (`I002`). Tests are
+  exempt, as they are from the docstring rules.
+- **Docstrings:** NumPy style for public names (`D`); at least an imperative line for
+  private functions over 10 lines.
+- **Layers:** every module of the package is declared `pure`, `io`, `ui` or
+  `orchestration` in `pyproject.toml` (`[tool.morphobricks.code-rules.layers]`). Pure
+  modules do no I/O and no UI; UI modules do not compute.
+- **Ownership:** shared logic lives in its owner repository; `RESERVED_NAMES` in
+  `tools/code_rules.py` fails a copy anywhere else. Write files with
+  `_io.write_text_atomic` and word messages with `validation.plural` and
+  `validation.agree`, never a local copy.
+- **Enforcement:** `tools/code_rules.py` is the shared file, identical in every MorphoBricks
+  repository (`tests/test_code_rules.py` checks its SHA-256). The violations that existed
+  when the rules came in are listed in `tools/code_rules_baseline.json`, with the number of
+  `# noqa` comments of the rules above. The baseline may only shrink: a new or grown
+  violation fails, and so does an entry the code no longer needs, until
+  `python tools/check.py --update-baseline` lowers it (it never adds an entry). A `# noqa`
+  must name its rules (`PGH004`), and line and file-level ones are counted, tests included.
+
 ## Design rules
 
 - Small dataclasses for settings and results; no global state.
diff --git a/notebooks/MorphoBricks_Preprocessing.ipynb b/notebooks/MorphoBricks_Preprocessing.ipynb
index f7a9ec26..f24ac29d 100644
--- a/notebooks/MorphoBricks_Preprocessing.ipynb
+++ b/notebooks/MorphoBricks_Preprocessing.ipynb
@@ -111,7 +111,7 @@
     "notebook_name = \"MorphoBricks_Preprocessing\"\n",
     "\n",
     "\n",
-    "def _start_preprocessing_notebook():\n",
+    "def _start_preprocessing_notebook() -> object:\n",
     "    \"\"\"Prepare this kernel's environment and return the notebook interface.\"\"\"\n",
     "    # This standalone cell can run before the package's Python requirement is checked.\n",
     "    if sys.version_info < (3, 11):  # noqa: UP036\n",
diff --git a/pyproject.toml b/pyproject.toml
index 13408511..c6743a1a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -67,7 +67,8 @@ addopts = "-ra"
 [tool.ruff]
 line-length = 100
 target-version = "py311"
-src = ["src", "tests"]
+src = ["src", "tests", "tools"]
+extend-exclude = ["tests/guard_fixtures"]
 
 [tool.ruff.lint]
 select = [
@@ -79,6 +80,11 @@ select = [
     "UP",  # modern syntax for the target Python
     "NPY", # numpy-specific checks
     "D",   # docstrings
+    "C90", # complexity (spec §9: at most 15)
+    "PLR0913", # at most 8 parameters
+    "PLR0915", # at most 50 statements
+    "ANN", # complete annotations
+    "PGH004", # a noqa names its rules, so the noqa ratchet sees every one
 ]
 ignore = [
     "D105", # magic methods need no docstring
@@ -88,6 +94,62 @@ ignore = [
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
+[tool.ruff.lint.mccabe]
+max-complexity = 15
+
+[tool.ruff.lint.pylint]
+max-args = 8
+max-statements = 50
+
+[tool.ruff.lint.isort]
+known-first-party = ["morphobricks_preprocessing", "code_rules", "check"]
+# Spec §9: annotations come with postponed evaluation (I002 enforces it).
+required-imports = ["from __future__ import annotations"]
+
 [tool.ruff.lint.per-file-ignores]
-"tests/**" = ["D"]
-"experiments/**" = ["D", "E501", "B905"]  # study scripts kept as they were run
+"tests/**" = ["D", "ANN", "I002"]
+"experiments/**" = ["D", "E501", "B905", "ANN", "C90", "PLR", "I002"]  # study scripts kept as they were run
+"notebooks/**" = ["I002"]  # notebook cells are not modules
+
+[tool.morphobricks.code-rules]
+# The shared tools/code_rules.py (spec §9), configured for this repository.
+owner = "preprocessing"
+package = "src/morphobricks_preprocessing"
+baseline = "tools/code_rules_baseline.json"
+
+[tool.morphobricks.code-rules.layers]
+# pure: no I/O, no UI; io: reads or writes files; ui: notebook and command line, no
+# computing; orchestration: ties the others together.
+"morphobricks_preprocessing" = "orchestration"
+"morphobricks_preprocessing.__main__" = "ui"
+"morphobricks_preprocessing._io" = "io"
+"morphobricks_preprocessing._moved" = "pure"
+"morphobricks_preprocessing.axes" = "pure"
+"morphobricks_preprocessing.axis_check" = "pure"
+"morphobricks_preprocessing.mask_checks" = "pure"
+"morphobricks_preprocessing.notebook_axes" = "ui"
+"morphobricks_preprocessing.cli" = "ui"
+"morphobricks_preprocessing.csv_io" = "pure"
+"morphobricks_preprocessing.dataset" = "pure"
+"morphobricks_preprocessing.design" = "io"
+"morphobricks_preprocessing.discovery" = "io"
+"morphobricks_preprocessing.dtypes" = "pure"
+"morphobricks_preprocessing.histogram" = "pure"
+"morphobricks_preprocessing.image_type" = "pure"
+"morphobricks_preprocessing.intensity" = "io"
+"morphobricks_preprocessing.manifest" = "io"
+"morphobricks_preprocessing.mask_scan" = "io"
+"morphobricks_preprocessing.masks" = "io"
+"morphobricks_preprocessing.metadata" = "io"
+"morphobricks_preprocessing.normalization" = "pure"
+"morphobricks_preprocessing.notebook_style" = "ui"
+"morphobricks_preprocessing.notebook_ui" = "ui"
+"morphobricks_preprocessing.physical_sizes" = "io"
+"morphobricks_preprocessing.planes" = "io"
+"morphobricks_preprocessing.pooling" = "pure"
+"morphobricks_preprocessing.records" = "pure"
+"morphobricks_preprocessing.report" = "pure"
+"morphobricks_preprocessing.run" = "orchestration"
+"morphobricks_preprocessing.validation" = "pure"
+"morphobricks_preprocessing.zarr_export" = "io"
+"morphobricks_preprocessing.zarr_input" = "io"
diff --git a/src/morphobricks_preprocessing/__init__.py b/src/morphobricks_preprocessing/__init__.py
index 4f76d2ae..c57e6ea5 100644
--- a/src/morphobricks_preprocessing/__init__.py
+++ b/src/morphobricks_preprocessing/__init__.py
@@ -6,6 +6,8 @@
 group statistics and normalization parameters without rereading the images.
 """
 
+from __future__ import annotations
+
 from importlib.metadata import PackageNotFoundError, version
 
 # The modules that moved to morphobricks_normalization stay importable as
diff --git a/src/morphobricks_preprocessing/__main__.py b/src/morphobricks_preprocessing/__main__.py
index 0fbfca45..bce50085 100644
--- a/src/morphobricks_preprocessing/__main__.py
+++ b/src/morphobricks_preprocessing/__main__.py
@@ -1,5 +1,7 @@
 """Allow ``python -m morphobricks_preprocessing``."""
 
+from __future__ import annotations
+
 import sys
 
 from .cli import main
diff --git a/src/morphobricks_preprocessing/_io.py b/src/morphobricks_preprocessing/_io.py
new file mode 100644
index 00000000..0596fbbc
--- /dev/null
+++ b/src/morphobricks_preprocessing/_io.py
@@ -0,0 +1,45 @@
+"""File writing shared by the brick's modules (private).
+
+Every file the brick writes is written atomically: to a temporary file in the same folder,
+then moved over the target with :func:`os.replace`, so a reader never sees half a file
+and an interrupted write leaves the earlier file as it was (contract §9). One function
+does it, so the rule is not copied per output file.
+"""
+
+from __future__ import annotations
+
+import os
+import tempfile
+from pathlib import Path
+
+
+def write_text_atomic(path: str | os.PathLike, text: str, *, parents: bool = False) -> Path:
+    """Write UTF-8 text to ``path`` atomically, with the line endings as given.
+
+    Parameters
+    ----------
+    path
+        The file to write; replaced only once the whole text is written.
+    text
+        The content. Line endings are written as they are (no translation), so a text
+        with LF line endings gives LF on every platform.
+    parents
+        Create the missing parent folders first.
+
+    Returns
+    -------
+    Path
+        The file written.
+    """
+    path = Path(path)
+    if parents:
+        path.parent.mkdir(parents=True, exist_ok=True)
+    handle, temporary = tempfile.mkstemp(prefix=f".{path.name}.", suffix=".tmp", dir=path.parent)
+    try:
+        with os.fdopen(handle, "w", newline="", encoding="utf-8") as stream:
+            stream.write(text)
+        os.replace(temporary, path)
+    except BaseException:
+        Path(temporary).unlink(missing_ok=True)
+        raise
+    return path
diff --git a/src/morphobricks_preprocessing/cli.py b/src/morphobricks_preprocessing/cli.py
index 86ffaabf..26b94caa 100644
--- a/src/morphobricks_preprocessing/cli.py
+++ b/src/morphobricks_preprocessing/cli.py
@@ -432,7 +432,7 @@ def progress(done: int, total: int, path: str) -> None:
     return 0
 
 
-def _run(args: argparse.Namespace) -> int:
+def _run(args: argparse.Namespace) -> int:  # noqa: PLR0915
     pre = preflight(args.experiment, args.output, exclude=args.exclude, masks_folder=args.masks)
     axes = reference_axes(pre.metadata.files)
     if axes is None:
@@ -532,7 +532,7 @@ def progress(done: int, total: int, path: str) -> None:
     return 0 if result.written else 1
 
 
-def _design_for_run(pre, args: argparse.Namespace) -> tuple[ExperimentDesign | None, str]:
+def _design_for_run(pre, args: argparse.Namespace) -> tuple[ExperimentDesign | None, str]:  # noqa: ANN001
     """Return the confirmed experiment design, or None and what the user has to do.
 
     Without a fully confirmed design, a template (keeping every answer already
@@ -595,7 +595,7 @@ def _image_type_note(review: ImageTypeReview, given: str | None) -> str:
     return "\n".join(lines)
 
 
-def _conversion_note(pre, conversion: ConversionSettings, output) -> str:
+def _conversion_note(pre, conversion: ConversionSettings, output) -> str:  # noqa: ANN001
     estimate = estimate_conversion(pre.discovery.root, pre.metadata.files, conversion)
     if not estimate.image_count:
         return "Conversion: there are no TIFF images to convert."
diff --git a/src/morphobricks_preprocessing/dataset.py b/src/morphobricks_preprocessing/dataset.py
index ca17f01f..e48393ae 100644
--- a/src/morphobricks_preprocessing/dataset.py
+++ b/src/morphobricks_preprocessing/dataset.py
@@ -271,7 +271,7 @@ def check_dataset(
     return DatasetReport(tuple(repeats), balance, tuple(issues))
 
