diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
new file mode 100644
index 00000000..a1c96fb0
--- /dev/null
+++ b/.github/workflows/docker-publish.yml
@@ -0,0 +1,54 @@
+name: Build and Publish Docker image
+
+on:
+  push:
+    branches: ["main", "dev"]
+    tags: ["v*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4.0.0
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v4.1.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v6.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=raw,value=edge,enable=${{ github.ref == 'refs/heads/dev' }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v7.1.0
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
diff --git a/.github/workflows/nextflow-ci.yml b/.github/workflows/nextflow-ci.yml
index 02b5b968..254ae072 100644
--- a/.github/workflows/nextflow-ci.yml
+++ b/.github/workflows/nextflow-ci.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0.2
 
       - uses: actions/setup-java@v5.2.0
         with:
@@ -41,26 +41,13 @@ jobs:
           sudo chmod +x /usr/local/bin/nf-test
 
       - name: Lint Nextflow files
-        # `nextflow lint` does not load Groovy classes from `lib/`, so it
-        # falsely reports `Helpers` as undefined wherever the workflow calls
-        # `Helpers.X(...)`. We strip ANSI colour codes from the output, drop
-        # those known false-positives, and re-derive the exit status.
+        # Pass -project-dir so that nextflow lint (26.04+) can resolve Groovy
+        # classes from lib/ (e.g. Helpers). Each workflow lives in its own
+        # subdirectory, so lint is invoked once per workflow.
         run: |
-          tmp=$(mktemp)
-          nextflow lint \
-            workflows/preproc/preproc_rawtiles.nf \
-            workflows/reconst_3d/soct_3d_reconst.nf \
-            workflows/reconst_2.5d/soct_2.5d_reconst.nf \
-            > "$tmp" 2>&1 || true
-          sed 's/\x1b\[[0-9;]*[a-zA-Z]//g' "$tmp" \
-            | awk '/`Helpers` is not defined/ { skip = 3; next } skip > 0 { skip--; next } { print }' \
-            > "$tmp.filt"
-          cat "$tmp.filt"
-          if grep -qE '^Error ' "$tmp.filt"; then
-            echo "::error::nextflow lint reported errors (excluding Helpers false-positives)"
-            exit 1
-          fi
-          echo "Lint passed (Helpers false-positives ignored: lib/ classes are loaded at runtime but not by 'nextflow lint')."
+          nextflow lint -project-dir workflows/preproc workflows/preproc/preproc_rawtiles.nf
+          nextflow lint -project-dir workflows/reconst_3d workflows/reconst_3d/soct_3d_reconst.nf
+          nextflow lint -project-dir workflows/reconst_2.5d workflows/reconst_2.5d/soct_2.5d_reconst.nf
 
       - name: Validate Nextflow configs
         run: |
diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml
index 295595e0..3f4d6c26 100644
--- a/.github/workflows/publish.yaml
+++ b/.github/workflows/publish.yaml
@@ -3,32 +3,28 @@ name: Build and Publish Toolkit
 on:
   push:
     tags:
-      - v1.*
-    workflow_dispatch:
+      - "v1.*"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
 jobs:
   build_and_publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v3
-        with:
-          python-version: "3.10"
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-          .
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+
+      - name: Set up Python 3.14
+        run: uv python install 3.14
+
+      - name: Build sdist and wheel
+        run: uv build --sdist --wheel --out-dir dist/
+
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         with:
           password: ${{ secrets.PYPI_TOKEN }}
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 575b8810..977d95b3 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -5,33 +5,39 @@ name: Python application
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main", "dev"]
   pull_request:
-    branches: [ "main" ]
+    branches: ["main", "dev"]
 
 permissions:
   contents: read
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v5
-    - name: Set up Python 3.12
-      run: uv python install 3.12
-    - name: Install dependencies
-      run: uv sync
-    - name: Lint with ruff
-      run: |
-        uv run ruff check .
-        uv run ruff format --check .
-    - name: Type check with ty
-      continue-on-error: true
-      run: uv run ty check
-    - name: Test with pytest
-      run: |
-        uv run pytest
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+        with:
+          enable-cache: true
+
+      - name: Set up Python 3.14
+        run: uv python install 3.14
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Lint with ruff
+        run: |
+          uv run ruff check .
+          uv run ruff format --check .
+
+      - name: Type check with ty
+        continue-on-error: true
+        run: uv run ty check
+
+      - name: Test with pytest
+        run: uv run pytest
diff --git a/.gitignore b/.gitignore
index 11725bae..589e7e91 100644
--- a/.gitignore
+++ b/.gitignore
@@ -173,6 +173,10 @@ cython_debug/
 .nextflow/
 *.nextflow.log*
 
+# nf-test
+.nf-test/
+.nf-test.log
+
 # Standalone tools (separate git repos)
 tools/
 workflows/work/
diff --git a/.pep8speaks.yml b/.pep8speaks.yml
deleted file mode 100644
index 7b47282d..00000000
--- a/.pep8speaks.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-# File : .pep8speaks.yml
-
-scanner:
-  diff_only: True # If False, the entire file touched by the Pull Request is scanned for errors. If True, only the diff is scanned.
-  linter: pycodestyle # Other option is flake8
-
-pycodestyle: # Same as scanner.linter value. Other option is flake8
-  max-line-length: 100 # Default is 79 in PEP 8
-  ignore: # Errors and warnings to ignore
-    - W504 # line break after binary operator
-    - E402 # module level import not at top of file
-    - E731 # do not assign a lambda expression, use a def
-    - C406 # Unnecessary list literal - rewrite as a dict literal.
-    - E741 # ambiguous variable name
-
-no_blank_comment: True # If True, no comment is made on PR without any errors.
-descending_issues_order: False # If True, PEP 8 issues in message will be displayed in descending order of line numbers in the file
-
-message: # Customize the comment made by the bot
-  opened: # Messages when a new PR is submitted
-    header:
-      "Hello @{name}! Thanks for opening this PR. "
-      # The keyword {name} is converted into the author's username
-    footer:
-      "Do see the [Hitchhiker's guide to code style](https://goo.gl/hqbW4r)"
-      # The messages can be written as they would over GitHub
-  updated: # Messages when new commits are added to the PR
-    header: "Hello @{name}! Thanks for updating this PR. "
-    footer: "" # Why to comment the link to the style guide everytime? :)
-  no_errors: "There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers: "
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index fe730638..b2c8cea0 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.14"
   jobs:
     create_environment:
       - asdf plugin add uv
diff --git a/Dockerfile b/Dockerfile
index 8632c109..bc3e0994 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12
+FROM python:3.14
 
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
@@ -19,5 +19,5 @@ RUN apt-get update && apt-get install -y \
 # Install with uv
 COPY linumpy ./linumpy
 COPY scripts ./scripts
-COPY pyproject.toml uv.lock README.md .python-version ./
+COPY pyproject.toml uv.lock README.md ./
 RUN uv sync --frozen --no-dev
diff --git a/README.md b/README.md
index 12f66f01..a628877a 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 ## Installation
 *Although a version of the library is available on PyPI, it has not been updated in a while. We highly discourage its use.*
 
-The library is tested for python 3.12. To install the library, clone the repository, change directory to the repository root and then install it with the command below:
+The library is tested for python 3.14. To install the library, clone the repository, change directory to the repository root and then install it with the command below:
 ```
 pip install .
 ```
diff --git a/docs/NEXTFLOW_WORKFLOWS.md b/docs/NEXTFLOW_WORKFLOWS.md
index 9e5fe1f3..627458ed 100644
--- a/docs/NEXTFLOW_WORKFLOWS.md
+++ b/docs/NEXTFLOW_WORKFLOWS.md
@@ -935,7 +935,7 @@ rm -rf work/
 
 ```bash
 # Pull container manually
-apptainer pull linumpy.sif docker://ghcr.io/linum/linumpy:latest
+apptainer pull linumpy.sif docker://ghcr.io/linum-uqam/linumpy:latest
 
 # Run with explicit container
 nextflow run workflow.nf -with-apptainer linumpy.sif
diff --git a/docs/conf.py b/docs/conf.py
index d69adaaa..8d4fad26 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -2,8 +2,6 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 """Sphinx configuration for the linumpy documentation."""
 
-from __future__ import annotations
-
 import sys
 from datetime import datetime
 from pathlib import Path
diff --git a/linumpy/cli/args.py b/linumpy/cli/args.py
index 9e7f76b5..8e7b0f01 100644
--- a/linumpy/cli/args.py
+++ b/linumpy/cli/args.py
@@ -1,7 +1,6 @@
 """Common argument-parsing helpers for linumpy CLI scripts."""
 
 import argparse
-import multiprocessing
 import os
 import shutil
 from pathlib import Path
@@ -19,7 +18,7 @@ def get_available_cpus() -> int:
     -------
         int: Number of available CPUs
     """
-    total_cpus = multiprocessing.cpu_count()
+    total_cpus = os.process_cpu_count() or os.cpu_count() or 1
 
     # Check for explicit max CPUs limit
     max_cpus = os.environ.get("LINUMPY_MAX_CPUS")
diff --git a/linumpy/config/threads.py b/linumpy/config/threads.py
index 82e9c20b..19fc03d4 100644
--- a/linumpy/config/threads.py
+++ b/linumpy/config/threads.py
@@ -31,7 +31,6 @@
 """
 
 import contextlib
-import multiprocessing
 import os
 import sys
 
@@ -39,6 +38,16 @@
 _thread_config_applied = False
 
 
+def _available_cpus() -> int:
+    """Return the number of CPUs usable by this process.
+
+    Prefers ``os.process_cpu_count()`` (Python 3.13+) which honours
+    ``sched_setaffinity`` and cgroup CPU limits, falling back to
+    ``os.cpu_count()`` and finally to 1.
+    """
+    return os.process_cpu_count() or os.cpu_count() or 1
+
+
 def get_max_threads() -> int:
     """
     Calculate the maximum number of threads to use based on environment variables.
@@ -47,7 +56,7 @@ def get_max_threads() -> int:
     -------
         int: Maximum number of threads to use
     """
-    total_cpus = multiprocessing.cpu_count()
+    total_cpus = _available_cpus()
 
     # Check for explicit max CPUs limit
     max_cpus = os.environ.get("LINUMPY_MAX_CPUS")
@@ -121,7 +130,7 @@ def configure_dask() -> None:
     try:
         import dask
 
-        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", _available_cpus()))
         dask.config.set(num_workers=max_threads)
         dask.config.set(scheduler="threads")  # Use thread scheduler, not process
         dask.config.set({"array.slicing.split_large_chunks": False})
@@ -142,7 +151,7 @@ def configure_sitk() -> None:
     try:
         import SimpleITK as sitk
 
-        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", _available_cpus()))
         sitk.ProcessObject.SetGlobalDefaultNumberOfThreads(max_threads)
     except ImportError:
         pass
@@ -157,10 +166,10 @@ def configure_torch() -> None:
     try:
         import torch
 
-        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", _available_cpus()))
         torch.set_num_threads(max_threads)
         torch.set_num_interop_threads(max_threads)
-    except (ImportError, RuntimeError):
+    except ImportError, RuntimeError:
         pass
 
 
@@ -179,7 +188,7 @@ def apply_threadpool_limits() -> object | None:
         from threadpoolctl import threadpool_limits
 
         # Get the configured thread limit
-        max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
+        max_threads = int(os.environ.get("OMP_NUM_THREADS", _available_cpus()))
 
         # Apply limits globally - this returns a context manager but also applies immediately
         limiter = threadpool_limits(limits=max_threads)
@@ -207,7 +216,7 @@ def configure_all_libraries() -> int:
     """
     global _thread_config_applied
 
-    max_threads = int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count()))
+    max_threads = int(os.environ.get("OMP_NUM_THREADS", _available_cpus()))
 
     # Configure SimpleITK if imported (CRITICAL - major source of CPU spikes)
     if "SimpleITK" in sys.modules:
@@ -227,7 +236,7 @@ def configure_all_libraries() -> int:
             from numba import set_num_threads
 
             set_num_threads(max_threads)
-        except (ImportError, Exception):
+        except ImportError, Exception:
             pass
 
     # Apply threadpoolctl limits (catches numpy, scipy, etc.)
@@ -248,8 +257,8 @@ def get_thread_info() -> dict:
         dict: Thread configuration information
     """
     info = {
-        "total_cpus": multiprocessing.cpu_count(),
-        "configured_threads": int(os.environ.get("OMP_NUM_THREADS", multiprocessing.cpu_count())),
+        "total_cpus": _available_cpus(),
+        "configured_threads": int(os.environ.get("OMP_NUM_THREADS", _available_cpus())),
         "env_vars": {},
         "libraries": {},
     }
diff --git a/linumpy/geometry/galvo.py b/linumpy/geometry/galvo.py
index e4429936..05d6d0e7 100644
--- a/linumpy/geometry/galvo.py
+++ b/linumpy/geometry/galvo.py
@@ -1,7 +1,5 @@
 """Galvanometric XY shift detection and correction."""
 
-from __future__ import annotations
-
 import numpy as np
 from scipy.ndimage import median_filter
 
diff --git a/linumpy/gpu/__init__.py b/linumpy/gpu/__init__.py
index ee83dc46..c7c63502 100644
--- a/linumpy/gpu/__init__.py
+++ b/linumpy/gpu/__init__.py
@@ -27,6 +27,7 @@
     Set USE_GPU=false environment variable to disable GPU globally.
 """
 
+import operator
 import os
 import warnings
 from typing import Any
@@ -319,7 +320,7 @@ def select_best_gpu(verbose: bool = True) -> Any:
         return None
 
     # Find GPU with most free memory
-    best_gpu = max(gpus, key=lambda g: g["free_gb"])
+    best_gpu = max(gpus, key=operator.itemgetter("free_gb"))
     best_id = best_gpu["id"]
 
     # Switch to best GPU
diff --git a/linumpy/gpu/bias_field.py b/linumpy/gpu/bias_field.py
index 32a76085..45589ea6 100644
--- a/linumpy/gpu/bias_field.py
+++ b/linumpy/gpu/bias_field.py
@@ -5,8 +5,6 @@
 CPU (NumPy + SciPy) when ``GPU_AVAILABLE`` is False.
 """
 
-from __future__ import annotations
-
 import numpy as np
 
 from . import GPU_AVAILABLE
diff --git a/linumpy/gpu/bspline.py b/linumpy/gpu/bspline.py
index 32a209ae..ece8235d 100644
--- a/linumpy/gpu/bspline.py
+++ b/linumpy/gpu/bspline.py
@@ -37,8 +37,6 @@
 weights regularise short-range support and recover the contrast.
 """
 
-from __future__ import annotations
-
 from typing import Any
 
 import numpy as np
diff --git a/linumpy/gpu/image_quality.py b/linumpy/gpu/image_quality.py
index d362d65a..3958ef62 100644
--- a/linumpy/gpu/image_quality.py
+++ b/linumpy/gpu/image_quality.py
@@ -35,7 +35,7 @@
     cupy_uniform_filter = None
 
 
-def _to_gpu(arr: np.ndarray) -> "cp.ndarray":
+def _to_gpu(arr: np.ndarray) -> cp.ndarray:
     """Transfer numpy array to GPU."""
     return cp.asarray(arr, dtype=cp.float32)
 
@@ -47,7 +47,7 @@ def _to_cpu(arr: Any) -> np.ndarray:
     return np.asarray(arr)
 
 
-def normalize_image_gpu(img: "cp.ndarray") -> "cp.ndarray":
+def normalize_image_gpu(img: cp.ndarray) -> cp.ndarray:
     """
     Normalize image to [0, 1] range on GPU.
 
diff --git a/linumpy/gpu/kvikio_zarr.py b/linumpy/gpu/kvikio_zarr.py
index 93a65b49..05fc81b7 100644
--- a/linumpy/gpu/kvikio_zarr.py
+++ b/linumpy/gpu/kvikio_zarr.py
@@ -28,8 +28,6 @@
   kvikio falls back to a posix bounce-buffer path with no speed-up.
 """
 
-from __future__ import annotations
-
 import json
 import sys
 from itertools import product
diff --git a/linumpy/gpu/n4.py b/linumpy/gpu/n4.py
index df491a77..af97da45 100644
--- a/linumpy/gpu/n4.py
+++ b/linumpy/gpu/n4.py
@@ -24,8 +24,6 @@
 i.e. ~12 GB for a (256, 1024, 1024) float32 volume.
 """
 
-from __future__ import annotations
-
 from typing import Any
 
 import numpy as np
diff --git a/linumpy/gpu/zarr_io.py b/linumpy/gpu/zarr_io.py
index 43b2e97e..30892857 100644
--- a/linumpy/gpu/zarr_io.py
+++ b/linumpy/gpu/zarr_io.py
@@ -26,8 +26,6 @@
 warm cache: kvikio ~9.9 GiB/s, zarr-gpu ~7.1 GiB/s.
 """
 
-from __future__ import annotations
-
 from contextlib import contextmanager
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Literal
@@ -65,7 +63,7 @@ def _array_is_kvikio_compatible(array_path: Path) -> bool:
 
     try:
         _load_array_spec(array_path)
-    except (NotImplementedError, FileNotFoundError, ValueError):
+    except NotImplementedError, FileNotFoundError, ValueError:
         return False
     return True
 
@@ -138,7 +136,7 @@ def read_zarr_to_gpu(array_path: str | Path, *, prefer: Backend = "auto") -> Any
 
         try:
             return read_zarr_via_kvikio(path)
-        except (RuntimeError, OSError, NotImplementedError):
+        except RuntimeError, OSError, NotImplementedError:
             pass
 
     return read_zarr_via_zarr_gpu(path)
diff --git a/linumpy/imaging/visualization.py b/linumpy/imaging/visualization.py
index 3476e252..8b6b5fd1 100644
--- a/linumpy/imaging/visualization.py
+++ b/linumpy/imaging/visualization.py
@@ -261,7 +261,7 @@ def _panel_labels_from_orientation(orientation: str) -> tuple | None:
     code = orientation.strip("'\" ").upper()
     try:
         parse_orientation_code(code)  # validation only
-    except (ValueError, KeyError):
+    except ValueError, KeyError:
         return None
 
     a0, a1, a2 = code  # anatomical letter for source dim0, dim1, dim2
@@ -415,9 +415,9 @@ def save_annotated_views(
     y_slice = y_slice if y_slice is not None else n_cols // 2
 
     # Derive panel titles and axis labels from orientation when available.
-    _orient = _panel_labels_from_orientation(orientation) if orientation else None
-    if _orient:
-        p1_name, p1_xlabel, p1_ylabel, p1_fixed, p2_name, p2_xlabel, p2_ylabel, p2_fixed = _orient
+    orient = _panel_labels_from_orientation(orientation) if orientation else None
+    if orient:
+        p1_name, p1_xlabel, p1_ylabel, p1_fixed, p2_name, p2_xlabel, p2_ylabel, p2_fixed = orient
         title1 = f"{p1_name} ({p1_ylabel}\u00d7{p1_xlabel}) view at {p1_fixed}={x_slice}"
         title2 = f"{p2_name} ({p2_ylabel}\u00d7{p2_xlabel}) view at {p2_fixed}={y_slice}"
         xlabel1, ylabel1 = p1_xlabel, p1_ylabel
diff --git a/linumpy/intensity/bias_field.py b/linumpy/intensity/bias_field.py
index 16cf95b2..4b8d6f78 100644
--- a/linumpy/intensity/bias_field.py
+++ b/linumpy/intensity/bias_field.py
@@ -12,8 +12,6 @@
     vol_out, _ = n4_correct(vol_ps, mask)
 """
 
-from __future__ import annotations
-
 import multiprocessing
 from typing import Any
 
diff --git a/linumpy/intensity/normalize.py b/linumpy/intensity/normalize.py
index 188466a8..1be737b5 100644
--- a/linumpy/intensity/normalize.py
+++ b/linumpy/intensity/normalize.py
@@ -221,13 +221,13 @@ def get_smooth_intensity_transition(vol: np.ndarray, slices_start: list[int]) ->
         L1 = np.exp(-(2 * z[:, :, 0 : nz / 2] - nz) / (1.0 * nz) * f1)
 
         # If z > N/2
-        nz_2 = factor[:, :, nz / 2 : :].shape[2]
+        nz_2 = factor[:, :, nz / 2 :].shape[2]
         f2 = np.log((a_next + b_current) / (2.0 * b_current + epsilon))
         f2 = np.tile(np.reshape(f2, (nx, ny, 1)), (1, 1, nz_2))
-        L2 = np.exp((2 * z[:, :, nz / 2 : :] - nz) / (1.0 * nz) * f2)
+        L2 = np.exp((2 * z[:, :, nz / 2 :] - nz) / (1.0 * nz) * f2)
 
         L[:, :, 0 : nz / 2] = L1
-        L[:, :, nz / 2 : :] = L2
+        L[:, :, nz / 2 :] = L2
 
         # Apply correction to this slice
         volume[:, :, z1:z2] = L * volume[:, :, z1:z2]
diff --git a/linumpy/io/slice_config.py b/linumpy/io/slice_config.py
index 61f28876..7b259002 100644
--- a/linumpy/io/slice_config.py
+++ b/linumpy/io/slice_config.py
@@ -33,8 +33,6 @@
 output path; otherwise the last writer wins.