 
-def _repeat_folder(leaf) -> str:
+def _repeat_folder(leaf) -> str:  # noqa: ANN001
     if leaf.condition == SINGLE:
         return ROOT
     parts = leaf.relative_path.split("/")
diff --git a/src/morphobricks_preprocessing/design.py b/src/morphobricks_preprocessing/design.py
index 6a8178fc..2142ac97 100644
--- a/src/morphobricks_preprocessing/design.py
+++ b/src/morphobricks_preprocessing/design.py
@@ -23,7 +23,6 @@
 import hashlib
 import io
 import os
-import tempfile
 from collections.abc import Iterable, Mapping
 from dataclasses import dataclass, replace
 from pathlib import Path
@@ -31,6 +30,7 @@
 
 from morphobricks_normalization.records import SINGLE
 
+from ._io import write_text_atomic
 from .dataset import BiologicalRepeat
 from .discovery import IdentityError, check_identity_case, check_identity_text
 from .validation import ValidationIssue, error, plural
@@ -686,16 +686,7 @@ def write_experiment_design(design: ExperimentDesign, path: str | os.PathLike) -
                 DESIGN_SCHEMA_VERSION,
             ]
         )
-    path.parent.mkdir(parents=True, exist_ok=True)
-    handle, temporary = tempfile.mkstemp(prefix=f".{path.name}.", suffix=".tmp", dir=path.parent)
-    try:
-        with os.fdopen(handle, "w", newline="", encoding="utf-8") as fh:
-            fh.write(buffer.getvalue())
-        os.replace(temporary, path)
-    except BaseException:
-        Path(temporary).unlink(missing_ok=True)
-        raise
-    return path
+    return write_text_atomic(path, buffer.getvalue(), parents=True)
 
 
 def load_design(
diff --git a/src/morphobricks_preprocessing/discovery.py b/src/morphobricks_preprocessing/discovery.py
index 56f43809..36c8020f 100644
--- a/src/morphobricks_preprocessing/discovery.py
+++ b/src/morphobricks_preprocessing/discovery.py
@@ -32,7 +32,7 @@
 import numpy as np
 from morphobricks_normalization.records import LEVELS, SINGLE
 
-from .validation import ValidationIssue, error, has_errors, plural, warning
+from .validation import ValidationIssue, agree, error, has_errors, plural, warning
 from .zarr_input import is_zarr_name
 
 logger = logging.getLogger(__name__)
@@ -470,7 +470,8 @@ def mask_name_issues(
         issues.append(
             warning(
                 "image_named_as_mask",
-                f"{plural(len(named), 'image')} {_are(named)} named as a mask of another "
+                f"{plural(len(named), 'image')} "
+                f"{agree(named, 'is', 'are')} named as a mask of another "
                 "image: that image's name followed by "
                 + ", ".join(sorted(suffixes))
                 + f" ({_few([f'{file} (of {owner})' for file, owner in named])}). A mask is "
@@ -591,7 +592,7 @@ def _few(items: list[str], shown: int = 5) -> str:
 class _Walker:
     """Collects leaf folders and problem paths during one walk."""
 
-    def __init__(self, root: Path):
+    def __init__(self, root: Path):  # noqa: ANN204
         self.root = root
         self.excluded: Path | None = None
         self.leaves: list[LeafFolder] = []
@@ -807,7 +808,8 @@ def finish(self) -> tuple[ValidationIssue, ...]:
             issues.append(
                 warning(
                     "empty_folder",
-                    f"{plural(len(self.empty), 'folder')} {_contain(self.empty)} no images "
+                    f"{plural(len(self.empty), 'folder')} "
+                    f"{agree(self.empty, 'contains', 'contain')} no images "
                     "and no subfolders and will not be analysed.",
                     self.empty,
                     "No action needed if this is expected. Otherwise add the missing images "
@@ -821,7 +823,8 @@ def finish(self) -> tuple[ValidationIssue, ...]:
                 # refuses it, so they are never dropped silently.
                 error(
                     "tiff_outside_leaf",
-                    f"{plural(len(self.outside_leaf), 'image')} {_are(self.outside_leaf)} "
+                    f"{plural(len(self.outside_leaf), 'image')} "
+                    f"{agree(self.outside_leaf, 'is', 'are')} "
                     "in folders that also contain subfolders. A folder holds either images "
                     "or subfolders, never both, so these images have no place in the "
                     "experiment's levels.",
@@ -842,11 +845,3 @@ def finish(self) -> tuple[ValidationIssue, ...]:
                 )
             )
         return tuple(issues)
-
-
-def _are(items: list) -> str:
-    return "is" if len(items) == 1 else "are"
-
-
-def _contain(items: list) -> str:
-    return "contains" if len(items) == 1 else "contain"
diff --git a/src/morphobricks_preprocessing/manifest.py b/src/morphobricks_preprocessing/manifest.py
index 8deb948d..dc2c182e 100644
--- a/src/morphobricks_preprocessing/manifest.py
+++ b/src/morphobricks_preprocessing/manifest.py
@@ -23,7 +23,6 @@
 import json
 import os
 import platform
-import tempfile
 from collections.abc import Iterable, Mapping, Sequence
 from dataclasses import asdict, dataclass, field
 from importlib.metadata import PackageNotFoundError, version
@@ -36,6 +35,7 @@
 from morphobricks_normalization.csv_io import SCHEMA_VERSION
 from morphobricks_normalization.ranges import HistogramSettings, RangeCheck
 
+from ._io import write_text_atomic
 from .axes import AxisMapping, file_mapping_for
 from .discovery import position_id
 from .metadata import inspect_image
@@ -412,7 +412,7 @@ def from_dict(cls, data: dict) -> RunManifest:
             raise ManifestFormatError(f"The manifest is incomplete or malformed: {exc}") from exc
 
 
-def file_entry_for(
+def file_entry_for(  # noqa: PLR0913
     root: str | os.PathLike,
     relative_path: str,
     labels: tuple[str, str, str],
@@ -465,7 +465,7 @@ def source_fingerprint(path: str | os.PathLike) -> tuple[int, int]:
     return size, newest
 
 
-def check_sources(
+def check_sources(  # noqa: C901
     manifest: RunManifest,
     experiment_root: str | os.PathLike,
     relative_paths: Iterable[str],
@@ -643,17 +643,8 @@ def file_sha256(path: str | os.PathLike) -> str:
 
 def write_manifest(manifest: RunManifest, path: str | os.PathLike) -> Path:
     """Write a manifest as JSON, replacing the file only once writing succeeded."""
-    path = Path(path)
     text = json.dumps(manifest.to_dict(), indent=2, ensure_ascii=False) + "\n"
-    handle, temporary = tempfile.mkstemp(prefix=f".{path.name}.", suffix=".tmp", dir=path.parent)
-    try:
-        with os.fdopen(handle, "w", newline="\n", encoding="utf-8") as fh:
-            fh.write(text)
-        os.replace(temporary, path)
-    except BaseException:
-        Path(temporary).unlink(missing_ok=True)
-        raise
-    return path
+    return write_text_atomic(path, text)
 
 
 def read_manifest(path: str | os.PathLike) -> RunManifest:
@@ -750,7 +741,7 @@ def _flag(value: object, key: str | None = None) -> bool:
     return value
 
 
-def _plain(value):
+def _plain(value):  # noqa: ANN001, ANN202
     """Return a range check value as JSON data: Python numbers, lists for tuples."""
     if isinstance(value, tuple):
         return [_plain(item) for item in value]
diff --git a/src/morphobricks_preprocessing/mask_scan.py b/src/morphobricks_preprocessing/mask_scan.py
index 97837f88..ba10aca4 100644
--- a/src/morphobricks_preprocessing/mask_scan.py
+++ b/src/morphobricks_preprocessing/mask_scan.py
@@ -44,7 +44,6 @@
 import json
 import logging
 import os
-import tempfile
 from collections.abc import Callable, Mapping
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -53,6 +52,7 @@
 import numpy as np
 from scipy import ndimage
 
+from ._io import write_text_atomic
 from .manifest import package_versions
 from .masks import MaskInventory, check_labels, read_mask
 
@@ -418,18 +418,8 @@ def scan_masks(
 
 def write_mask_report(report: MaskReport, path: str | os.PathLike) -> Path:
     """Write the report as UTF-8 JSON (two-space indent, LF), atomically; return the path."""
-    target = Path(path)
-    target.parent.mkdir(parents=True, exist_ok=True)
     text = json.dumps(report.to_dict(), indent=2, ensure_ascii=False) + "\n"
-    handle, temporary = tempfile.mkstemp(prefix=".mask_report-", dir=target.parent)
-    try:
-        with os.fdopen(handle, "w", encoding="utf-8", newline="\n") as stream:
-            stream.write(text)
-        os.replace(temporary, target)
-    finally:
-        if os.path.exists(temporary):
-            os.remove(temporary)
-    return target
+    return write_text_atomic(path, text, parents=True)
 
 
 def _scan_plane(
diff --git a/src/morphobricks_preprocessing/masks.py b/src/morphobricks_preprocessing/masks.py
index 2dda8d13..72260e92 100644
--- a/src/morphobricks_preprocessing/masks.py
+++ b/src/morphobricks_preprocessing/masks.py
@@ -42,7 +42,7 @@
 from .axes import AxisMapping
 from .discovery import DiscoveryResult, is_system_name, is_tiff_name, position_id
 from .metadata import TiffMetadata, named_axes
-from .validation import ValidationIssue, error, has_errors, plural, warning
+from .validation import ValidationIssue, agree, error, has_errors, plural, warning
 from .zarr_input import (
     NgffError,
     ZarrUnavailableError,
@@ -540,12 +540,14 @@ def _suffix_matches(relative: Path, by_leaf: Mapping[str, list]) -> list[tuple[s
 
 
 def _layout_issues(loose: list[str], unpaired: list[str]) -> list[ValidationIssue]:
+    """Warn about files that are not masks and masks that match no analysed image."""
     issues = []
     if loose:
         issues.append(
             warning(
                 "mask_outside_type_folder",
-                f"{plural(len(loose), 'file')} in the masks folder {_are(loose)} not masks "
+                f"{plural(len(loose), 'file')} in the masks folder "
+                f"{agree(loose, 'is', 'are')} not masks "
                 "and will not be used.",
                 loose,
                 "Keep only masks there: Nuclei/<condition>/.../<image>.tif, or "
@@ -556,7 +558,8 @@ def _layout_issues(loose: list[str], unpaired: list[str]) -> list[ValidationIssu
         issues.append(
             warning(
                 "mask_without_image",
-                f"{plural(len(unpaired), 'file')} in the masks folder {_match(unpaired)} no "
+                f"{plural(len(unpaired), 'file')} in the masks folder "
+                f"{agree(unpaired, 'matches', 'match')} no "
                 "analysed image (same folders and image name) and will not be used.",
                 unpaired,
                 "Check the folder names and file names against the experiment, or remove "
@@ -826,8 +829,10 @@ def mask_plane_issues(
     return [
         error(
             "mask_planes_mismatch",
-            f"{plural(len(mismatched), 'mask')} {_do(mismatched)} not have the depth slices "
-            f"and time points of {_their(mismatched)} image: a 2D mask fits only an image with "
+            f"{plural(len(mismatched), 'mask')} "
+            f"{agree(mismatched, 'does', 'do')} not have the depth slices "
+            f"and time points of "
+            f"{agree(mismatched, 'its', 'their')} image: a 2D mask fits only an image with "
             "one plane, and a mask with depth (Z) or time (T) needs the same number of slices "
             "or time points as its image.",
             mismatched,
@@ -854,6 +859,7 @@ def _image_yx(meta: TiffMetadata) -> tuple[int, int] | None:
 def _missing_issues(
     types: tuple[str, ...], files: list[MaskFile], images: Mapping[str, TiffMetadata]
 ) -> list[ValidationIssue]:
+    """Warn about images without a mask of a type that other images have."""
     have = {(f.image, f.mask_type) for f in files}
     issues = []
     for mask_type in types:
@@ -862,30 +868,11 @@ def _missing_issues(
             issues.append(
                 warning(
                     "mask_missing",
-                    f"{plural(len(missing), 'image')} {_have(missing)} no {mask_type} mask; "
+                    f"{plural(len(missing), 'image')} "
+                    f"{agree(missing, 'has', 'have')} no {mask_type} mask; "
                     f"their {mask_type} objects cannot be measured.",
                     missing,
                     f"Add the {mask_type} masks of these images, or exclude the images.",
                 )
             )
     return issues
-
-
-def _do(items: list) -> str:
-    return "does" if len(items) == 1 else "do"
-
-
-def _their(items: list) -> str:
-    return "its" if len(items) == 1 else "their"
-
-
-def _are(items: list) -> str:
-    return "is" if len(items) == 1 else "are"
-
-
-def _match(items: list) -> str:
-    return "matches" if len(items) == 1 else "match"
-
-
-def _have(items: list) -> str:
-    return "has" if len(items) == 1 else "have"
diff --git a/src/morphobricks_preprocessing/notebook_style.py b/src/morphobricks_preprocessing/notebook_style.py
index 0dc25348..a495392f 100644
--- a/src/morphobricks_preprocessing/notebook_style.py
+++ b/src/morphobricks_preprocessing/notebook_style.py
@@ -221,7 +221,7 @@ def checklist(items: Iterable[tuple[bool, str]]) -> str:
     return f"<ul class='mb-check'>{lines}</ul>"
 
 
-def button(description: str, *, style: str = "", icon: str = "", tooltip: str = "", main=False):
+def button(description: str, *, style: str = "", icon: str = "", tooltip: str = "", main=False):  # noqa: ANN001, ANN201
     """Build a button; ``main`` buttons are full width and taller, for a step's main action."""
     layout = widgets.Layout(width="99%", height="42px") if main else widgets.Layout(width="auto")
     return widgets.Button(
@@ -282,7 +282,7 @@ class ConfirmToggle:
         Text of the button that takes the confirmation back.
     """
 
-    def __init__(
+    def __init__(  # noqa: ANN204
         self,
         question: str,
         explanation: str,
@@ -336,7 +336,7 @@ def explain(self, explanation: str) -> None:
             f"<div class='mb-help' style='margin-bottom:0'>{explanation}</div></div>"
         )
 
-    def observe(self, callback) -> None:
+    def observe(self, callback) -> None:  # noqa: ANN001
         """Call ``callback(value)`` whenever the answer changes."""
         self._callbacks.append(callback)
 
@@ -362,7 +362,7 @@ def set(self, value: bool, *, notify: bool = True) -> None:
                 callback(value)
 
 
-def ask_open_file(initial: str = "", filetypes=(("All files", "*.*"),)) -> str | None:
+def ask_open_file(initial: str = "", filetypes=(("All files", "*.*"),)) -> str | None:  # noqa: ANN001
     """Open the system's file dialog; return the chosen file, ``""`` if cancelled.
 
     Returns None when no dialog can be shown, like :func:`ask_directory`.
diff --git a/src/morphobricks_preprocessing/notebook_ui.py b/src/morphobricks_preprocessing/notebook_ui.py
index 12d4ec75..a327a325 100644
--- a/src/morphobricks_preprocessing/notebook_ui.py
+++ b/src/morphobricks_preprocessing/notebook_ui.py
@@ -221,7 +221,7 @@ class PreprocessingNotebook:
         Result of the last run, or None.
     """
 
-    def __init__(self, experiment_folder: str = "", output_folder: str = ""):
+    def __init__(self, experiment_folder: str = "", output_folder: str = ""):  # noqa: ANN204
         self.preflight: Preflight | None = None
         self.design: ExperimentDesign | None = None
         # True while the saved design cannot be read and has not been replaced by an answer.
@@ -1505,7 +1505,7 @@ def _render_preview(self) -> None:
         self.preview_caption.value = preview_caption(header.relative_path, plane)
         self._show_log()
 
-    def _preview_header(self):
+    def _preview_header(self):  # noqa: ANN202
         value = self.preview_file.value
         return next((f for f in self.preflight.metadata.files if f.relative_path == value), None)
 
@@ -2617,7 +2617,7 @@ class IntensityPanel:
         Help line under it (HTML).
     """
 
-    def __init__(self, title: str, explanation: str):
+    def __init__(self, title: str, explanation: str):  # noqa: ANN204
         self.records: list[PlaneRecord] = []
         self.report: IntensityReport | None = None
         defaults = IntensityCheckSettings()
@@ -3181,7 +3181,7 @@ def distribution_png(groups: dict[tuple[str, ...], list]) -> bytes | None:
 class _LogCapture(logging.Handler):
     """Collects the package's log messages for the "Technical details" panel."""
 
-    def __init__(self):
+    def __init__(self):  # noqa: ANN204
         super().__init__(logging.DEBUG)
         self.lines: list[str] = []
         self.setFormatter(logging.Formatter("%(asctime)s %(levelname)s %(name)s: %(message)s"))
@@ -3189,22 +3189,22 @@ def __init__(self):
     def emit(self, record: logging.LogRecord) -> None:
         self.lines.append(self.format(record))
 
-    def attached(self):
+    def attached(self):  # noqa: ANN202
         return _Attached(self)
 
 
 class _Attached:
-    def __init__(self, handler: logging.Handler):
+    def __init__(self, handler: logging.Handler):  # noqa: ANN204
         self.handler = handler
         self.logger = logging.getLogger(_PACKAGE_LOGGER)
 
-    def __enter__(self):
+    def __enter__(self):  # noqa: ANN204
         self.level = self.logger.level
         self.logger.addHandler(self.handler)
         self.logger.setLevel(logging.DEBUG)
         return self.handler
 
-    def __exit__(self, *exc):
+    def __exit__(self, *exc):  # noqa: ANN002, ANN204
         self.logger.removeHandler(self.handler)
         self.logger.setLevel(self.level)
         return False
@@ -3299,7 +3299,7 @@ def _conversion_help(available: bool) -> str:
     return "<ul>" + "".join(f"<li>{item}</li>" for item in items) + "</ul>"
 
 
-def _bins_help(dtype) -> str:
+def _bins_help(dtype) -> str:  # noqa: ANN001
     if is_integer(dtype):
         top = min(MAX_BIN_COUNT, 2 ** (dtype.itemsize * 8))
         exact = (
diff --git a/src/morphobricks_preprocessing/physical_sizes.py b/src/morphobricks_preprocessing/physical_sizes.py
index 2f67df18..ab679903 100644
--- a/src/morphobricks_preprocessing/physical_sizes.py
+++ b/src/morphobricks_preprocessing/physical_sizes.py
@@ -569,7 +569,7 @@ def _ngff_scale(entry: dict, ndim: int) -> list[float | None] | None:
     return None
 
 
-def _scale_value(value) -> float | None:
+def _scale_value(value) -> float | None:  # noqa: ANN001
     """Return one scale value as a float; None when it is not a usable number."""
     if isinstance(value, bool) or not isinstance(value, int | float):
         return None
@@ -646,7 +646,7 @@ def _imagej_sizes(tif: tifffile.TiffFile) -> PhysicalSizes:
     )
 
 
-def _ngff_unit(value, table: dict[str, str]) -> str | None:
+def _ngff_unit(value, table: dict[str, str]) -> str | None:  # noqa: ANN001
     """Return an OME-NGFF axis unit with common spellings as UDUNITS-2 names.
 
     ``"µm"``, ``"um"`` and ``"micron"`` become ``"micrometer"``, ``"s"``
@@ -660,7 +660,7 @@ def _ngff_unit(value, table: dict[str, str]) -> str | None:
     return known or text
 
 
-def _written(value) -> str | None:
+def _written(value) -> str | None:  # noqa: ANN001
     """Return a unit as the metadata write it (escapes decoded); None when blank."""
     if value is None:
         return None
@@ -668,11 +668,11 @@ def _written(value) -> str | None:
     return text or None
 
 
-def _imagej_unit(value) -> str | None:
+def _imagej_unit(value) -> str | None:  # noqa: ANN001
     return _SPACE_UNITS.get(_imagej_text(value))
 
 
-def _imagej_text(value) -> str:
+def _imagej_text(value) -> str:  # noqa: ANN001
     r"""Return an ImageJ unit in lower case, with its ``\uXXXX`` escapes decoded.
 
     ImageJ writes non-ASCII characters as ``\u00B5`` in the TIFF description, and
@@ -686,7 +686,7 @@ def _decode_escapes(text: str) -> str:
     return re.sub(r"\\u([0-9a-fA-F]{4})", lambda m: chr(int(m.group(1), 16)), text)
 
 
-def _resolution(tag) -> float | None:
+def _resolution(tag) -> float | None:  # noqa: ANN001
     if tag is None:
         return None
     try:
@@ -696,7 +696,7 @@ def _resolution(tag) -> float | None:
         return None
 
 
-def _number(value) -> float | None:
+def _number(value) -> float | None:  # noqa: ANN001
     if isinstance(value, bool):  # True would otherwise read as a size of 1
         return None
     try:
diff --git a/src/morphobricks_preprocessing/planes.py b/src/morphobricks_preprocessing/planes.py
index a8469024..4ecf6906 100644
--- a/src/morphobricks_preprocessing/planes.py
+++ b/src/morphobricks_preprocessing/planes.py
@@ -733,7 +733,7 @@ def _open(path: str | os.PathLike) -> tifffile.TiffFile:
     return tif
 
 
-def _check_fit(shape: tuple[int, ...], axes: str, mapping: AxisMapping, path) -> tuple[int, int]:
+def _check_fit(shape: tuple[int, ...], axes: str, mapping: AxisMapping, path) -> tuple[int, int]:  # noqa: ANN001
     """Check that ``mapping`` fits an image; return the Y and X dimensions."""
     if axes != mapping.axes:
         raise PlaneReadError(
@@ -756,7 +756,7 @@ def _check_fit(shape: tuple[int, ...], axes: str, mapping: AxisMapping, path) ->
 def _layout(
     series: tifffile.TiffPageSeries,
     mapping: AxisMapping,
-    path,
+    path,  # noqa: ANN001
     binning: _Binning,
     memory_limit: int = DEFAULT_MEMORY_LIMIT,
 ) -> PlaneLayout:
@@ -839,7 +839,7 @@ def _finished_histograms_nbytes(dtype: np.dtype, bin_count: int | None, channels
     return channels * 8 * (default_bin_count(dtype) if bin_count is None else bin_count)
 
 
-def _check_limit(layout: PlaneLayout, path) -> None:
+def _check_limit(layout: PlaneLayout, path) -> None:  # noqa: ANN001
     if not layout.fits:
         raise PlaneMemoryError(
             f"Reading one plane of {Path(path).name} needs about "
@@ -880,7 +880,10 @@ def at(position: dict[int, int], channel: int) -> dict[int, int]:
 
 
 def _tiff_reader(
-    series: tifffile.TiffPageSeries, layout: PlaneLayout, mapping: AxisMapping, path
+    series: tifffile.TiffPageSeries,
+    layout: PlaneLayout,
+    mapping: AxisMapping,
+    path,  # noqa: ANN001
 ) -> Callable[[dict[int, int]], Plane]:
     """Return a function reading the plane at a position, keeping the last page decoded.
 
@@ -906,7 +909,7 @@ def _read_one(
     series: tifffile.TiffPageSeries,
     layout: PlaneLayout,
     mapping: AxisMapping,
-    path,
+    path,  # noqa: ANN001
     wanted: Mapping[str, int | None],
 ) -> Plane:
     position = _position(layout, mapping, wanted)
@@ -949,7 +952,7 @@ def _page_index(layout: PlaneLayout, position: Mapping[int, int]) -> int:
     return int(np.ravel_multi_index([position[d] for d in range(k)], layout.shape[:k]))
 
 
-def _read_page(series: tifffile.TiffPageSeries, index: int, layout: PlaneLayout, path):
+def _read_page(series: tifffile.TiffPageSeries, index: int, layout: PlaneLayout, path):  # noqa: ANN001, ANN202
     page = series.pages[index]
     if page is None:
         raise PlaneReadError(f"Page {index} of {path} is missing from the file.")
@@ -1118,7 +1121,7 @@ def _block_plane(
 
 def _whole_or_preview(
     layout: PlaneLayout,
-    path,
+    path,  # noqa: ANN001
     preview: bool,
     reblock: Callable[[int], PlaneLayout],
 ) -> PlaneLayout:
@@ -1182,7 +1185,11 @@ def _whole_or_reduced(plane: Plane, layout: PlaneLayout) -> Plane:
 
 
 def _tiff_blocking(
-    keyframe, shape: tuple[int, ...], split: int, y: int, x: int
+    keyframe: tifffile.TiffPage,
+    shape: tuple[int, ...],
+    split: int,
+    y: int,
+    x: int,
 ) -> _Blocking | None:
     """Work out how the pages of a series are stored in strips or tiles, if they can be split.
 