 """
 
-from __future__ import annotations
-
 import csv
 from collections import OrderedDict
 from pathlib import Path
diff --git a/linumpy/io/zarr.py b/linumpy/io/zarr.py
index da391567..5c3f731e 100644
--- a/linumpy/io/zarr.py
+++ b/linumpy/io/zarr.py
@@ -201,9 +201,9 @@ def save_omezarr(
     metadata = {"method": "ome_zarr.writer.write_image", "version": ome_zarr_version, "args": pyramid_kw}
 
     create_directory(store_path, overwrite)
-    _loc = parse_url(store_path, mode="w")
-    assert _loc is not None
-    store = _loc.store
+    loc = parse_url(store_path, mode="w")
+    assert loc is not None
+    store = loc.store
     zarr_group = zarr.group(store=store)
 
     write_image(
@@ -241,9 +241,9 @@ def resolve_omezarr_level_path(zarr_path: Path, level: int = 0) -> Path:
     Path
         On-disk path of the level's zarr array.
     """
-    _zarr_loc = parse_url(zarr_path)
-    assert _zarr_loc is not None
-    reader = Reader(_zarr_loc)
+    zarr_loc = parse_url(zarr_path)
+    assert zarr_loc is not None
+    reader = Reader(zarr_loc)
     nodes = list(reader())
     image_node = nodes[0]
 
@@ -270,9 +270,9 @@ def read_omezarr(zarr_path: Path, level: int = 0) -> tuple:
     :type res: tuple (3,)
     :return res: Voxel size of zarr array.
     """
-    _zarr_loc = parse_url(zarr_path)
-    assert _zarr_loc is not None
-    reader = Reader(_zarr_loc)
+    zarr_loc = parse_url(zarr_path)
+    assert zarr_loc is not None
+    reader = Reader(zarr_loc)
     nodes = list(reader())
     image_node = nodes[0]
 
@@ -402,9 +402,9 @@ def __init__(
             else:
                 raise ValueError(f"Overwrite set to False and {store_path} non-empty.")
 
-        _store_loc = parse_url(store_path, mode="w", fmt=self.fmt)
-        assert _store_loc is not None
-        store = _store_loc.store
+        store_loc = parse_url(store_path, mode="w", fmt=self.fmt)
+        assert store_loc is not None
+        store = store_loc.store
         self.root = zarr.group(store=store)
 
         shape = tuple(int(v) for v in shape)
@@ -536,8 +536,7 @@ def _downsample_to_resolution(
         """Downsample from *source_path* to *target_path* with a specific target shape."""
         group_path = str(parent.store_path)
         # Remove file:// prefix if present (from zarr URL format)
-        if group_path.startswith("file://"):
-            group_path = group_path[7:]
+        group_path = group_path.removeprefix("file://")
         img_path = parent.store_path / parent.path
         image_path = Path(group_path) / parent.path
 
@@ -648,8 +647,7 @@ def finalize(
         # Get the path to level 0 (base resolution) for downsampling source
         # Remove file:// prefix if present (from zarr URL format)
         group_path = str(self.root.store_path)
-        if group_path.startswith("file://"):
-            group_path = group_path[7:]  # Remove "file://" prefix
+        group_path = group_path.removeprefix("file://")  # Remove "file://" prefix
 
         for i, target_um in enumerate(valid_targets):
             path = f"{i}"
diff --git a/linumpy/metrics/__init__.py b/linumpy/metrics/__init__.py
index 114a31de..142dff12 100644
--- a/linumpy/metrics/__init__.py
+++ b/linumpy/metrics/__init__.py
@@ -615,13 +615,13 @@ def collect_interface_crop_metrics(
     metrics.add_metric("end_index", int(end_idx), unit="voxels", description="End index for cropping")
 
     # Quality checks
-    _min_depth = PipelineMetrics.DEFAULT_THRESHOLDS["interface_min_depth_px"]["error"]
-    _max_fraction = PipelineMetrics.DEFAULT_THRESHOLDS["interface_max_depth_fraction"]["error"]
-    if detected_interface < _min_depth:
+    min_depth = PipelineMetrics.DEFAULT_THRESHOLDS["interface_min_depth_px"]["error"]
+    max_fraction = PipelineMetrics.DEFAULT_THRESHOLDS["interface_max_depth_fraction"]["error"]
+    if detected_interface < min_depth:
         metrics.add_metric(
             "interface_quality", "warning", description="Interface detected very close to start - may be incorrect"
         )
-    elif detected_interface > input_shape[0] * _max_fraction:
+    elif detected_interface > input_shape[0] * max_fraction:
         metrics.add_metric("interface_quality", "warning", description="Interface detected past halfway - check detection")
     else:
         metrics.add_metric("interface_quality", "ok", description="Interface detection appears reasonable")
diff --git a/linumpy/microscope/oct.py b/linumpy/microscope/oct.py
index 01934cea..748fb211 100644
--- a/linumpy/microscope/oct.py
+++ b/linumpy/microscope/oct.py
@@ -40,8 +40,7 @@ def read_scan_info(self, filename: Path) -> None:
         filename
             Path to the scan_file written by the OCT (.txt)
         """
-        with Path(filename).open() as f:
-            foo = f.read()
+        foo = Path(filename).read_text()
 
         # Process the file input
         foo = foo.split("\n")
diff --git a/linumpy/mosaic/discovery.py b/linumpy/mosaic/discovery.py
index 89a67873..92aa8431 100644
--- a/linumpy/mosaic/discovery.py
+++ b/linumpy/mosaic/discovery.py
@@ -101,10 +101,10 @@ def get_mosaic_info(directory: Path, z: int, overlap_fraction: float = 0.2, use_
 
     assert oct_tile is not None
     # Compute the mosaic shape
-    x_min = min([x for x, _ in tiles_positions_px])
-    y_min = min([y for _, y in tiles_positions_px])
-    x_max = max([x for x, _ in tiles_positions_px]) + oct_tile.shape[0]
-    y_max = max([y for _, y in tiles_positions_px]) + oct_tile.shape[1]
+    x_min = min(x for x, _ in tiles_positions_px)
+    y_min = min(y for _, y in tiles_positions_px)
+    x_max = max(x for x, _ in tiles_positions_px) + oct_tile.shape[0]
+    y_max = max(y for _, y in tiles_positions_px) + oct_tile.shape[1]
     mosaic_nrows = x_max - x_min
     mosaic_ncols = y_max - y_min
 
diff --git a/linumpy/mosaic/interpolation.py b/linumpy/mosaic/interpolation.py
index ac932a09..e1068dde 100644
--- a/linumpy/mosaic/interpolation.py
+++ b/linumpy/mosaic/interpolation.py
@@ -26,8 +26,6 @@
 ``interpolation_failed``, ``interpolation_fallback_reason`` columns).
 """
 
-from __future__ import annotations
-
 import logging
 from typing import Any
 
diff --git a/linumpy/mosaic/motor.py b/linumpy/mosaic/motor.py
index ab34a16d..63acb42d 100644
--- a/linumpy/mosaic/motor.py
+++ b/linumpy/mosaic/motor.py
@@ -232,7 +232,7 @@ def _is_empty(ov: np.ndarray) -> bool:
                     dy *= scale
                     refinements["stats"]["clamped_pairs"] += 1
 
-                refinements["horizontal"][(i, j)] = {"dx": float(dx), "dy": float(dy)}
+                refinements["horizontal"][i, j] = {"dx": float(dx), "dy": float(dy)}
                 refinements["stats"]["valid_pairs"] += 1
                 all_shifts.append(magnitude)
             except Exception as e:
@@ -278,7 +278,7 @@ def _is_empty(ov: np.ndarray) -> bool:
                     dy *= scale
                     refinements["stats"]["clamped_pairs"] += 1
 
-                refinements["vertical"][(i, j)] = {"dx": float(dx), "dy": float(dy)}
+                refinements["vertical"][i, j] = {"dx": float(dx), "dy": float(dy)}
                 refinements["stats"]["valid_pairs"] += 1
                 all_shifts.append(magnitude)
             except Exception as e:
diff --git a/linumpy/mosaic/quick_stitch.py b/linumpy/mosaic/quick_stitch.py
index 07c26a01..82922a1a 100644
--- a/linumpy/mosaic/quick_stitch.py
+++ b/linumpy/mosaic/quick_stitch.py
@@ -110,10 +110,10 @@ def get_mosaic_info(directory: Path, z: int, overlap_fraction: float = 0.2, use_
 
     # Compute the mosaic shape
     assert oct_tile is not None
-    x_min = min([x for x, _ in tiles_positions_px])
-    y_min = min([y for _, y in tiles_positions_px])
-    x_max = max([x for x, _ in tiles_positions_px]) + oct_tile.shape[0]
-    y_max = max([y for _, y in tiles_positions_px]) + oct_tile.shape[1]
+    x_min = min(x for x, _ in tiles_positions_px)
+    y_min = min(y for _, y in tiles_positions_px)
+    x_max = max(x for x, _ in tiles_positions_px) + oct_tile.shape[0]
+    y_max = max(y for _, y in tiles_positions_px) + oct_tile.shape[1]
     mosaic_nrows = x_max - x_min
     mosaic_ncols = y_max - y_min
 
@@ -206,10 +206,10 @@ def quick_stitch(
 
     # Compute the mosaic shape
     assert oct_tile is not None
-    x_min = min([x for x, _ in tiles_positions_px])
-    y_min = min([y for _, y in tiles_positions_px])
-    x_max = max([x for x, _ in tiles_positions_px]) + oct_tile.shape[0]
-    y_max = max([y for _, y in tiles_positions_px]) + oct_tile.shape[1]
+    x_min = min(x for x, _ in tiles_positions_px)
+    y_min = min(y for _, y in tiles_positions_px)
+    x_max = max(x for x, _ in tiles_positions_px) + oct_tile.shape[0]
+    y_max = max(y for _, y in tiles_positions_px) + oct_tile.shape[1]
     mosaic_nrows = x_max - x_min
     mosaic_ncols = y_max - y_min
     mosaic = np.zeros((mosaic_nrows, mosaic_ncols), dtype=np.float32)
diff --git a/linumpy/reference/allen.py b/linumpy/reference/allen.py
index 9b403992..e1aaf8c6 100644
--- a/linumpy/reference/allen.py
+++ b/linumpy/reference/allen.py
@@ -79,8 +79,7 @@ def download_template(resolution: int, cache: bool = True, cache_dir: str = ".da
         # Download the template
         response = requests.get(url, stream=True)
         with Path(nrrd_file).open("wb") as f:
-            for data in tqdm(response.iter_content()):
-                f.write(data)
+            f.writelines(tqdm(response.iter_content()))
 
     # Loading the nrrd file
     vol = sitk.ReadImage(str(nrrd_file))
diff --git a/linumpy/stack_alignment/io.py b/linumpy/stack_alignment/io.py
index db6d24c3..6f2781e8 100644
--- a/linumpy/stack_alignment/io.py
+++ b/linumpy/stack_alignment/io.py
@@ -34,7 +34,7 @@ def load_shifts_csv(shifts_path: Path) -> tuple[dict, list]:
     for _, row in df.iterrows():
         fixed_id = int(row["fixed_id"])
         moving_id = int(row["moving_id"])
-        shift_lookup[(fixed_id, moving_id)] = (row["x_shift_mm"], row["y_shift_mm"])
+        shift_lookup[fixed_id, moving_id] = (row["x_shift_mm"], row["y_shift_mm"])
 
     cumsum = {all_ids[0]: (0.0, 0.0)}
     for i in range(len(all_ids) - 1):
@@ -80,7 +80,7 @@ def build_cumulative_shifts(
     for _, row in shifts_df.iterrows():
         fixed_id = int(row["fixed_id"])
         moving_id = int(row["moving_id"])
-        shift_lookup[(fixed_id, moving_id)] = (row["x_shift_mm"], row["y_shift_mm"])
+        shift_lookup[fixed_id, moving_id] = (row["x_shift_mm"], row["y_shift_mm"])
 
     all_slice_ids = set()
     for _, row in shifts_df.iterrows():
diff --git a/linumpy/tests/test_bias_field.py b/linumpy/tests/test_bias_field.py
index 992b64d7..454184cb 100644
--- a/linumpy/tests/test_bias_field.py
+++ b/linumpy/tests/test_bias_field.py
@@ -1,7 +1,5 @@
 """Tests for linumpy/intensity/bias_field.py (and gpu/bias_field.py)."""