@@ -1227,7 +1234,7 @@ def _tiff_blocking(
     )
 
 
-def _tiff_reblock(series, mapping: AxisMapping, path) -> Callable[[int], PlaneLayout]:
+def _tiff_reblock(series, mapping: AxisMapping, path) -> Callable[[int], PlaneLayout]:  # noqa: ANN001
     return lambda limit: _layout(series, mapping, path, _Binning(), limit)
 
 
@@ -1236,7 +1243,7 @@ def _tiff_block_plane(
     layout: PlaneLayout,
     mapping: AxisMapping,
     position: Mapping[int, int],
-    path,
+    path,  # noqa: ANN001
 ) -> Plane:
     index = _page_index(layout, position)
     page = series.pages[index]
@@ -1255,7 +1262,7 @@ def _tiff_block_plane(
     )
 
 
-def _read_tiff_block(page, layout: PlaneLayout, where: list[int], box, path) -> np.ndarray:
+def _read_tiff_block(page, layout: PlaneLayout, where: list[int], box, path) -> np.ndarray:  # noqa: ANN001
     """Read rows ``r0 .. r1`` and columns ``c0 .. c1`` of one plane of a page, piece by piece."""
     r0, r1, c0, c1 = box
     keyframe = page.keyframe
@@ -1289,7 +1296,7 @@ def _read_tiff_block(page, layout: PlaneLayout, where: list[int], box, path) ->
     return out
 
 
-def _read_segment(page, index: int, z: int, rows: tuple[int, int], blocking: _Blocking, path):
+def _read_segment(page, index: int, z: int, rows: tuple[int, int], blocking: _Blocking, path):  # noqa: ANN001, ANN202
     """Read rows of one strip or tile as (rows, columns, contiguous samples), or None if empty.
 
     Uncompressed pieces are read straight from the file, only the rows wanted;
@@ -1328,7 +1335,7 @@ def _read_segment(page, index: int, z: int, rows: tuple[int, int], blocking: _Bl
 # OME-Zarr ------------------------------------------------------------------------------
 
 
-def _open_zarr(path) -> NgffImage:
+def _open_zarr(path) -> NgffImage:  # noqa: ANN001
     try:
         return open_ngff(path)
     except (NgffError, ZarrUnavailableError) as exc:
@@ -1338,7 +1345,7 @@ def _open_zarr(path) -> NgffImage:
 def _zarr_layout(
     image: NgffImage,
     mapping: AxisMapping,
-    path,
+    path,  # noqa: ANN001
     binning: _Binning,
     memory_limit: int = DEFAULT_MEMORY_LIMIT,
 ) -> PlaneLayout:
@@ -1385,12 +1392,16 @@ def _zarr_layout(
     return _with_blocks(layout, blocking, binning)
 
 
-def _zarr_reblock(image: NgffImage, mapping: AxisMapping, path) -> Callable[[int], PlaneLayout]:
+def _zarr_reblock(image: NgffImage, mapping: AxisMapping, path) -> Callable[[int], PlaneLayout]:  # noqa: ANN001
     return lambda limit: _zarr_layout(image, mapping, path, _Binning(), limit)
 
 
 def _zarr_plane(
-    image: NgffImage, layout: PlaneLayout, mapping: AxisMapping, position: Mapping[int, int], path
+    image: NgffImage,
+    layout: PlaneLayout,
+    mapping: AxisMapping,
+    position: Mapping[int, int],
+    path,  # noqa: ANN001
 ) -> Plane:
     if layout.in_blocks:
         rows, cols = layout.blocking.rows, layout.blocking.cols
@@ -1404,7 +1415,7 @@ def read(r0: int, r1: int, c0: int, c1: int) -> np.ndarray:
     return _finish(_zarr_read(image, selection, path), layout, mapping, position)
 
 
-def _zarr_read(image: NgffImage, selection: tuple, path) -> np.ndarray:
+def _zarr_read(image: NgffImage, selection: tuple, path) -> np.ndarray:  # noqa: ANN001
     try:
         return read_selection(image.array, selection)
     except Exception as exc:  # decoding errors come from many codecs and stores
diff --git a/src/morphobricks_preprocessing/report.py b/src/morphobricks_preprocessing/report.py
index 1eecfbf9..dadf1885 100644
--- a/src/morphobricks_preprocessing/report.py
+++ b/src/morphobricks_preprocessing/report.py
@@ -439,7 +439,7 @@ def _relationship_line(pair: PairRelation) -> str:
     return text + (f"; {', '.join(extra)}" if extra else "")
 
 
-def _hierarchy_lines(hierarchy) -> list[str]:
+def _hierarchy_lines(hierarchy) -> list[str]:  # noqa: ANN001
     """Return the mask types as an indented tree; a type with two parents shows twice."""
     children: dict[str, list[str]] = {name: [] for name in hierarchy}
     for name, parents in hierarchy.items():
diff --git a/src/morphobricks_preprocessing/run.py b/src/morphobricks_preprocessing/run.py
index 2ff3a4ca..01ffcb49 100644
--- a/src/morphobricks_preprocessing/run.py
+++ b/src/morphobricks_preprocessing/run.py
@@ -336,7 +336,7 @@ def preflight(
     )
 
 
-def run_experiment(
+def run_experiment(  # noqa: C901, PLR0913, PLR0915
     experiment_root: str | os.PathLike,
     mapping: AxisMapping,
     *,
@@ -495,7 +495,7 @@ def run_experiment(
             )
         )
 
-    def stop(**counts) -> RunResult:
+    def stop(**counts) -> RunResult:  # noqa: ANN003
         return RunResult(output, False, _sorted(issues), excluded=pre.excluded, **counts)
 
     if has_errors(issues):
@@ -858,7 +858,7 @@ class _CopyStaging:
     which reuses this folder; :meth:`discard` removes it when the run stops early.
     """
 
-    def __init__(self, output: Path, experiment_root: Path, settings: ConversionSettings):
+    def __init__(self, output: Path, experiment_root: Path, settings: ConversionSettings):  # noqa: ANN204
         self.output = output
         self.experiment_root = experiment_root
         self.settings = settings
@@ -952,7 +952,7 @@ def _load_previous(
     return manifest, by_file, None
 
 
-def _bin_count(dtype, bin_count: int | None) -> tuple[int | None, list[ValidationIssue]]:
+def _bin_count(dtype, bin_count: int | None) -> tuple[int | None, list[ValidationIssue]]:  # noqa: ANN001
     if bin_count is None:
         return default_bin_count(dtype), []
     try:
diff --git a/src/morphobricks_preprocessing/validation.py b/src/morphobricks_preprocessing/validation.py
index b8f2e6a4..09c81dbd 100644
--- a/src/morphobricks_preprocessing/validation.py
+++ b/src/morphobricks_preprocessing/validation.py
@@ -7,7 +7,7 @@
 
 from __future__ import annotations
 
-from collections.abc import Iterable
+from collections.abc import Iterable, Sized
 from dataclasses import dataclass
 from enum import StrEnum
 
@@ -81,3 +81,23 @@ def plural(count: int, singular: str, plural_form: str | None = None) -> str:
     """Return e.g. ``"1 file"`` or ``"3 files"`` for plain-language messages."""
     word = singular if count == 1 else (plural_form or f"{singular}s")
     return f"{count:,} {word}"
+
+
+def agree(items: Sized, one: str, several: str) -> str:
+    """Return the word that agrees with how many items there are.
+
+    The one grammar helper of the brick's messages, beside :func:`plural`.
+
+    Parameters
+    ----------
+    items
+        The items the word is about.
+    one, several
+        The word for one item and for several, e.g. ``"is"`` and ``"are"``.
+
+    Returns
+    -------
+    str
+        ``one`` for exactly one item, ``several`` otherwise.
+    """
+    return one if len(items) == 1 else several
diff --git a/src/morphobricks_preprocessing/zarr_export.py b/src/morphobricks_preprocessing/zarr_export.py
index 5b5f05e4..69b14b6a 100644
--- a/src/morphobricks_preprocessing/zarr_export.py
+++ b/src/morphobricks_preprocessing/zarr_export.py
@@ -580,14 +580,14 @@ def copy_channels_current(copy: str | os.PathLike, channel_names: Sequence[str |
 # zarr 2 / 3 ---------------------------------------------------------------------------
 
 
-def _create_group(path: Path):
+def _create_group(path: Path):  # noqa: ANN202
     zarr = _zarr()
     if _zarr_major() >= 3:
         return zarr.open_group(str(path), mode="w", zarr_format=2)
     return zarr.open_group(str(path), mode="w")
 
 
-def _compressor(settings: ConversionSettings):
+def _compressor(settings: ConversionSettings):  # noqa: ANN202
     """Return the numcodecs compressor for ``settings``; None means no compression."""
     if settings.compression == "none":
         return None
@@ -600,7 +600,7 @@ def _compressor(settings: ConversionSettings):
     )
 
 
-def _create_array(group, name: str, shape, chunks, dtype, compressor):
+def _create_array(group, name: str, shape, chunks, dtype, compressor):  # noqa: ANN001, ANN202
     if _zarr_major() >= 3:
         return group.create_array(
             name,
diff --git a/src/morphobricks_preprocessing/zarr_input.py b/src/morphobricks_preprocessing/zarr_input.py
index 2e9e13b3..bef7aec2 100644
--- a/src/morphobricks_preprocessing/zarr_input.py
+++ b/src/morphobricks_preprocessing/zarr_input.py
@@ -281,7 +281,7 @@ def _image_group(path: str | os.PathLike) -> tuple[str, Any, dict, int]:
     return prefix, group, meta, image_count
 
 
-def _level0(group, meta: dict, prefix: str, image_count: int) -> NgffImage:
+def _level0(group, meta: dict, prefix: str, image_count: int) -> NgffImage:  # noqa: ANN001
     """Describe level 0 of the multiscales image in ``group``."""
     multiscales = meta.get("multiscales")
     if not multiscales:
@@ -335,7 +335,7 @@ def _physical_sizes(multiscale: dict, axes: str, where: str) -> PhysicalSizes:
         return PhysicalSizes()
 
 
-def _labels_group(group):
+def _labels_group(group):  # noqa: ANN001, ANN202
     """Return the ``labels`` group next to an image, or None when it has none."""
     try:
         labels = group["labels"]
@@ -344,7 +344,7 @@ def _labels_group(group):
     return labels if hasattr(labels, "group_keys") else None
 
 
-def ngff_axes(axes: Any, ndim: int) -> str:
+def ngff_axes(axes: Any, ndim: int) -> str:  # noqa: ANN401
     """Translate OME-NGFF axis metadata into one-letter codes.
 