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 
diff --git a/linumpy/tests/test_bias_field_backend.py b/linumpy/tests/test_bias_field_backend.py
index fe2ed006..a4d7a3a4 100644
--- a/linumpy/tests/test_bias_field_backend.py
+++ b/linumpy/tests/test_bias_field_backend.py
@@ -1,7 +1,5 @@
 """Integration tests for the n4_correct backend dispatcher."""
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 
diff --git a/linumpy/tests/test_gpu_bspline.py b/linumpy/tests/test_gpu_bspline.py
index 7d02f5c2..353f9a80 100644
--- a/linumpy/tests/test_gpu_bspline.py
+++ b/linumpy/tests/test_gpu_bspline.py
@@ -1,7 +1,5 @@
 """Tests for linumpy.gpu.bspline."""
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 
diff --git a/linumpy/tests/test_gpu_n4.py b/linumpy/tests/test_gpu_n4.py
index 92802614..f1509fc2 100644
--- a/linumpy/tests/test_gpu_n4.py
+++ b/linumpy/tests/test_gpu_n4.py
@@ -1,7 +1,5 @@
 """Tests for linumpy.gpu.n4."""
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 
diff --git a/linumpy/tests/test_io_allen.py b/linumpy/tests/test_io_allen.py
index 8155bc1a..4b4d0e9d 100644
--- a/linumpy/tests/test_io_allen.py
+++ b/linumpy/tests/test_io_allen.py
@@ -6,8 +6,6 @@
 produces a RAS+ volume (``+X = Right``, ``+Y = Anterior``, ``+Z = Superior``).
 """
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 import SimpleITK as sitk
diff --git a/linumpy/tests/test_io_slice_config.py b/linumpy/tests/test_io_slice_config.py
index b054d1d7..717deee4 100644
--- a/linumpy/tests/test_io_slice_config.py
+++ b/linumpy/tests/test_io_slice_config.py
@@ -1,7 +1,5 @@
 """Tests for linumpy/io/slice_config.py."""
 
-from __future__ import annotations
-
 import csv
 from pathlib import Path
 
diff --git a/linumpy/tests/test_n4_gpu_equivalency.py b/linumpy/tests/test_n4_gpu_equivalency.py
index 8c17567e..0bf24530 100644
--- a/linumpy/tests/test_n4_gpu_equivalency.py
+++ b/linumpy/tests/test_n4_gpu_equivalency.py
@@ -26,8 +26,6 @@
   a small tolerance.
 """
 
-from __future__ import annotations
-
 import numpy as np
 import pytest
 
diff --git a/linumpy/tests/test_n4_gpu_perf.py b/linumpy/tests/test_n4_gpu_perf.py
index e923c552..9e5e8e2c 100644
--- a/linumpy/tests/test_n4_gpu_perf.py
+++ b/linumpy/tests/test_n4_gpu_perf.py
@@ -6,8 +6,6 @@
 seconds, not minutes.
 """
 
-from __future__ import annotations
-
 import time
 
 import numpy as np
diff --git a/pyproject.toml b/pyproject.toml
index a12c823c..74f5b858 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ version = "0.1.1"
 description = "linumpy: microscopy tools and utilities"
 readme = "README.md"
 license = "GPL-3.0-or-later"
-requires-python = ">=3.12"
+requires-python = ">=3.14"
 authors = [
     { name = "The LINUM developers" },
 ]
@@ -21,6 +21,7 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
     "Programming Language :: Python",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
 ]
 dependencies = [
@@ -199,17 +200,20 @@ include = ["linumpy*", "scripts*"]
 
 # --- Ruff ---
 [tool.ruff]
-target-version = "py312"
+target-version = "py314"
 line-length = 127
 fix = true
 include = ["linumpy*", "scripts*"]
 
 [tool.ruff.lint]
 select = ["E", "F", "W", "I", "UP", "B", "RUF", "SIM", "C4", "PIE", "PTH", 
-            "N", "PERF", "FLY", "TCH", "G", "D", "ANN", "ARG", "ERA"]
+            "N", "PERF", "FLY", "G", "D", "ANN", "ARG", "ERA", "FURB"]
 # N813: SimpleITK as sitk is the universal Python convention — excluded globally.
 # D212/D213 conflict: numpy convention picks D213 (summary on second line of multi-line docstrings).
 # ANN401: Any is legitimately unavoidable in a few callback/override signatures.
+# Note: flake8-type-checking (TCH/TC) is intentionally not selected — under
+# PEP 649 (Python 3.14 default), annotations are lazily evaluated, so gating
+# typing-only imports inside TYPE_CHECKING blocks no longer reduces import cost.
 ignore = ["N813", "ANN401"]
 extend-select = ["D417"]
 # Scientific codebase: Greek letters and the info-icon glyph are intentional;
@@ -255,7 +259,7 @@ convention = "numpy"
 # before numpy/scipy/SimpleITK or the env vars have no effect.
 known-first-party = ["linumpy"]
 sections.thread-config = ["linumpy.config.threads"]
-section-order = ["future", "thread-config", "standard-library", "third-party", "first-party", "local-folder"]
+section-order = ["thread-config", "standard-library", "third-party", "first-party", "local-folder"]
 
 [tool.ruff.format]
 # Use default (black-compatible) formatting
@@ -265,7 +269,7 @@ section-order = ["future", "thread-config", "standard-library", "third-party", "
 include = ["linumpy", "scripts"]
 
 [tool.ty.environment]
-python-version = "3.12"
+python-version = "3.14"
 
 [tool.ty.rules]
 # possibly-unresolved-reference defaults to "warn" in ty; raise it to "error"
diff --git a/scripts/diagnostics/linum_aggregate_dilation_analysis.py b/scripts/diagnostics/linum_aggregate_dilation_analysis.py
index 7134eed9..fc17d9c7 100644
--- a/scripts/diagnostics/linum_aggregate_dilation_analysis.py
+++ b/scripts/diagnostics/linum_aggregate_dilation_analysis.py
@@ -234,19 +234,27 @@ def generate_report(stats: Any, corrections: Any, _per_slice: Any, output_dir: P
     dev_x = corrections["deviation_from_unity"]["x_percent"]
 
     if abs(dev_y) > 1.0 or abs(dev_x) > 1.0:
-        lines.append("⚠ SIGNIFICANT DILATION DETECTED")
-        lines.append(f"  Y-direction: {abs(dev_y):.2f}% {'contraction' if dev_y > 0 else 'expansion'}")
-        lines.append(f"  X-direction: {abs(dev_x):.2f}% {'contraction' if dev_x > 0 else 'expansion'}")
-        lines.append("")
-        lines.append("  This will cause edge misalignment in 3D reconstruction.")
-        lines.append("  Apply the recommended correction factors below.")
+        lines.extend(
+            (
+                "⚠ SIGNIFICANT DILATION DETECTED",
+                f"  Y-direction: {abs(dev_y):.2f}% {'contraction' if dev_y > 0 else 'expansion'}",
+                f"  X-direction: {abs(dev_x):.2f}% {'contraction' if dev_x > 0 else 'expansion'}",
+                "",
+                "  This will cause edge misalignment in 3D reconstruction.",
+                "  Apply the recommended correction factors below.",
+            )
+        )
     else:
         lines.append("✓ Scale factors close to 1.0 - minimal dilation detected")
 
     if stats["anisotropy"]["mean"] > 0.01:
-        lines.append("")
-        lines.append(f"⚠ ANISOTROPIC SCALING: X and Y scales differ by {stats['anisotropy']['mean'] * 100:.2f}%")
-        lines.append("  Use different correction factors for X and Y directions.")
+        lines.extend(
+            (
+                "",
+                f"⚠ ANISOTROPIC SCALING: X and Y scales differ by {stats['anisotropy']['mean'] * 100:.2f}%",
+                "  Use different correction factors for X and Y directions.",
+            )
+        )
 
     lines.extend(
         [
@@ -296,8 +304,7 @@ def generate_report(stats: Any, corrections: Any, _per_slice: Any, output_dir: P
     )
 
     report_path = Path(output_dir) / "aggregated_dilation_report.txt"
-    with Path(report_path).open("w") as f:
-        f.write("\n".join(lines))
+    Path(report_path).write_text("\n".join(lines))
 
     logger.info("Report saved to %s", report_path)
     return report_path
diff --git a/scripts/diagnostics/linum_analyze_acquisition_rotation.py b/scripts/diagnostics/linum_analyze_acquisition_rotation.py
index c43b2a14..2c6f8c71 100644
--- a/scripts/diagnostics/linum_analyze_acquisition_rotation.py
+++ b/scripts/diagnostics/linum_analyze_acquisition_rotation.py
@@ -370,8 +370,7 @@ def generate_report(analysis: Any, reg_comparison: Any, output_dir: Path) -> Pat
     lines.extend(["", "=" * 70])
 
     report_path = output_dir / "acquisition_rotation_analysis.txt"
-    with Path(report_path).open("w") as f:
-        f.write("\n".join(lines))
+    Path(report_path).write_text("\n".join(lines))
 
     logger.info("Report saved to %s", report_path)
     return report_path
diff --git a/scripts/diagnostics/linum_analyze_registration_transforms.py b/scripts/diagnostics/linum_analyze_registration_transforms.py
index d8526fbe..3f33f16e 100644
--- a/scripts/diagnostics/linum_analyze_registration_transforms.py
+++ b/scripts/diagnostics/linum_analyze_registration_transforms.py
@@ -336,8 +336,7 @@ def generate_report(df: Any, analysis: Any, correlation: Any, output_dir: Path)
     lines.append("=" * 70)
 
     report_path = output_dir / "rotation_analysis.txt"
-    with Path(report_path).open("w") as f:
-        f.write("\n".join(lines))
+    Path(report_path).write_text("\n".join(lines))
 
     logger.info("Report saved to %s", report_path)
     return report_path
diff --git a/scripts/diagnostics/linum_analyze_tile_dilation.py b/scripts/diagnostics/linum_analyze_tile_dilation.py
index 389fa90d..f2a3dfe6 100644
--- a/scripts/diagnostics/linum_analyze_tile_dilation.py
+++ b/scripts/diagnostics/linum_analyze_tile_dilation.py
@@ -191,15 +191,27 @@ def generate_report(
     if scale_deviation < 0.001:
         lines.append("✓ Scale factor ~1.0: No significant dilation detected")
     elif scale_factors["mean_scale"] > 1.0:
-        lines.append(f"⚠ Scale > 1.0: Tiles spread MORE than expected ({scale_deviation * 100:.2f}% expansion)")
-        lines.append("  → Possible cause: Tissue relaxation/expansion after cutting")
+        lines.extend(
+            (
+                f"⚠ Scale > 1.0: Tiles spread MORE than expected ({scale_deviation * 100:.2f}% expansion)",
+                "  → Possible cause: Tissue relaxation/expansion after cutting",
+            )
+        )
     else:
-        lines.append(f"⚠ Scale < 1.0: Tiles spread LESS than expected ({scale_deviation * 100:.2f}% contraction)")
-        lines.append("  → Possible cause: Stage calibration error or tissue shrinkage")
+        lines.extend(
+            (
+                f"⚠ Scale < 1.0: Tiles spread LESS than expected ({scale_deviation * 100:.2f}% contraction)",
+                "  → Possible cause: Stage calibration error or tissue shrinkage",
+            )
+        )
 
     if scale_factors["anisotropy"] > 0.005:
-        lines.append(f"⚠ Anisotropic scaling detected: X/Y scales differ by {scale_factors['anisotropy']:.4f}")
-        lines.append("  → May cause edge misalignment in 3D reconstruction")
+        lines.extend(
+            (
+                f"⚠ Anisotropic scaling detected: X/Y scales differ by {scale_factors['anisotropy']:.4f}",
+                "  → May cause edge misalignment in 3D reconstruction",
+            )
+        )
 
     lines.extend(
         [
@@ -237,8 +249,7 @@ def generate_report(
     )
 
     report_path = Path(output_dir) / "dilation_analysis.txt"
-    with Path(report_path).open("w") as f:
-        f.write("\n".join(lines))
+    Path(report_path).write_text("\n".join(lines))
 
     logger.info("Report saved to %s", report_path)
     return report_path
diff --git a/scripts/diagnostics/linum_benchmark_gpu.py b/scripts/diagnostics/linum_benchmark_gpu.py
index 71d0e094..0eee6b10 100644
--- a/scripts/diagnostics/linum_benchmark_gpu.py
+++ b/scripts/diagnostics/linum_benchmark_gpu.py
@@ -57,7 +57,7 @@ class BenchmarkTimer:
     def __init__(self) -> None:
         self.elapsed = 0
 
-    def __enter__(self) -> "BenchmarkTimer":
+    def __enter__(self) -> BenchmarkTimer:
         """Magic method function."""
         self.start = time.perf_counter()
         return self
diff --git a/scripts/diagnostics/linum_benchmark_n4_gpu.py b/scripts/diagnostics/linum_benchmark_n4_gpu.py
index 0ecbad8f..399c5e1d 100644
--- a/scripts/diagnostics/linum_benchmark_n4_gpu.py
+++ b/scripts/diagnostics/linum_benchmark_n4_gpu.py
@@ -16,8 +16,6 @@
         --live-zarr /scratch/workspace/sub-22/output/01/fix_illumination/mosaic_grid_z01_illum_fix.ome.zarr
 """
 
-from __future__ import annotations
-
 import argparse
 import json
 import time
@@ -255,7 +253,7 @@ def main():
     if args.live_zarr is not None and args.live_zarr.exists():
         print(f"\n=== Live OCT volume: {args.live_zarr} (level={args.live_level}) ===")
         vol, mask = _load_live_volume(args.live_zarr, level=args.live_level, slice_index=args.live_slice_index)
-        zc, yc, xc = (min(s, c) for s, c in zip(vol.shape, args.max_live_shape, strict=True))
+        zc, yc, xc = map(min, vol.shape, args.max_live_shape, strict=True)
         vol = vol[:zc, :yc, :xc].copy()
         mask = mask[:zc, :yc, :xc].copy()
         print(f"  live volume shape={vol.shape}, mask coverage={float(mask.mean()):.2%}")
@@ -277,10 +275,12 @@ def main():
     json_path.write_text(json.dumps(records, indent=2))
 
     lines = ["# N4 GPU vs SimpleITK benchmark", ""]
-    lines.append(
-        "| Volume | shrink | iters | CPU (s) | GPU (s) | Speedup | r(bias) | median |Δ|/mean | CV bias CPU | CV bias GPU |"
+    lines.extend(
+        (
+            "| Volume | shrink | iters | CPU (s) | GPU (s) | Speedup | r(bias) | median |Δ|/mean | CV bias CPU | CV bias GPU |",
+            "|---|---|---|---|---|---|---|---|---|---|",
+        )
     )
-    lines.append("|---|---|---|---|---|---|---|---|---|---|")
     for r in records:
         shape = "x".join(str(s) for s in r["shape"])
         n_iter_str = ",".join(str(n) for n in r["n_iter"])
diff --git a/scripts/diagnostics/linum_diagnose_pipeline.py b/scripts/diagnostics/linum_diagnose_pipeline.py
index b1cecc87..5624789c 100644
--- a/scripts/diagnostics/linum_diagnose_pipeline.py
+++ b/scripts/diagnostics/linum_diagnose_pipeline.py
@@ -21,7 +21,6 @@
 import argparse
 import glob
 import json
-import multiprocessing
 import os
 import subprocess
 import sys
@@ -73,7 +72,7 @@ def check_cpu(self) -> Any:
         print_header("CPU Configuration")
 
         # Physical CPU info
-        total_cpus = multiprocessing.cpu_count()
+        total_cpus = os.process_cpu_count() or os.cpu_count() or 1
         self.results["cpu"]["total_cores"] = total_cpus
         print(f"  Total CPU cores detected: {total_cpus}")
 
@@ -170,7 +169,7 @@ def check_gpu(self) -> None:
                                     f"{int(float(parts[2])) / 1024:.1f} GB free"
                                 )
                                 print(f"    Driver: {parts[3]}, CUDA: {parts[4]}")
-                            except (ValueError, IndexError):
+                            except ValueError, IndexError:
                                 print(f"  ⚠️  Could not parse GPU {i} info: {line}")
 
                     self.results["gpu"]["available"] = len(gpus) > 0
diff --git a/scripts/diagnostics/linum_diagnose_reconstruction.py b/scripts/diagnostics/linum_diagnose_reconstruction.py
index f9fd1229..7060a651 100644
--- a/scripts/diagnostics/linum_diagnose_reconstruction.py
+++ b/scripts/diagnostics/linum_diagnose_reconstruction.py
@@ -376,8 +376,7 @@ def generate_summary_report(results: Any, output_dir: Path) -> Path:
     lines.extend(["", "=" * 70])
 
     report_path = Path(output_dir) / "diagnostic_report.txt"
-    with Path(report_path).open("w") as f:
-        f.write("\n".join(lines))
+    Path(report_path).write_text("\n".join(lines))
 
     # Also save JSON
     json_path = Path(output_dir) / "diagnostic_results.json"
diff --git a/scripts/diagnostics/linum_n4_gpu_visual_compare.py b/scripts/diagnostics/linum_n4_gpu_visual_compare.py
index b1431377..86d394d5 100644
--- a/scripts/diagnostics/linum_n4_gpu_visual_compare.py
+++ b/scripts/diagnostics/linum_n4_gpu_visual_compare.py
@@ -6,8 +6,6 @@
 |CPU - GPU|) for documentation.