     ``axes`` is the ``multiscales[0]["axes"]`` entry: a list of objects with
@@ -373,7 +373,7 @@ def ngff_axes(axes: Any, ndim: int) -> str:
     return "".join(letters)
 
 
-def read_selection(array: Any, selection: tuple) -> np.ndarray:
+def read_selection(array: Any, selection: tuple) -> np.ndarray:  # noqa: ANN401
     """Read part of a zarr array as a NumPy array in native byte order."""
     data = np.asarray(array[selection])
     return data.astype(canonical_dtype(data.dtype.newbyteorder("=")), copy=False)
@@ -382,7 +382,7 @@ def read_selection(array: Any, selection: tuple) -> np.ndarray:
 # zarr 2 / 3 ---------------------------------------------------------------------------
 
 
-def _zarr():
+def _zarr():  # noqa: ANN202
     try:
         import zarr
     except ImportError as exc:
@@ -397,14 +397,14 @@ def _zarr_major() -> int:
     return int(_zarr().__version__.split(".")[0])
 
 
-def _ome_attrs(group) -> dict:
+def _ome_attrs(group) -> dict:  # noqa: ANN001
     """Return the OME metadata of a group (nested under ``"ome"`` in OME-NGFF 0.5)."""
     attrs = dict(group.attrs)
     ome = attrs.get("ome")
     return dict(ome) if isinstance(ome, dict) else attrs
 
 
-def _descend(group, path: str):
+def _descend(group, path: str):  # noqa: ANN001, ANN202
     try:
         child = group[path]
     except KeyError as exc:
diff --git a/tests/guard_fixtures/README.md b/tests/guard_fixtures/README.md
new file mode 100644
index 00000000..95454f45
--- /dev/null
+++ b/tests/guard_fixtures/README.md
@@ -0,0 +1,3 @@
+Deliberately bad modules for `tests/test_code_rules.py`: each one breaks one code rule, to
+prove the rule fires. Ruff skips this folder (`extend-exclude`), and the code rules leave it
+out of the repository check.
diff --git a/tests/guard_fixtures/blanket_noqa.py b/tests/guard_fixtures/blanket_noqa.py
new file mode 100644
index 00000000..10e6713a
--- /dev/null
+++ b/tests/guard_fixtures/blanket_noqa.py
@@ -0,0 +1,8 @@
+"""A noqa that names no rule."""
+
+from __future__ import annotations
+
+
+def add(a: int, b: int) -> int:  # noqa
+    """Add two numbers."""
+    return a + b
diff --git a/tests/guard_fixtures/long_function.py b/tests/guard_fixtures/long_function.py
new file mode 100644
index 00000000..bb98967a
--- /dev/null
+++ b/tests/guard_fixtures/long_function.py
@@ -0,0 +1,70 @@
+"""A function of more than 60 executable lines."""
+
+from __future__ import annotations
+
+
+def long() -> int:
+    """Add many numbers."""
+    total = 0
+    total += 0
+    total += 1
+    total += 2
+    total += 3
+    total += 4
+    total += 5
+    total += 6
+    total += 7
+    total += 8
+    total += 9
+    total += 10
+    total += 11
+    total += 12
+    total += 13
+    total += 14
+    total += 15
+    total += 16
+    total += 17
+    total += 18
+    total += 19
+    total += 20
+    total += 21
+    total += 22
+    total += 23
+    total += 24
+    total += 25
+    total += 26
+    total += 27
+    total += 28
+    total += 29
+    total += 30
+    total += 31
+    total += 32
+    total += 33
+    total += 34
+    total += 35
+    total += 36
+    total += 37
+    total += 38
+    total += 39
+    total += 40
+    total += 41
+    total += 42
+    total += 43
+    total += 44
+    total += 45
+    total += 46
+    total += 47
+    total += 48
+    total += 49
+    total += 50
+    total += 51
+    total += 52
+    total += 53
+    total += 54
+    total += 55
+    total += 56
+    total += 57
+    total += 58
+    total += 59
+    total += 60
+    return total
diff --git a/tests/guard_fixtures/many_arguments.py b/tests/guard_fixtures/many_arguments.py
new file mode 100644
index 00000000..20c088bd
--- /dev/null
+++ b/tests/guard_fixtures/many_arguments.py
@@ -0,0 +1,8 @@
+"""A function with nine parameters."""
+
+from __future__ import annotations
+
+
+def nine(a: int, b: int, c: int, d: int, e: int, f: int, g: int, h: int, i: int) -> int:
+    """Add nine numbers."""
+    return a + b + c + d + e + f + g + h + i
diff --git a/tests/guard_fixtures/missing_annotation.py b/tests/guard_fixtures/missing_annotation.py
new file mode 100644
index 00000000..a61b465b
--- /dev/null
+++ b/tests/guard_fixtures/missing_annotation.py
@@ -0,0 +1,6 @@
+"""A function without annotations, in a module without `from __future__ import annotations`."""
+
+
+def add(a, b):
+    """Add two numbers."""
+    return a + b
diff --git a/tests/guard_fixtures/private_without_docstring.py b/tests/guard_fixtures/private_without_docstring.py
new file mode 100644
index 00000000..04a28b55
--- /dev/null
+++ b/tests/guard_fixtures/private_without_docstring.py
@@ -0,0 +1,19 @@
+"""A private function over 10 lines without a docstring."""
+
+from __future__ import annotations
+
+
+def _helper() -> int:
+    total = 0
+    total += 0
+    total += 1
+    total += 2
+    total += 3
+    total += 4
+    total += 5
+    total += 6
+    total += 7
+    total += 8
+    total += 9
+    total += 10
+    return total
diff --git a/tests/guard_fixtures/pure_with_io.py b/tests/guard_fixtures/pure_with_io.py
new file mode 100644
index 00000000..1b2b0a6e
--- /dev/null
+++ b/tests/guard_fixtures/pure_with_io.py
@@ -0,0 +1,11 @@
+"""A module declared pure that writes a file."""
+
+from __future__ import annotations
+
+import os
+
+
+def save(text: str) -> None:
+    """Write text."""
+    with open(os.devnull, "w", encoding="utf-8") as stream:
+        stream.write(text)
diff --git a/tests/guard_fixtures/reserved_copy.py b/tests/guard_fixtures/reserved_copy.py
new file mode 100644
index 00000000..0775aebf
--- /dev/null
+++ b/tests/guard_fixtures/reserved_copy.py
@@ -0,0 +1,8 @@
+"""A copy of a function owned by another repository."""
+
+from __future__ import annotations
+
+
+def min_max(values: list[float]) -> tuple[float, float]:
+    """Return the smallest and largest value."""
+    return min(values), max(values)
diff --git a/tests/guard_fixtures/too_complex.py b/tests/guard_fixtures/too_complex.py
new file mode 100644
index 00000000..f4e7f68a
--- /dev/null
+++ b/tests/guard_fixtures/too_complex.py
@@ -0,0 +1,38 @@
+"""A function above the complexity limit of 15."""
+
+from __future__ import annotations
+
+
+def branches(x: int) -> int:
+    """Return a number through many branches."""
+    if x == 0:
+        return 0
+    if x == 1:
+        return 1
+    if x == 2:
+        return 2
+    if x == 3:
+        return 3
+    if x == 4:
+        return 4
+    if x == 5:
+        return 5
+    if x == 6:
+        return 6
+    if x == 7:
+        return 7
+    if x == 8:
+        return 8
+    if x == 9:
+        return 9
+    if x == 10:
+        return 10
+    if x == 11:
+        return 11
+    if x == 12:
+        return 12
+    if x == 13:
+        return 13
+    if x == 14:
+        return 14
+    return 15
diff --git a/tests/guard_fixtures/ui_computing.py b/tests/guard_fixtures/ui_computing.py
new file mode 100644
index 00000000..7488db9c
--- /dev/null
+++ b/tests/guard_fixtures/ui_computing.py
@@ -0,0 +1,10 @@
+"""A module declared ui that computes with scipy."""
+
+from __future__ import annotations
+
+from scipy import ndimage
+
+
+def label(mask: object) -> object:
+    """Label a mask."""
+    return ndimage.label(mask)
diff --git a/tests/guard_fixtures/uses_suppress.py b/tests/guard_fixtures/uses_suppress.py
new file mode 100644
index 00000000..aa342640
--- /dev/null
+++ b/tests/guard_fixtures/uses_suppress.py
@@ -0,0 +1,11 @@
+"""A module that hides exceptions."""
+
+from __future__ import annotations
+
+import contextlib
+
+
+def quiet() -> None:
+    """Hide an error."""
+    with contextlib.suppress(ValueError):
+        int("x")
diff --git a/tests/test_code_rules.py b/tests/test_code_rules.py
new file mode 100644
index 00000000..0d7a97d0
--- /dev/null
+++ b/tests/test_code_rules.py
@@ -0,0 +1,179 @@
+"""The code standards (spec §9): the shared rules, their baseline, and each guard.
+
+``tests/guard_fixtures`` holds deliberately bad modules; Ruff skips them in normal runs
+(``extend-exclude``) and these tests lint them explicitly to prove each rule fires.
+"""
+
+from __future__ import annotations
+
+import hashlib
+import subprocess
+import sys
+from pathlib import Path
+
+import pytest
+
+ROOT = Path(__file__).resolve().parents[1]
+GUARDS = Path(__file__).parent / "guard_fixtures"
+sys.path.insert(0, str(ROOT / "tools"))
+
+import check  # noqa: E402
+from code_rules import (  # noqa: E402
+    baseline_key,
+    check_source,
+    compare_with_baseline,
+    layer_problems,
+    missing_private_docstrings,
+    noqa_counts,
+    reserved_name_problems,
+    shrunk_baseline,
+)
+
+SHARED_SHA256 = "cc04a420a4d25d5ef200bfa370f052d9911786fde0c57385dcaf155716d6e0a2"
+"""SHA-256 of the shared ``tools/code_rules.py``, identical in every MorphoBricks repository."""
+
+
+def test_the_shared_rules_file_is_the_shared_copy():
+    # With LF line endings, as committed (a Windows checkout may convert them).
+    data = (ROOT / "tools" / "code_rules.py").read_bytes().replace(b"\r\n", b"\n")
+    digest = hashlib.sha256(data).hexdigest()
+    assert digest == SHARED_SHA256
+
+
+def test_the_repository_matches_its_baseline():
+    """No new violation, none grown, and the baseline as small as the code allows."""
+    assert check.baseline_problems() == []
+
+
+def test_every_package_module_has_a_layer():
+    layers = check.config()["layers"]
+    package = ROOT / check.config()["package"]
+    modules = {check._module_name(path, package) for path in package.rglob("*.py")}
+    assert modules == set(layers)
+
+
+def ruff_codes(path: Path) -> set[str]:
+    result = subprocess.run(
+        [
+            sys.executable,
+            *("-m", "ruff", "check", "--no-cache", "--output-format=concise"),
+            # The fixtures live under tests/, whose ignores would hide the rules.
+            *("--config", "lint.per-file-ignores = {}", str(path)),
+        ],
+        cwd=ROOT,
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+    lines = [line for line in result.stdout.splitlines() if ": " in line]
+    return {line.split(": ", 1)[1].split(" ", 1)[0] for line in lines}
+
+
+@pytest.mark.parametrize(
+    ("fixture", "code"),
+    [
+        ("missing_annotation.py", "ANN001"),
+        ("too_complex.py", "C901"),
+        ("many_arguments.py", "PLR0913"),
+        # A blanket noqa would hide every rule from the noqa ratchet.
+        ("blanket_noqa.py", "PGH004"),
+        ("missing_annotation.py", "I002"),
+    ],
+)
+def test_ruff_guard_catches(fixture, code):
+    assert code in ruff_codes(GUARDS / fixture)
+
+
+def guard(name):
+    return (GUARDS / name).read_text(encoding="utf-8"), name
+
+
+@pytest.mark.parametrize(
+    ("fixture", "text"),
+    [
+        ("long_function.py", "executable lines (max 60)"),
+        ("many_arguments.py", "9 parameters (max 8)"),
+        ("uses_suppress.py", "contextlib.suppress"),
+    ],
+)
+def test_size_and_suppress_guards(fixture, text):
+    assert any(text in problem for problem in check_source(*guard(fixture)))
+
+
+def test_private_functions_need_a_docstring():
+    (problem,) = missing_private_docstrings(*guard("private_without_docstring.py"))
+    assert "_helper: private function of 13 lines without a docstring" in problem
+    assert missing_private_docstrings(*guard("long_function.py")) == []
+
+
+def test_layers():
+    assert layer_problems(*guard("pure_with_io.py"), "pure") == [
+        "pure_with_io.py: pure module imports os",
+        "pure_with_io.py: pure module calls open()",
+    ]
+    assert layer_problems(*guard("pure_with_io.py"), "io") == []
+    assert layer_problems(*guard("ui_computing.py"), "ui") == [
+        "ui_computing.py: UI module imports scipy"
+    ]
+    assert "no layer declared" in layer_problems(*guard("ui_computing.py"), None)[0]
+
+
+def test_reserved_names_belong_to_their_owner():
+    (problem,) = reserved_name_problems(*guard("reserved_copy.py"), "preprocessing")
+    assert "min_max: owned by normalization" in problem
+    assert reserved_name_problems(*guard("reserved_copy.py"), "normalization") == []
+
+
+def test_the_baseline_only_shrinks():
+    problems = ["a.py: 700 lines (max 600)", "a.py:12 f: 70 executable lines (max 60)"]
+    noqa = {"C901": 1, "PLR0913": 0, "PLR0915": 0, "ANN": 2}
+    baseline = shrunk_baseline(problems, noqa, {"problems": {}, "noqa": {}})
+    assert baseline["problems"] == {}  # nothing is ever added
+    recorded = {
+        "problems": {baseline_key(p)[0]: baseline_key(p)[1] for p in problems},
+        "noqa": dict(noqa),
+    }
+    assert compare_with_baseline(problems, noqa, recorded) == []
+    # The function moved (another line number): still the same entry.
+    moved = ["a.py: 700 lines (max 600)", "a.py:40 f: 70 executable lines (max 60)"]
+    assert compare_with_baseline(moved, noqa, recorded) == []
+    grown = ["a.py: 710 lines (max 600)", problems[1]]
+    assert compare_with_baseline(grown, noqa, recorded) == [
+        "grew from 700 to 710: a.py: # lines (max #)"
+    ]
+    new = [*problems, "b.py:3 g: 9 parameters (max 8)"]
+    assert compare_with_baseline(new, noqa, recorded) == [
+        "new violation: b.py g: # parameters (max #)"
+    ]
+    smaller = ["a.py: 650 lines (max 600)"]
+    found = compare_with_baseline(smaller, noqa, recorded)
+    assert len(found) == 2 and all("baseline can shrink" in f for f in found)
+    lowered = shrunk_baseline(smaller, noqa, recorded)
+    assert lowered["problems"] == {"a.py: # lines (max #)": 650}
+    more_noqa = {**noqa, "ANN": 3}
+    assert compare_with_baseline(problems, more_noqa, recorded) == [f"{NOQA}: ANN grew from 2 to 3"]
+
+
+NOQA = "# " + "noqa"
+"""Built, not written out, so this file's test data is not counted by the noqa ratchet."""
+
+
+def test_noqa_counts():
+    sources = [("a.py", f"x = 1  {NOQA}: ANN001, E501\ndef f():  {NOQA}:C901,PLR0915\n")]
+    assert noqa_counts(sources) == {"C901": 1, "PLR0913": 0, "PLR0915": 1, "ANN": 1}
+
+
+def test_file_level_noqa_counts():
+    sources = [("a.py", "# ruff: " + "noqa: ANN001, PLR0913\n")]
+    assert noqa_counts(sources) == {"C901": 0, "PLR0913": 1, "PLR0915": 0, "ANN": 1}
+
+
+def test_line_numbers_are_never_a_baseline_size():
+    """Moving a duplicated helper or a module with a digit in its name changes no size."""
+    duplicate = "identical bodies: tests/a.py:36 helper, tests/b.py:20 helper"
+    moved = "identical bodies: tests/a.py:90 helper, tests/b.py:20 helper"
+    assert baseline_key(duplicate) == baseline_key(moved)
+    assert baseline_key(duplicate)[1] == 0
+    assert baseline_key("import cycle: p.v2 -> p.c -> p.v2")[1] == 0
+    assert baseline_key("p.py:3 f_v2: 70 executable lines (max 60)")[1] == 70
+    assert baseline_key("p.py:3 _h: private function of 13 lines without a docstring")[1] == 13
diff --git a/tests/test_shared_helpers.py b/tests/test_shared_helpers.py
new file mode 100644
index 00000000..ff0bc43f
--- /dev/null
+++ b/tests/test_shared_helpers.py
@@ -0,0 +1,42 @@
+"""The helpers that replaced copies (plan-structure audit D1 and D7)."""
+
+from __future__ import annotations
+
+import os
+
+import pytest
+
+from morphobricks_preprocessing._io import write_text_atomic
+from morphobricks_preprocessing.validation import agree
+
+
+def test_write_text_atomic_writes_lf_and_replaces(tmp_path):
+    path = write_text_atomic(tmp_path / "a" / "b.txt", "one\ntwo\n", parents=True)
+    assert path.read_bytes() == b"one\ntwo\n"
+    write_text_atomic(path, "three\n")
+    assert path.read_text(encoding="utf-8") == "three\n"
+    assert sorted(p.name for p in path.parent.iterdir()) == ["b.txt"]
+
+
+def test_write_text_atomic_keeps_the_earlier_file_on_failure(tmp_path, monkeypatch):
+    path = write_text_atomic(tmp_path / "b.txt", "earlier\n")
+
+    def broken(source, destination):
+        raise OSError("simulated")
+
+    monkeypatch.setattr(os, "replace", broken)
+    with pytest.raises(OSError, match="simulated"):
+        write_text_atomic(path, "later\n")
+    assert path.read_text(encoding="utf-8") == "earlier\n"
+    assert sorted(p.name for p in tmp_path.iterdir()) == ["b.txt"]
+
+
+def test_write_text_atomic_needs_the_folder_unless_asked(tmp_path):
+    with pytest.raises(FileNotFoundError):
+        write_text_atomic(tmp_path / "missing" / "b.txt", "x")
+
+
+def test_agree():
+    assert agree(["a"], "is", "are") == "is"
+    assert agree([], "is", "are") == "are"
+    assert agree(["a", "b"], "has", "have") == "have"
diff --git a/tests/zarr_tree.py b/tests/zarr_tree.py
index 0cf0d7c0..15f48d31 100644
--- a/tests/zarr_tree.py
+++ b/tests/zarr_tree.py
@@ -15,7 +15,7 @@ def zarr_major() -> int:
     return int(zarr.__version__.split(".")[0])
 
 
-def write_ngff(
+def write_ngff(  # noqa: PLR0913
     path,
     data,
     axes="czyx",
diff --git a/tools/check.py b/tools/check.py
new file mode 100644
index 00000000..860a11a6
--- /dev/null
+++ b/tools/check.py
@@ -0,0 +1,119 @@
+"""Run every local check a pull request must pass: Ruff, the code rules and pytest.
+
+Usage:
+
+- ``python tools/check.py``: everything; exits non-zero when any check fails, after
+  running all of them so one run lists every problem;
+- ``python tools/check.py --rules``: only the code rules against their baseline (CI);
+- ``python tools/check.py --update-baseline``: lower the baseline to the current code. It
+  never adds or raises an entry: new violations must be fixed.
+
+The code rules are the shared ``tools/code_rules.py``, configured in ``pyproject.toml``
+under ``[tool.morphobricks.code-rules]`` (owner, package, layers, baseline file).
+"""
+
+from __future__ import annotations
+
+import json
+import subprocess
+import sys
+import tomllib
+from pathlib import Path
+
+from code_rules import (
+    check_source,
+    compare_with_baseline,
+    duplicate_bodies,
+    import_cycles,
+    layer_problems,
+    missing_private_docstrings,
+    noqa_counts,
+    read_baseline,
+    reserved_name_problems,
+    shrunk_baseline,
+)
+
+ROOT = Path(__file__).resolve().parents[1]
+LINTED = ("src", "tests", "tools")
+
+
+def config() -> dict:
+    """Return this repository's code-rules settings from ``pyproject.toml``."""
+    data = tomllib.loads((ROOT / "pyproject.toml").read_text(encoding="utf-8"))
+    return data["tool"]["morphobricks"]["code-rules"]
+
+
+def _python_files() -> list[Path]:
+    """Return the repository's checked Python files (guard fixtures are deliberately bad)."""
+    files = [path for folder in LINTED for path in sorted((ROOT / folder).rglob("*.py"))]
+    return [path for path in files if "guard_fixtures" not in path.parts]
+
+
+def _module_name(path: Path, package_dir: Path) -> str:
+    """Return the dotted module name of a file of the package."""
+    parts = path.relative_to(package_dir.parent).with_suffix("").parts
+    return ".".join(parts[:-1] if parts[-1] == "__init__" else parts)
+
+
+def code_rule_problems() -> tuple[list[str], dict[str, int]]:
+    """Return every code-rule violation in the repository and the ``# noqa`` counts."""
+    settings = config()
+    package_dir = ROOT / settings["package"]
+    layers = settings.get("layers", {})
+    sources = [
+        (str(path.relative_to(ROOT).as_posix()), path.read_text(encoding="utf-8"))
+        for path in _python_files()
+    ]
+    problems = []
+    for name, text in sources:
+        problems += check_source(text, name)
+        problems += missing_private_docstrings(text, name)
+        problems += reserved_name_problems(text, name, settings["owner"])
+        path = ROOT / name
+        if package_dir in path.parents:
+            problems += layer_problems(text, name, layers.get(_module_name(path, package_dir)))
+    problems += duplicate_bodies(sources)
+    problems += import_cycles(package_dir)
+    return problems, noqa_counts(sources)
+
+
+def baseline_problems() -> list[str]:
+    """Return what breaks the code-rules baseline (empty when the code matches it)."""
+    problems, noqa = code_rule_problems()
+    baseline = read_baseline(ROOT / config()["baseline"])
+    return compare_with_baseline(problems, noqa, baseline)
+
+
+def update_baseline() -> Path:
+    """Lower the baseline file to the current code, never raising an entry."""
+    problems, noqa = code_rule_problems()
+    path = ROOT / config()["baseline"]
+    lowered = shrunk_baseline(problems, noqa, read_baseline(path))
+    path.write_text(json.dumps(lowered, indent=2, sort_keys=True) + "\n", encoding="utf-8")
+    return path
+
+
+def main(argv: list[str]) -> int:
+    """Run the checks and return the process exit code."""
+    if "--update-baseline" in argv:
+        print(f"Baseline lowered: {update_baseline()}")
+        return 0
+    failed = False
+    if "--rules" not in argv:
+        commands = (
+            [sys.executable, "-m", "ruff", "check", "."],
+            [sys.executable, "-m", "ruff", "format", "--check", "."],
+            [sys.executable, "-m", "pytest", "-q"],
+        )
+        for command in commands:
+            print("$", " ".join(command[2:]), flush=True)
+            failed |= subprocess.run(command, cwd=ROOT, check=False).returncode != 0
+    print("$ code rules", flush=True)
+    problems = baseline_problems()
+    for problem in problems:
+        print(problem)
+    return 1 if failed or problems else 0
+
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv[1:]))
diff --git a/tools/code_rules.py b/tools/code_rules.py
new file mode 100644
index 00000000..cea2c162
--- /dev/null
+++ b/tools/code_rules.py
@@ -0,0 +1,550 @@
+"""MorphoBricks code standards that Ruff does not check, as AST checks (spec §9).
+
+The shared copy of this file is identical in every MorphoBricks repository (a SHA-256 test
+keeps it so); each repository configures it in ``pyproject.toml`` under
+``[tool.morphobricks.code-rules]``.
+
+Ruff (configured in ``pyproject.toml``) checks line length, annotations, docstrings,
+complexity, statements and blind or silent exception handling. This module checks the
+rest:
+
+- at most 600 lines per file, 60 executable lines per function (docstring excluded),
+  eight named parameters per function (``self``/``cls`` excluded);
+- no ``contextlib.suppress``, no identical function bodies, no import cycles;
+- a docstring (at least an imperative line) on private functions over 10 lines;
+- layers: every module is ``pure``, ``io``, ``ui`` or ``orchestration``; pure modules do
+  no I/O and no UI, and UI modules do not compute;
+- ownership: :data:`RESERVED_NAMES` may only be defined in their owner repository.
+
+Existing violations are listed in a baseline that may only shrink
+(:func:`compare_with_baseline`), and the ``# noqa`` comments of the ratcheted Ruff rules
+are counted against it (:func:`noqa_counts`).
+"""
+
+from __future__ import annotations
+
+import ast
+import json
+import re
+from collections.abc import Iterable, Iterator, Mapping
+from pathlib import Path
+
+MAX_FILE_LINES = 600
+MAX_FUNCTION_LINES = 60
+MAX_PARAMETERS = 8
+PRIVATE_DOCSTRING_LINES = 10
+"""Private functions longer than this many executable lines need a docstring."""
+# Bodies shorter than this many statements are too small to count as duplicated logic.
+MIN_DUPLICATE_STATEMENTS = 3
+
+FunctionNode = ast.FunctionDef | ast.AsyncFunctionDef
+
+
+def _functions(tree: ast.AST) -> Iterator[FunctionNode]:
+    """Yield every function and method in ``tree``, nested ones included."""
+    for node in ast.walk(tree):
+        if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef)):
+            yield node
+
+
+def _body_without_docstring(function: FunctionNode) -> list[ast.stmt]:
+    """Return the function's statements after its docstring."""
+    body = function.body
+    first = body[0]
+    is_docstring = (
+        isinstance(first, ast.Expr)
+        and isinstance(first.value, ast.Constant)
+        and isinstance(first.value.value, str)
+    )
+    return body[1:] if is_docstring else body
+
+
+def _executable_lines(function: FunctionNode, lines: list[str]) -> int:
+    """Count non-blank, non-comment source lines of the body after the docstring."""
+    body = _body_without_docstring(function)
+    if not body:
+        return 0
+    start, end = body[0].lineno, max(stmt.end_lineno or stmt.lineno for stmt in body)
+    code = (line.strip() for line in lines[start - 1 : end])
+    return sum(1 for line in code if line and not line.startswith("#"))
+
+
+def _parameter_count(function: FunctionNode, method: bool) -> int:
+    """Count named parameters, excluding a method's ``self``/``cls``."""
+    arguments = [*function.args.posonlyargs, *function.args.args, *function.args.kwonlyargs]
+    if method and arguments and arguments[0].arg in {"self", "cls"}:
+        arguments = arguments[1:]
+    return len(arguments)
+
+
+def _methods(tree: ast.AST) -> set[ast.AST]:
+    """Return functions defined directly in a class body."""
+    return {
+        item
+        for node in ast.walk(tree)
+        if isinstance(node, ast.ClassDef)
+        for item in node.body
+        if isinstance(item, (ast.FunctionDef, ast.AsyncFunctionDef))
+    }
+
+
+def _uses_suppress(tree: ast.AST) -> bool:
+    """Return whether the module refers to ``contextlib.suppress`` in any form."""
+    for node in ast.walk(tree):
+        if isinstance(node, ast.Attribute) and node.attr == "suppress":
+            return True
+        if isinstance(node, ast.ImportFrom) and node.module == "contextlib":
+            if any(alias.name == "suppress" for alias in node.names):
+                return True
+    return False
+
+
+def check_source(text: str, name: str) -> list[str]:
+    """Return every rule violation of one module's source.
+
+    Parameters
+    ----------
+    text
+        Python source.
+    name
+        Name used in the messages, usually the relative path.
+
+    Returns
+    -------
+    list of str
+        One message per violation; empty when the module follows the rules.
+    """
+    lines = text.splitlines()
+    tree = ast.parse(text, filename=name)
+    problems = []
+    if len(lines) > MAX_FILE_LINES:
+        problems.append(f"{name}: {len(lines)} lines (max {MAX_FILE_LINES})")
+    methods = _methods(tree)
+    for function in _functions(tree):
+        where = f"{name}:{function.lineno} {function.name}"
+        length = _executable_lines(function, lines)
+        if length > MAX_FUNCTION_LINES:
+            problems.append(f"{where}: {length} executable lines (max {MAX_FUNCTION_LINES})")
+        count = _parameter_count(function, function in methods)
+        if count > MAX_PARAMETERS:
+            problems.append(f"{where}: {count} parameters (max {MAX_PARAMETERS})")
+    if _uses_suppress(tree):
+        problems.append(f"{name}: contextlib.suppress hides exceptions; handle them explicitly")
+    return problems
+
+
+def duplicate_bodies(sources: Iterable[tuple[str, str]]) -> list[str]:
+    """Return functions whose bodies (docstring excluded) are identical.
+
+    Parameters
+    ----------
+    sources
+        ``(name, source)`` pairs of the modules to compare.
+
+    Returns
+    -------
+    list of str
+        One message per group of identical bodies.
+    """
+    seen: dict[str, list[str]] = {}
+    for name, text in sources:
+        for function in _functions(ast.parse(text, filename=name)):
+            body = _body_without_docstring(function)
+            if len(body) >= MIN_DUPLICATE_STATEMENTS:
+                dump = "\n".join(ast.dump(statement) for statement in body)
+                seen.setdefault(dump, []).append(f"{name}:{function.lineno} {function.name}")
+    return [f"identical bodies: {', '.join(where)}" for where in seen.values() if len(where) > 1]
+
+
+def _imported_modules(tree: ast.AST, package: str) -> set[str]:
+    """Return the modules of ``package`` that a module imports."""
+    imported = set()
+    for node in ast.walk(tree):
+        if isinstance(node, ast.ImportFrom) and node.module and node.level == 0:
+            imported.add(node.module)
+        elif isinstance(node, ast.Import):
+            imported.update(alias.name for alias in node.names)
+    return {module for module in imported if module.split(".")[0] == package}
+
+
+def _cycle_from(start: str, graph: dict[str, set[str]]) -> list[str]:
+    """Return one import cycle through ``start``, or an empty list."""
+    stack = [(start, [start])]
+    while stack:
+        module, path = stack.pop()
+        for target in sorted(graph.get(module, ())):
+            if target == start:
+                return [*path, start]
+            if target not in path:
+                stack.append((target, [*path, target]))
+    return []
+
+
+def import_cycles(package_dir: Path) -> list[str]:
+    """Return import cycles among the modules of one package.
+
+    Parameters
+    ----------
+    package_dir
+        Directory of the package, such as ``src/morphofeature``.
+
+    Returns
+    -------
+    list of str
+        One message per module that lies on a cycle.
+    """
+    package = package_dir.name
+    graph = {}
+    for path in sorted(package_dir.rglob("*.py")):
+        parts = path.relative_to(package_dir.parent).with_suffix("").parts
+        module = ".".join(parts[:-1] if parts[-1] == "__init__" else parts)
+        tree = ast.parse(path.read_text(encoding="utf-8"), filename=str(path))
+        graph[module] = _imported_modules(tree, package) - {module}
+    # The package's __init__ re-exports its modules; only cycles among them matter.
+    graph.pop(package, None)
+    cycles = (_cycle_from(module, graph) for module in sorted(graph))
+    return [f"import cycle: {' -> '.join(cycle)}" for cycle in cycles if cycle]
+
+
+RESERVED_NAMES: Mapping[str, str] = {
+    # morphobricks-normalization: histograms, the table, pooling and normalization.
+    "compute_plane_histogram": "normalization",
+    "compute_block_histogram": "normalization",
+    "histogram_with_range_check": "normalization",
+    "PooledHistogram": "normalization",
+    "pooled_statistics": "normalization",
+    "NormalizationParameters": "normalization",
+    "min_max": "normalization",
+    "percentile_range": "normalization",
+    "z_score": "normalization",
+    "robust_z_score": "normalization",
+    "make_plane_id": "normalization",
+    "write_plane_histograms": "normalization",
+    "read_plane_histograms": "normalization",
+    "image_summaries": "normalization",
+    "intensity_checks": "normalization",
+    # morphobricks-preprocessing: identities, axes, units, labels, masks, sources.
+    "check_identity_text": "preprocessing",
+    "check_identity_case": "preprocessing",
+    "check_plane_index": "preprocessing",
+    "position_id": "preprocessing",
+    "named_axes": "preprocessing",
+    "header_axes": "preprocessing",
+    "space_unit": "preprocessing",
+    "to_micrometers": "preprocessing",
+    "same_pixel_size": "preprocessing",
+    "pixel_size_groups": "preprocessing",
+    "check_labels": "preprocessing",
+    "find_masks": "preprocessing",
+    "read_mask": "preprocessing",
+    "read_confirmed_design": "preprocessing",
+    "source_fingerprint": "preprocessing",
+    "check_sources": "preprocessing",
+    "discover_experiment": "preprocessing",
+    # CellPatcher: patches and their table.
+    "object_sides": "cellpatcher",
+    "check_patch_bounds": "cellpatcher",
+    "read_patch_table": "cellpatcher",
+}
+"""Names of shared logic, by the repository that owns it (spec §9, "Ownership"). A function
+or class of one of these names defined in any other repository is a copy, and fails."""
+
+LAYERS = ("pure", "io", "ui", "orchestration")
+
+IO_MODULES = frozenset(
+    {"os", "shutil", "tempfile", "subprocess", "tifffile", "zarr", "numcodecs", "socket"}
+)
+"""Modules whose import makes a module do I/O."""
+
+UI_MODULES = frozenset({"ipywidgets", "matplotlib", "IPython", "tkinter"})
+"""Modules whose import makes a module a user interface."""
+
+COMPUTE_MODULES = frozenset({"scipy"})
+"""Modules a UI module may not import: UI modules show results, they do not compute them."""
+
+IO_CALLS = frozenset(
+    {
+        "open",
+        "print",
+        "read_text",
+        "write_text",
+        "read_bytes",
+        "write_bytes",
+        "mkdir",
+        "unlink",
+        "rmdir",
+        "iterdir",
+        "rglob",
+        "glob",
+        "stat",
+    }
+)
+"""Calls (by name or attribute) that a pure module may not make."""
+
+RATCHETED_NOQA = ("C901", "PLR0913", "PLR0915", "ANN")
+"""Ruff rules whose ``# noqa`` comments are counted against the baseline."""
+
+
+def missing_private_docstrings(text: str, name: str) -> list[str]:
+    """Return private functions over :data:`PRIVATE_DOCSTRING_LINES` lines without a docstring.
+
+    Public names are Ruff's (``D`` rules); a private function needs at least an imperative
+    line once it is longer than a few lines.
+
+    Parameters
+    ----------
+    text
+        Python source.
+    name
+        Name used in the messages, usually the relative path.
+
+    Returns
+    -------
+    list of str
+        One message per function.
+    """
+    lines = text.splitlines()
+    problems = []
+    for function in _functions(ast.parse(text, filename=name)):
+        private = function.name.startswith("_") and not function.name.startswith("__")
+        if not private or ast.get_docstring(function) is not None:
+            continue
+        length = _executable_lines(function, lines)
+        if length > PRIVATE_DOCSTRING_LINES:
+            problems.append(
+                f"{name}:{function.lineno} {function.name}: private function of {length} "
+                "lines without a docstring"
+            )
+    return problems
+
+
+def _imports(tree: ast.AST) -> set[str]:
+    """Return the top-level names of every module a module imports (absolute imports)."""
+    found = set()
+    for node in ast.walk(tree):
+        if isinstance(node, ast.Import):
+            found.update(alias.name.split(".")[0] for alias in node.names)
+        elif isinstance(node, ast.ImportFrom) and node.module and node.level == 0:
+            found.add(node.module.split(".")[0])
+    return found
+
+
+def _called_names(tree: ast.AST) -> set[str]:
+    """Return the names of every call: ``f(...)`` gives ``f``, ``a.b(...)`` gives ``b``."""
+    names = set()
+    for node in ast.walk(tree):
+        if isinstance(node, ast.Call):
+            if isinstance(node.func, ast.Name):
+                names.add(node.func.id)
+            elif isinstance(node.func, ast.Attribute):
+                names.add(node.func.attr)
+    return names
+
+
+def layer_problems(text: str, name: str, layer: str | None) -> list[str]:
+    """Return the layer violations of one module.
+
+    Parameters
+    ----------
+    text
+        Python source.
+    name
+        Name used in the messages, usually the relative path.
+    layer
+        The module's declared layer (:data:`LAYERS`), or None when it has none.
+
+    Returns
+    -------
+    list of str
+        A missing or unknown layer; I/O or UI in a pure module; computing imports in a UI
+        module.
+    """
+    if layer not in LAYERS:
+        return [f"{name}: no layer declared (one of {', '.join(LAYERS)})"]
+    tree = ast.parse(text, filename=name)
+    imports = _imports(tree)
+    problems = []
+    if layer == "pure":
+        for module in sorted(imports & (IO_MODULES | UI_MODULES)):
+            problems.append(f"{name}: pure module imports {module}")
+        for call in sorted(_called_names(tree) & IO_CALLS):
+            problems.append(f"{name}: pure module calls {call}()")
+    if layer == "ui":
+        for module in sorted(imports & COMPUTE_MODULES):
+            problems.append(f"{name}: UI module imports {module}")
+    return problems
+
+
+def reserved_name_problems(text: str, name: str, owner: str) -> list[str]:
+    """Return definitions of :data:`RESERVED_NAMES` that this repository does not own.
+
+    Parameters
+    ----------
+    text
+        Python source.
+    name
+        Name used in the messages, usually the relative path.
+    owner
+        This repository's owner name (``"preprocessing"``, ``"normalization"``, ...).
+
+    Returns
+    -------
+    list of str
+        One message per copied definition.
+    """
+    problems = []
+    for node in ast.walk(ast.parse(text, filename=name)):
+        defined = isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef))
+        if defined and RESERVED_NAMES.get(node.name, owner) != owner:
+            problems.append(
+                f"{name}:{node.lineno} {node.name}: owned by {RESERVED_NAMES[node.name]}; "
+                "call it there instead of copying it"
+            )
+    return problems
+
+
+def noqa_counts(sources: Iterable[tuple[str, str]]) -> dict[str, int]:
+    """Count the ``# noqa`` codes of :data:`RATCHETED_NOQA` in the sources.
+
+    Parameters
+    ----------
+    sources
+        ``(name, source)`` pairs.
+
+    Returns
+    -------
+    dict
+        ``{code prefix: count}`` for every ratcheted prefix (0 when none).
+    """
+    counts = dict.fromkeys(RATCHETED_NOQA, 0)
+    for _, text in sources:
+        # Line comments and file-level ones (``ruff: noqa: ANN001`` after the hash) count.
+        for comment in re.findall(r"#\s*(?:(?:ruff|flake8):\s*)?noqa:\s*([A-Z0-9, ]+)", text):
+            for code in (part.strip() for part in comment.split(",")):
+                prefix = next((p for p in RATCHETED_NOQA if code.startswith(p)), None)
+                if prefix is not None:
+                    counts[prefix] += 1
+    return counts
+
+
+def baseline_key(problem: str) -> tuple[str, int]:
+    """Split a violation into a stable key and its size.
+
+    Line numbers are dropped and the first remaining number (a length or count) becomes the
+    size, so a violation keeps its key while its code moves or shrinks. A line number
+    (``path:12``) or a digit inside a name is never a size: a message without a length or
+    count, such as identical bodies or an import cycle, has size 0.
+
+    Parameters
+    ----------
+    problem
+        A message of the checks above.
+
+    Returns
+    -------
+    tuple
+        ``(key, size)``; the size is 0 when the message has no number.
+    """
+    text = re.sub(r"^([^:]+):\d+ ", r"\1 ", problem)
+    found = re.search(r"(?<![\w.:])\d+(?![\w.])", text.split(": ", 1)[-1])
+    size = int(found.group()) if found else 0
+    key = re.sub(r"\d+", "#", text)
+    return key, size
+
+
+def compare_with_baseline(
+    problems: Iterable[str], noqa: Mapping[str, int], baseline: Mapping
+) -> list[str]:
+    """Return what breaks the baseline: new violations, growth, and entries that can shrink.
+
+    The baseline may only shrink: a violation not in it, or larger than recorded, fails;
+    so does an entry that is no longer needed (or larger than needed), until it is lowered
+    with ``tools/check.py --update-baseline``. ``# noqa`` counts work the same way.
+
+    Parameters
+    ----------
+    problems
+        The current violations.
+    noqa
+        The current :func:`noqa_counts`.
+    baseline
+        ``{"problems": {key: size}, "noqa": {prefix: count}}``.
+
+    Returns
+    -------
+    list of str
+        One message per difference; empty when the code matches the baseline.
+    """
+    allowed = dict(baseline.get("problems", {}))
+    current: dict[str, int] = {}
+    for problem in problems:
+        key, size = baseline_key(problem)
+        current[key] = max(current.get(key, 0), size)
+    found = []
+    for key, size in sorted(current.items()):
+        if key not in allowed:
+            found.append(f"new violation: {key}")
+        elif size > allowed[key]:
+            found.append(f"grew from {allowed[key]} to {size}: {key}")
+    for key, size in sorted(allowed.items()):
+        if key not in current or current[key] < size:
+            found.append(f"baseline can shrink (run tools/check.py --update-baseline): {key}")
+    for prefix, count in sorted(noqa.items()):
+        limit = baseline.get("noqa", {}).get(prefix, 0)
+        if count > limit:
+            found.append(f"# noqa: {prefix} grew from {limit} to {count}")
+        elif count < limit:
+            found.append(
+                f"# noqa: {prefix} can shrink from {limit} to {count} "
+                "(run tools/check.py --update-baseline)"
+            )
+    return found
+
+
+def shrunk_baseline(problems: Iterable[str], noqa: Mapping[str, int], baseline: Mapping) -> dict:
+    """Return the baseline lowered to the current code, never raised.
+
+    Parameters
+    ----------
+    problems
+        The current violations.
+    noqa
+        The current :func:`noqa_counts`.
+    baseline
+        The recorded baseline.
+
+    Returns
+    -------
+    dict
+        The new baseline: entries no longer violated removed, sizes and counts lowered; new
+        or grown violations are not added.
+    """
+    allowed = dict(baseline.get("problems", {}))
+    current: dict[str, int] = {}
+    for problem in problems:
+        key, size = baseline_key(problem)
+        current[key] = max(current.get(key, 0), size)
+    kept = {k: min(v, current[k]) for k, v in allowed.items() if k in current}
+    limits = baseline.get("noqa", {})
+    return {
+        "problems": dict(sorted(kept.items())),
+        "noqa": {p: min(limits.get(p, 0), noqa.get(p, 0)) for p in RATCHETED_NOQA},
+    }
+
+
+def read_baseline(path: Path) -> dict:
+    """Read a baseline file; an absent file is an empty baseline.
+
+    Parameters
+    ----------
+    path
+        The JSON file.
+
+    Returns
+    -------
+    dict
+        ``{"problems": {...}, "noqa": {...}}``.
+    """
+    if not path.exists():
+        return {"problems": {}, "noqa": {}}
+    return json.loads(path.read_text(encoding="utf-8"))
diff --git a/tools/code_rules_baseline.json b/tools/code_rules_baseline.json
new file mode 100644
index 00000000..301152e4
--- /dev/null
+++ b/tools/code_rules_baseline.json
@@ -0,0 +1,123 @@
+{
+  "noqa": {
+    "ANN": 63,
+    "C901": 2,
+    "PLR0913": 3,
+    "PLR0915": 2
+  },
+  "problems": {
+    "identical bodies: tests/test_axis_check.py:# imagej, tests/test_header_axes.py:# imagej": 0,
+    "identical bodies: tests/test_axis_check.py:# plain, tests/test_header_axes.py:# plain": 0,
+    "identical bodies: tests/test_cli.py:# bright_tree, tests/test_notebook_ui.py:# bright_tree": 0,
+    "identical bodies: tests/test_zarr_export.py:# random_data, tests/test_zarr_input.py:# random_data": 0,
+    "src/morphobricks_preprocessing/axes.py _check_declared_axes: private function of # lines without a docstring": 20,
+    "src/morphobricks_preprocessing/axes.py _declared_axes_problem: private function of # lines without a docstring": 20,
+    "src/morphobricks_preprocessing/axes.py check_mapping: # executable lines (max #)": 72,
+    "src/morphobricks_preprocessing/axes.py review_axes: # executable lines (max #)": 108,
+    "src/morphobricks_preprocessing/axes.py: # lines (max #)": 868,
+    "src/morphobricks_preprocessing/cli.py _check: private function of # lines without a docstring": 52,
+    "src/morphobricks_preprocessing/cli.py _common: private function of # lines without a docstring": 19,
+    "src/morphobricks_preprocessing/cli.py _conversion_note: private function of # lines without a docstring": 15,
+    "src/morphobricks_preprocessing/cli.py _masks: private function of # lines without a docstring": 39,
+    "src/morphobricks_preprocessing/cli.py _run: # executable lines (max #)": 93,
+    "src/morphobricks_preprocessing/cli.py _run: private function of # lines without a docstring": 93,
+    "src/morphobricks_preprocessing/cli.py build_parser: # executable lines (max #)": 147,
+    "src/morphobricks_preprocessing/cli.py: # lines (max #)": 637,
+    "src/morphobricks_preprocessing/dataset.py _missing_issues: private function of # lines without a docstring": 32,
+    "src/morphobricks_preprocessing/dataset.py _unbalanced_issues: private function of # lines without a docstring": 19,
+    "src/morphobricks_preprocessing/design.py _check_strict_values: private function of # lines without a docstring": 19,
+    "src/morphobricks_preprocessing/design.py _count: private function of # lines without a docstring": 11,
+    "src/morphobricks_preprocessing/design.py _parse_row: private function of # lines without a docstring": 36,
+    "src/morphobricks_preprocessing/design.py: # lines (max #)": 964,
+    "src/morphobricks_preprocessing/discovery.py _check_names: private function of # lines without a docstring": 14,
+    "src/morphobricks_preprocessing/discovery.py finish: # executable lines (max #)": 145,
+    "src/morphobricks_preprocessing/discovery.py: # lines (max #)": 847,
+    "src/morphobricks_preprocessing/image_type.py _rgb_problem: private function of # lines without a docstring": 12,
+    "src/morphobricks_preprocessing/manifest.py _file_dict: private function of # lines without a docstring": 18,
+    "src/morphobricks_preprocessing/manifest.py _file_entry: private function of # lines without a docstring": 21,
+    "src/morphobricks_preprocessing/manifest.py file_entry_for: # parameters (max #)": 10,
+    "src/morphobricks_preprocessing/manifest.py: # lines (max #)": 754,
+    "src/morphobricks_preprocessing/masks.py _duplicate_issues: private function of # lines without a docstring": 19,
+    "src/morphobricks_preprocessing/masks.py _folder_issues: private function of # lines without a docstring": 19,
+    "src/morphobricks_preprocessing/masks.py _name_issues: private function of # lines without a docstring": 15,
+    "src/morphobricks_preprocessing/masks.py: # lines (max #)": 878,
+    "src/morphobricks_preprocessing/metadata.py _check_channel_names: private function of # lines without a docstring": 32,
+    "src/morphobricks_preprocessing/metadata.py _check_dimensions: private function of # lines without a docstring": 30,
+    "src/morphobricks_preprocessing/metadata.py _check_image_sizes: private function of # lines without a docstring": 15,
+    "src/morphobricks_preprocessing/metadata.py _check_pixel_sizes: # executable lines (max #)": 71,
+    "src/morphobricks_preprocessing/metadata.py _check_plane_counts: private function of # lines without a docstring": 27,
+    "src/morphobricks_preprocessing/metadata.py check_metadata: # executable lines (max #)": 98,
+    "src/morphobricks_preprocessing/metadata.py: # lines (max #)": 936,
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+    "src/morphobricks_preprocessing/notebook_ui.py _build_image_type_card: private function of # lines without a docstring": 30,
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+    "src/morphobricks_preprocessing/physical_sizes.py _ome_sizes: private function of # lines without a docstring": 20,
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+    "src/morphobricks_preprocessing/planes.py _tiff_block_plane: private function of # lines without a docstring": 14,
+    "src/morphobricks_preprocessing/planes.py _zarr_layout: private function of # lines without a docstring": 40,
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+    "src/morphobricks_preprocessing/run.py _exclusion_issues: private function of # lines without a docstring": 34,
+    "src/morphobricks_preprocessing/run.py _pixel_issues: private function of # lines without a docstring": 38,
+    "src/morphobricks_preprocessing/run.py run_experiment: # executable lines (max #)": 250,
+    "src/morphobricks_preprocessing/run.py run_experiment: # parameters (max #)": 17,
+    "src/morphobricks_preprocessing/run.py: # lines (max #)": 1075,
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+    "src/morphobricks_preprocessing/zarr_export.py _open: private function of # lines without a docstring": 12,
+    "src/morphobricks_preprocessing/zarr_export.py _track_channel: private function of # lines without a docstring": 13,
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+    "tests/test_masks.py: # lines (max #)": 618,
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+    "tests/test_zarr_input.py: # lines (max #)": 934,
+    "tests/zarr_tree.py write_ngff: # parameters (max #)": 12
+  }
+}