 """
 
-from __future__ import annotations
-
 import argparse
 from pathlib import Path
 
@@ -32,7 +30,7 @@ def _load_slab(zarr_path: Path, level: int, z0: int, dz: int):
 
             with zipfile.ZipFile(str(zarr_path)) as zf:
                 names = zf.namelist()
-            top = sorted({n.split("/", 1)[0] for n in names if "/" in n})[0]
+            top = min(n.split("/", 1)[0] for n in names if "/" in n)
             root = zarr.open(store, mode="r", path=top)
     else:
         root = zarr.open(str(zarr_path), mode="r")
diff --git a/scripts/diagnostics/linum_stack_motor_only.py b/scripts/diagnostics/linum_stack_motor_only.py
index 4303b7aa..d9a5f7c7 100644
--- a/scripts/diagnostics/linum_stack_motor_only.py
+++ b/scripts/diagnostics/linum_stack_motor_only.py
@@ -272,7 +272,7 @@ def main() -> None:
 
     # Get resolution from first slice
     # NOTE: read_omezarr returns resolution in MILLIMETERS (OME-NGFF standard)
-    first_slice_id = sorted(slice_files.keys())[0]
+    first_slice_id = min(slice_files.keys())
     _first_vol, first_res = read_omezarr(Path(slice_files[first_slice_id]), level=0)
 
     # Resolution: res is [z, y, x] in mm from OME-NGFF, convert to µm
diff --git a/scripts/diagnostics/linum_stitch_motor_only.py b/scripts/diagnostics/linum_stitch_motor_only.py
index ecae5054..e153cba3 100644
--- a/scripts/diagnostics/linum_stitch_motor_only.py
+++ b/scripts/diagnostics/linum_stitch_motor_only.py
@@ -119,10 +119,10 @@ def main() -> None:
             logger.warning(comparison["dilation_warning"])
 
     # Compute output mosaic shape
-    posx_min = min([pos[0] for pos in motor_positions])
-    posx_max = max([pos[0] + tile_shape[1] for pos in motor_positions])
-    posy_min = min([pos[1] for pos in motor_positions])
-    posy_max = max([pos[1] + tile_shape[2] for pos in motor_positions])
+    posx_min = min(pos[0] for pos in motor_positions)
+    posx_max = max(pos[0] + tile_shape[1] for pos in motor_positions)
+    posy_min = min(pos[1] for pos in motor_positions)
+    posy_max = max(pos[1] + tile_shape[2] for pos in motor_positions)
     mosaic_shape = (volume.shape[0], int(posx_max - posx_min), int(posy_max - posy_min))
 
     logger.info("Output mosaic shape: %s", mosaic_shape)
diff --git a/scripts/linum_aip.py b/scripts/linum_aip.py
index b0d20e17..c3db5735 100644
--- a/scripts/linum_aip.py
+++ b/scripts/linum_aip.py
@@ -39,9 +39,9 @@ def _compute_aip(vol: Any, use_gpu: bool) -> tuple[zarr.Array, tuple]:
     shape = vol.shape[1:3]
     tile_shape = vol.chunks
     zarr_store = create_tempstore(suffix=".zarr")
-    _aip = zarr.open(zarr_store, mode="w", shape=shape, dtype=np.float32, chunks=vol.chunks[1:3])
-    assert isinstance(_aip, zarr.Array)
-    aip = _aip
+    aip_ = zarr.open(zarr_store, mode="w", shape=shape, dtype=np.float32, chunks=vol.chunks[1:3])
+    assert isinstance(aip_, zarr.Array)
+    aip = aip_
 
     nx = vol.shape[1] // tile_shape[1]
     ny = vol.shape[2] // tile_shape[2]
diff --git a/scripts/linum_align_to_ras.py b/scripts/linum_align_to_ras.py
index eced9d97..37da2329 100755
--- a/scripts/linum_align_to_ras.py
+++ b/scripts/linum_align_to_ras.py
@@ -331,7 +331,7 @@ def get_pyramid_resolutions_from_zarr(zarr_path: Path) -> list[float] | None:
         try:
             with Path(metadata_path).open(encoding="utf-8") as f:
                 metadata = json.load(f)
-        except (OSError, json.JSONDecodeError):
+        except OSError, json.JSONDecodeError:
             continue
 
         multiscales = metadata.get("multiscales", [])
diff --git a/scripts/linum_analyze_shifts.py b/scripts/linum_analyze_shifts.py
index 03b97e7d..916d2d27 100644
--- a/scripts/linum_analyze_shifts.py
+++ b/scripts/linum_analyze_shifts.py
@@ -114,8 +114,7 @@ def generate_report(df: Any, df_filtered: Any, outlier_mask: Any, stats: Any, re
     ]
 
     if outlier_mask.sum() > 0:
-        report_lines.append("")
-        report_lines.append("Outlier shifts:")
+        report_lines.extend(("", "Outlier shifts:"))
         shift_mag = np.sqrt(df["x_shift_mm"] ** 2 + df["y_shift_mm"] ** 2)
         for idx in df[outlier_mask].index:
             row = df.loc[idx]
diff --git a/scripts/linum_apply_slices_transforms.py b/scripts/linum_apply_slices_transforms.py
index dc01fe70..6e9de052 100644
--- a/scripts/linum_apply_slices_transforms.py
+++ b/scripts/linum_apply_slices_transforms.py
@@ -55,9 +55,9 @@ def main() -> None:
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    _in = zarr.open(args.in_zarr, mode="r")
-    assert isinstance(_in, zarr.Array)
-    in_zarr = _in
+    in_ = zarr.open(args.in_zarr, mode="r")
+    assert isinstance(in_, zarr.Array)
+    in_zarr = in_
     imin, imax = np.min(np.asarray(in_zarr)), np.max(np.asarray(in_zarr))
 
     checkpoint = np.load(args.in_corrections)
diff --git a/scripts/linum_assess_slice_quality.py b/scripts/linum_assess_slice_quality.py
index d1edb1fd..ec30f15d 100644
--- a/scripts/linum_assess_slice_quality.py
+++ b/scripts/linum_assess_slice_quality.py
@@ -37,8 +37,6 @@
     linum_assess_slice_quality.py /path/to/mosaics slice_config.csv --no-use_gpu
 """
 
-from __future__ import annotations
-
 # Configure thread limits before numpy/scipy imports
 import linumpy.config.threads  # noqa: F401
 
@@ -261,7 +259,7 @@ def main() -> None:
 
     existing_config = None
     if args.update_existing:
-        config_to_load = args.existing_config if args.existing_config else output_file
+        config_to_load = args.existing_config or output_file
         if Path(config_to_load).exists():
             existing_config = read_existing_config(Path(config_to_load))
             print(f"Loaded existing config with {len(existing_config)} entries")
diff --git a/scripts/linum_auto_exclude_slices.py b/scripts/linum_auto_exclude_slices.py
index 7df63234..27d4be42 100644
--- a/scripts/linum_auto_exclude_slices.py
+++ b/scripts/linum_auto_exclude_slices.py
@@ -20,6 +20,7 @@
 import argparse
 import json
 import logging
+import operator
 import os
 import re
 from pathlib import Path
@@ -88,7 +89,7 @@ def load_registration_metrics(transforms_dir: Path) -> Any:
         if z_corr is not None:
             metrics.append((slice_id, float(z_corr)))
 
-    metrics.sort(key=lambda x: x[0])
+    metrics.sort(key=operator.itemgetter(0))
     return metrics
 
 
diff --git a/scripts/linum_benchmark_kvikio_zarr.py b/scripts/linum_benchmark_kvikio_zarr.py
index 8147d6ff..29847d0b 100755
--- a/scripts/linum_benchmark_kvikio_zarr.py
+++ b/scripts/linum_benchmark_kvikio_zarr.py
@@ -30,8 +30,6 @@
         --runs 3
 """
 
-from __future__ import annotations
-
 import argparse
 import contextlib
 import sys
diff --git a/scripts/linum_convert_tiff_to_omezarr.py b/scripts/linum_convert_tiff_to_omezarr.py
index 2cc734ff..5062a040 100755
--- a/scripts/linum_convert_tiff_to_omezarr.py
+++ b/scripts/linum_convert_tiff_to_omezarr.py
@@ -89,7 +89,7 @@ def check_folders(parser: Any, folder: Path) -> list:
             parser.error("No tiff files or subfolder found in the folder.")
         else:
             logging.info("Found subfolders in the folder.")
-            for _index, subfolder in enumerate(subfolders):
+            for subfolder in subfolders:
                 if not list(Path(subfolder).glob("*.tif")):
                     parser.error("No tiff files found in the subfolder.")
                 else:
diff --git a/scripts/linum_detect_rehoming.py b/scripts/linum_detect_rehoming.py
index 52e2f5a2..6307d2f4 100644
--- a/scripts/linum_detect_rehoming.py
+++ b/scripts/linum_detect_rehoming.py
@@ -43,6 +43,7 @@
 
 import argparse
 import json
+import operator
 from pathlib import Path
 
 import numpy as np
@@ -169,7 +170,7 @@ def _save_diagnostics(
                 "corrected_y_shift_mm": float(row_after["y_shift_mm"]),
             }
         )
-    records.sort(key=lambda r: r["index"])
+    records.sort(key=operator.itemgetter("index"))
     report = {
         "n_corrected": len(records),
         "corrected_spikes": [r for r in records if r["correction_type"] == "spike"],
diff --git a/scripts/linum_export_manual_align.py b/scripts/linum_export_manual_align.py
index 41d9b8fe..203becb4 100644
--- a/scripts/linum_export_manual_align.py
+++ b/scripts/linum_export_manual_align.py
@@ -372,7 +372,7 @@ def _read_overlap_z_offsets(offsets_file: Path) -> tuple[int, int]:
         arr_off = np.loadtxt(str(offsets_file), dtype=int)
         if arr_off.size >= 2:
             return int(arr_off[0]), int(arr_off[1])
-    except (OSError, ValueError):
+    except OSError, ValueError:
         pass
     return 0, 0
 
@@ -451,7 +451,7 @@ def main(argv: Any = None) -> None:
     interp_remote_dir = (
         str(Path(args.interpolated_slices_remote_dir)) if args.interpolated_slices_remote_dir else slices_remote_dir
     )
-    workers = args.workers or max(1, (os.cpu_count() or 4) - 2)
+    workers = args.workers or max(1, (os.process_cpu_count() or os.cpu_count() or 4) - 2)
     overlap_px = args.xy_overlap_px
     logger.info("XY overlap slab: %s voxels at pyramid level %s", overlap_px, args.level)
 
diff --git a/scripts/linum_generate_pipeline_report.py b/scripts/linum_generate_pipeline_report.py
index 0691e7ac..b4acf7c1 100644
--- a/scripts/linum_generate_pipeline_report.py
+++ b/scripts/linum_generate_pipeline_report.py
@@ -27,6 +27,7 @@
 except ImportError:
     _PIL_AVAILABLE = False
 
+import operator
 from typing import Any
 
 import numpy as np
@@ -177,7 +178,7 @@ def group_issues(issues: list[str]) -> list[dict]:
     groups = defaultdict(list)
     for issue in issues:
         parsed = parse_issue(issue)
-        key = parsed["metric"] if parsed["metric"] else "__other__"
+        key = parsed["metric"] or "__other__"
         groups[key].append(parsed)
 
     result = []
@@ -330,11 +331,11 @@ def to_svg_y(v: Any) -> Any:
         )
 
     # Y-axis labels
-    elements.append(
-        f'<text x="{pad_x - 3}" y="{to_svg_y(max_y):.1f}" text-anchor="end" font-size="8" fill="#888">{max_y:.3g}</text>'
-    )
-    elements.append(
-        f'<text x="{pad_x - 3}" y="{to_svg_y(min_y):.1f}" text-anchor="end" font-size="8" fill="#888">{min_y:.3g}</text>'
+    elements.extend(
+        (
+            f'<text x="{pad_x - 3}" y="{to_svg_y(max_y):.1f}" text-anchor="end" font-size="8" fill="#888">{max_y:.3g}</text>',
+            f'<text x="{pad_x - 3}" y="{to_svg_y(min_y):.1f}" text-anchor="end" font-size="8" fill="#888">{min_y:.3g}</text>',
+        )
     )
 
     title_text = f"n={len(numeric)}, range [{min_y:.3g}, {max_y:.3g}]"
@@ -360,7 +361,7 @@ def _extract(metrics_list: Any, key: str) -> list:
             val = m.get("metrics", {}).get(key, {}).get("value")
             if isinstance(val, (int, float)):
                 pairs.append((src, val))
-        pairs.sort(key=lambda p: p[0])  # sort by source file path
+        pairs.sort(key=operator.itemgetter(0))  # sort by source file path
         return [v for _, v in pairs]
 
     # XY tile transform: scale and shear across slices
@@ -543,7 +544,7 @@ def _to_float(value: object) -> float | None:
             return None
         try:
             return float(value)
-        except (TypeError, ValueError):
+        except TypeError, ValueError:
             return None
 
     for r in rows:
@@ -1018,12 +1019,16 @@ def _render_interpolation_section_text(interpolation: dict) -> str:
     imp_mean = summary.get("ncc_improvement_mean")
 
     lines = []
-    lines.append("")
-    lines.append(f"{get_status_emoji('info')} SLICE INTERPOLATION")
-    lines.append("-" * 70)
-    lines.append(f"  Gaps detected          : {count}")
-    lines.append(f"  Successfully interp'd  : {n_succeeded}")
-    lines.append(f"  Hard-skipped (gap)     : {n_failed}")
+    lines.extend(
+        (
+            "",
+            f"{get_status_emoji('info')} SLICE INTERPOLATION",
+            "-" * 70,
+            f"  Gaps detected          : {count}",
+            f"  Successfully interp'd  : {n_succeeded}",
+            f"  Hard-skipped (gap)     : {n_failed}",
+        )
+    )
     if pre_mean is not None:
         lines.append(f"  Mean pre-reg NCC       : {pre_mean:.3f}")
     if post_mean is not None:
@@ -1041,9 +1046,9 @@ def _render_interpolation_section_text(interpolation: dict) -> str:
         lines.append(f"  Hard-skip reasons      : {fb_parts}")
 
     if rows:
-        lines.append("")
-        lines.append(f"  {'Slice':<6} {'Status':<8} {'Used':<14} {'Reason':<28} {'PreNCC':>7} {'PostNCC':>7}")
-        lines.append("  " + "-" * 80)
+        lines.extend(
+            ("", f"  {'Slice':<6} {'Status':<8} {'Used':<14} {'Reason':<28} {'PreNCC':>7} {'PostNCC':>7}", "  " + "-" * 80)
+        )
         for r in rows[:50]:
             sid = (r.get("slice_id", "") or "?")[:6]
             failed = bool(r.get("interpolation_failed"))
@@ -1054,11 +1059,11 @@ def _render_interpolation_section_text(interpolation: dict) -> str:
             post = r.get("post_reg_ncc", "")
             try:
                 pre_fmt = f"{float(pre):.3f}" if pre not in ("", None) else "-"
-            except (TypeError, ValueError):
+            except TypeError, ValueError:
                 pre_fmt = "-"
             try:
                 post_fmt = f"{float(post):.3f}" if post not in ("", None) else "-"
-            except (TypeError, ValueError):
+            except TypeError, ValueError:
                 post_fmt = "-"
             lines.append(f"  {sid:<6} {status:<8} {method_used:<14} {fb:<28} {pre_fmt:>7} {post_fmt:>7}")
         if len(rows) > 50:
@@ -1806,41 +1811,49 @@ def generate_text_report(
     aggregated = sort_steps(aggregated)
 
     lines = []
-    lines.append("=" * 70)
-    lines.append(title.center(70))
-    lines.append(f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}".center(70))
-    lines.append("=" * 70)
-    lines.append("")
+    lines.extend(
+        ("=" * 70, title.center(70), f"Generated: {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}".center(70), "=" * 70, "")
+    )
 
     _, error_count, warning_count, ok_count = compute_overall_status(aggregated)
 
-    lines.append("SUMMARY")
-    lines.append("-" * 70)
-    lines.append(f"  Pipeline Steps: {len(aggregated)}")
-    lines.append(f"  Total Metrics Files: {sum(len(v) for v in aggregated.values())}")
-    lines.append(
-        f"  Status: {get_status_emoji('ok')} OK: {ok_count}  "
-        f"{get_status_emoji('warning')} Warnings: {warning_count}  "
-        f"{get_status_emoji('error')} Errors: {error_count}"
+    lines.extend(
+        (
+            "SUMMARY",
+            "-" * 70,
+            f"  Pipeline Steps: {len(aggregated)}",
+            f"  Total Metrics Files: {sum(len(v) for v in aggregated.values())}",
+            f"  Status: {get_status_emoji('ok')} OK: {ok_count}  "
+            f"{get_status_emoji('warning')} Warnings: {warning_count}  "
+            f"{get_status_emoji('error')} Errors: {error_count}",
+            "",
+        )
     )
-    lines.append("")
 
     for step_name, metrics_list in aggregated.items():
         summary = compute_summary_statistics(metrics_list)
         step_status = get_step_status(metrics_list)
 
-        lines.append("")
-        lines.append(f"{get_status_emoji(step_status)} {step_name.replace('_', ' ').upper()}")
-        lines.append("-" * 70)
-        lines.append(f"  Items: {summary['count']} | Status: {step_status.upper()}")
+        lines.extend(
+            (
+                "",
+                f"{get_status_emoji(step_status)} {step_name.replace('_', ' ').upper()}",
+                "-" * 70,
+                f"  Items: {summary['count']} | Status: {step_status.upper()}",
+            )
+        )
 
         # Quality metrics stats
         quality_metrics, _ = separate_metrics_by_type(metrics_list)
         if quality_metrics:
-            lines.append("")
-            lines.append("  Quality Metrics:")
-            lines.append(f"  {'Metric':<25} {'Mean':>12} {'Median':>12} {'Std':>12} {'Min':>12} {'Max':>12}")
-            lines.append("  " + "-" * 77)
+            lines.extend(
+                (
+                    "",
+                    "  Quality Metrics:",
+                    f"  {'Metric':<25} {'Mean':>12} {'Median':>12} {'Std':>12} {'Min':>12} {'Max':>12}",
+                    "  " + "-" * 77,
+                )
+            )
             for metric_name, mdata in quality_metrics.items():
                 entries = mdata["entries"]
                 numeric_vals = [e["value"] for e in entries if isinstance(e.get("value"), (int, float))]
@@ -1859,8 +1872,7 @@ def generate_text_report(
         all_warnings, all_errors = collect_issues(metrics_list)
 
         if all_errors:
-            lines.append("")
-            lines.append(f"  {get_status_emoji('error')} ERRORS:")
+            lines.extend(("", f"  {get_status_emoji('error')} ERRORS:"))
             for g in group_issues(all_errors):
                 if g["count"] == 1:
                     lines.append(f"    - {g['details'][0]}")
@@ -1870,8 +1882,7 @@ def generate_text_report(
                     lines.append(f"    - {g['metric']}: {g['count']} slices ({val_str})")
 
         if all_warnings:
-            lines.append("")
-            lines.append(f"  {get_status_emoji('warning')} WARNINGS:")
+            lines.extend(("", f"  {get_status_emoji('warning')} WARNINGS:"))
             for g in group_issues(all_warnings):
                 if g["count"] == 1:
                     lines.append(f"    - {g['details'][0]}")
@@ -1881,8 +1892,7 @@ def generate_text_report(
                     lines.append(f"    - {g['metric']}: {g['count']} slices ({val_str})")
 
         if verbose:
-            lines.append("")
-            lines.append("  Individual Results:")
+            lines.extend(("", "  Individual Results:"))
             for m in metrics_list:
                 source = extract_slice_id(m.get("source_file", "unknown"))
                 m_status = m.get("overall_status", "unknown")
@@ -1896,10 +1906,7 @@ def generate_text_report(
     if interpolation:
         lines.append(_render_interpolation_section_text(interpolation))
 
-    lines.append("")
-    lines.append("=" * 70)
-    lines.append("End of Report".center(70))
-    lines.append("=" * 70)
+    lines.extend(("", "=" * 70, "End of Report".center(70), "=" * 70))
 
     return "\n".join(lines)
 
@@ -1996,8 +2003,8 @@ def main() -> None:
             image_mode=image_mode,
             max_overview_width=args.max_overview_width,
             max_thumb_width=args.max_thumb_width,
-            trends=trends if trends else None,
-            diagnostics=diagnostics if diagnostics else None,
+            trends=trends or None,
+            diagnostics=diagnostics or None,
             interpolation=interpolation,
         )
         if output_format == "zip":
@@ -2005,12 +2012,10 @@ def main() -> None:
                 output_file = output_file.with_suffix(".zip")
             generate_zip_bundle(report, images, output_file)
         else:
-            with Path(output_file).open("w") as f:
-                f.write(report)
+            Path(output_file).write_text(report)
     else:
         report = generate_text_report(aggregated, args.title, args.verbose, interpolation=interpolation)
-        with Path(output_file).open("w") as f:
-            f.write(report)
+        Path(output_file).write_text(report)
 
     print(f"Report saved to: {output_file}")
 
diff --git a/scripts/linum_reorient_nifti_to_ras.py b/scripts/linum_reorient_nifti_to_ras.py
index 782df023..6ff760e5 100644
--- a/scripts/linum_reorient_nifti_to_ras.py
+++ b/scripts/linum_reorient_nifti_to_ras.py
@@ -87,9 +87,7 @@ def main() -> None:
     # Get the resolution of the original volume
     resolutions = img.header["pixdim"][1:4]
     new_resolutions = []
-    new_resolutions.append(resolutions[axis_lr])
-    new_resolutions.append(resolutions[axis_pa])
-    new_resolutions.append(resolutions[axis_is])
+    new_resolutions.extend((resolutions[axis_lr], resolutions[axis_pa], resolutions[axis_is]))
 
     # Save the new volume
     affine = np.eye(4)
diff --git a/scripts/linum_stack_slices_motor.py b/scripts/linum_stack_slices_motor.py
index 709a8633..bf0a14e8 100644
--- a/scripts/linum_stack_slices_motor.py
+++ b/scripts/linum_stack_slices_motor.py
@@ -383,7 +383,7 @@ def load_registration_transforms(
                 status = metrics_data.get("overall_status", "ok")
                 try:
                     confidence = float(metrics_data["metrics"]["registration_confidence"]["value"])
-                except (KeyError, TypeError, ValueError):
+                except KeyError, TypeError, ValueError:
                     confidence = 1.0  # fallback for older JSONs without confidence score
 
                 # Always extract translations and zcorr for accumulation,
@@ -392,11 +392,11 @@ def load_registration_transforms(
                 try:
                     metrics_tx = float(metrics_data["metrics"]["translation_x"]["value"])
                     metrics_ty = float(metrics_data["metrics"]["translation_y"]["value"])
-                except (KeyError, TypeError, ValueError):
+                except KeyError, TypeError, ValueError:
                     metrics_tx, metrics_ty = 0.0, 0.0
                 try:
                     metrics_zcorr = float(metrics_data["metrics"]["z_correlation"]["value"])
-                except (KeyError, TypeError, ValueError):
+                except KeyError, TypeError, ValueError:
                     metrics_zcorr = 0.0
                 all_pairwise_translations[slice_id] = (metrics_tx, metrics_ty, metrics_zcorr)
 
@@ -404,11 +404,11 @@ def load_registration_transforms(
                     # Metric-based gating: accept based on z_correlation and rotation
                     try:
                         zcorr = float(metrics_data["metrics"]["z_correlation"]["value"])
-                    except (KeyError, TypeError, ValueError):
+                    except KeyError, TypeError, ValueError:
                         zcorr = 0.0
                     try:
                         rot_deg = float(metrics_data["metrics"]["rotation"]["value"])
-                    except (KeyError, TypeError, ValueError):
+                    except KeyError, TypeError, ValueError:
                         rot_deg = 999.0
                     if zcorr < load_min_zcorr or abs(rot_deg) > load_max_rotation:
                         logger.warning(
diff --git a/scripts/linum_stitch_3d.py b/scripts/linum_stitch_3d.py
index 61464214..b9c4c449 100644
--- a/scripts/linum_stitch_3d.py
+++ b/scripts/linum_stitch_3d.py
@@ -76,10 +76,10 @@ def main() -> None:
     # Axis-1 of the mosaic is the tile-grid *row* direction (tile_shape[1])
     # and axis-2 is the *column* direction (tile_shape[2]); name the bounds
     # accordingly so the later `pos[0] -= posr_min` reads naturally.
-    posr_min = min([pos[0] for pos in positions])
-    posr_max = max([pos[0] + tile_shape[1] for pos in positions])
-    posc_min = min([pos[1] for pos in positions])
-    posc_max = max([pos[1] + tile_shape[2] for pos in positions])
+    posr_min = min(pos[0] for pos in positions)
+    posr_max = max(pos[0] + tile_shape[1] for pos in positions)
+    posc_min = min(pos[1] for pos in positions)
+    posc_max = max(pos[1] + tile_shape[2] for pos in positions)
     mosaic_shape = [volume.shape[0], int(posr_max - posr_min), int(posc_max - posc_min)]
 
     # Stitch the mosaic
diff --git a/scripts/linum_stitch_3d_refined.py b/scripts/linum_stitch_3d_refined.py
index dfc859f8..1f64dd19 100644
--- a/scripts/linum_stitch_3d_refined.py
+++ b/scripts/linum_stitch_3d_refined.py
@@ -136,22 +136,22 @@ def stitch_with_refinements(
 
                 # From horizontal neighbor to the left
                 if j > 0 and (i, j - 1) in refinements.get("horizontal", {}):
-                    ref = refinements["horizontal"][(i, j - 1)]
+                    ref = refinements["horizontal"][i, j - 1]
                     tile_refinements.append({"dy": -ref["dy"], "dx": -ref["dx"]})
 
                 # From horizontal neighbor to the right
                 if (i, j) in refinements.get("horizontal", {}):
-                    ref = refinements["horizontal"][(i, j)]
+                    ref = refinements["horizontal"][i, j]
                     tile_refinements.append(ref)
 
                 # From vertical neighbor above
                 if i > 0 and (i - 1, j) in refinements.get("vertical", {}):
-                    ref = refinements["vertical"][(i - 1, j)]
+                    ref = refinements["vertical"][i - 1, j]
                     tile_refinements.append({"dy": -ref["dy"], "dx": -ref["dx"]})
 
                 # From vertical neighbor below
                 if (i, j) in refinements.get("vertical", {}):
-                    ref = refinements["vertical"][(i, j)]
+                    ref = refinements["vertical"][i, j]
                     tile_refinements.append(ref)
 
                 tile = apply_blend_shift_refinement(tile, tile_refinements)
@@ -162,13 +162,13 @@ def stitch_with_refinements(
                 tile_refinements = []
 
                 if j > 0 and (i, j - 1) in refinements.get("horizontal", {}):
-                    tile_refinements.append(refinements["horizontal"][(i, j - 1)])
+                    tile_refinements.append(refinements["horizontal"][i, j - 1])
                 if (i, j) in refinements.get("horizontal", {}):
-                    tile_refinements.append(refinements["horizontal"][(i, j)])
+                    tile_refinements.append(refinements["horizontal"][i, j])
                 if i > 0 and (i - 1, j) in refinements.get("vertical", {}):
-                    tile_refinements.append(refinements["vertical"][(i - 1, j)])
+                    tile_refinements.append(refinements["vertical"][i - 1, j])
                 if (i, j) in refinements.get("vertical", {}):
-                    tile_refinements.append(refinements["vertical"][(i, j)])
+                    tile_refinements.append(refinements["vertical"][i, j])
 
                 if tile_refinements:
                     avg_dy = np.mean([r["dy"] for r in tile_refinements]) / 2
diff --git a/scripts/linum_view_omezarr.py b/scripts/linum_view_omezarr.py
index e271989b..9033f4aa 100644
--- a/scripts/linum_view_omezarr.py
+++ b/scripts/linum_view_omezarr.py
@@ -27,9 +27,9 @@ def main() -> None:
     args = p.parse_args()
 
     # read the image data
-    _loc = parse_url(args.input_zarr)
-    assert _loc is not None
-    reader = Reader(_loc)
+    loc = parse_url(args.input_zarr)
+    assert loc is not None
+    reader = Reader(loc)
     # nodes may include images, labels etc
     nodes = list(reader())
 
diff --git a/scripts/tests/test_align_to_ras.py b/scripts/tests/test_align_to_ras.py
index 05626cbd..74df8436 100644
--- a/scripts/tests/test_align_to_ras.py
+++ b/scripts/tests/test_align_to_ras.py
@@ -5,8 +5,6 @@
 functions (no ``zarr`` I/O) without relying on the console entry point.
 """
 
-from __future__ import annotations
-
 import importlib.util
 from pathlib import Path
 
diff --git a/uv.lock b/uv.lock
index 4c96bff3..b996754a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,10 +1,6 @@
 version = 1
 revision = 3
-requires-python = ">=3.12"
-resolution-markers = [
-    "python_full_version >= '3.13'",
-    "python_full_version < '3.13'",
-]
+requires-python = ">=3.14"
 
 [manifest]
 overrides = [
@@ -66,40 +62,6 @@ dependencies = [
 ]
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diff --git a/workflows/preproc/preproc_rawtiles.nf b/workflows/preproc/preproc_rawtiles.nf
index ff400709..a6dbfdbd 100644
--- a/workflows/preproc/preproc_rawtiles.nf
+++ b/workflows/preproc/preproc_rawtiles.nf
@@ -1,6 +1,47 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl = 2
 
+
+workflow {
+    if (params.use_old_folder_structure) {
+        inputSlices = channel.fromPath("${params.input}/tile_x*_y*_z*/", type: 'dir')
+            .map { path -> tuple(path.toString().substring(path.toString().length() - 2), path) }
+            .groupTuple()
+    }
+    else {
+        inputSlices = channel.fromPath("${params.input}/**/tile_x*_y*_z*/", type: 'dir')
+            .map { path -> tuple(path.toString().substring(path.toString().length() - 2), path) }
+            .groupTuple()
+    }
+    input_dir_channel = channel.fromPath("${params.input}", type: 'dir')
+
+    // Generate a 3D mosaic grid at full resolution
+    create_mosaic_grid(inputSlices)
+
+    // [Optional] Generate AIP images from mosaic grids for QC visualization
+    if (params.generate_aips) {
+        generate_aip(create_mosaic_grid.out)
+    }
+
+    // [Optional] Generate orthogonal view previews of mosaic grids.
+    // maxForks 1 on the process keeps screenshots sequential to avoid spawning
+    // 52 concurrent I/O-heavy jobs. Each task depends only on its own zarr
+    // being complete, which Nextflow already guarantees via channel ordering.
+    if (params.generate_previews) {
+        generate_mosaic_preview(create_mosaic_grid.out)
+    }
+
+    // Estimate XY shifts from metadata
+    estimate_xy_shifts_from_metadata(input_dir_channel)
+
+    // Generate slice configuration file (for controlling which slices to use in reconstruction)
+    if (params.generate_slice_config) {
+        // Combine shifts file with input directory for optional galvo detection
+        slice_config_input = estimate_xy_shifts_from_metadata.out.combine(input_dir_channel)
+        generate_slice_config(slice_config_input)
+    }
+}
+
 // Workflow Description
 // Convert raw S-OCT tiles into mosaic grids and xy shifts
 // Input: Directory containing raw data set tiles
@@ -9,23 +50,25 @@ nextflow.enable.dsl = 2
 // Parameters are defined in nextflow.config
 
 process create_mosaic_grid {
-    publishDir "${params.output}", mode: 'link'  // Hard link: no duplication, file stays accessible
-    
+    publishDir "${params.output}", mode: 'link'
+
     input:
-        tuple val(slice_id), path(tiles)
+    tuple val(slice_id), path(tiles)
+
     output:
-        tuple val(slice_id), path("*.ome.zarr")
+    tuple val(slice_id), path("*.ome.zarr")
+
     script:
-    String options = ""
-    options += params.fix_galvo_shift? "--fix_galvo_shift":"--no-fix_galvo_shift"
+    def options: String = ""
+    options += params.fix_galvo_shift ? "--fix_galvo_shift" : "--no-fix_galvo_shift"
     options += " "
-    options += params.fix_camera_shift? "--fix_camera_shift":"--no-fix_camera_shift"
+    options += params.fix_camera_shift ? "--fix_camera_shift" : "--no-fix_camera_shift"
     options += " "
-    options += params.preprocess? "--preprocess":"--no-preprocess"
+    options += params.preprocess ? "--preprocess" : "--no-preprocess"
     // Select GPU or CPU script based on use_gpu parameter
-    String gpu_opts = params.use_gpu ? "--use_gpu --galvo_threshold ${params.galvo_confidence_threshold}" : "--no-use_gpu"
+    def gpu_opts: String = params.use_gpu ? "--use_gpu --galvo_threshold ${params.galvo_confidence_threshold}" : "--no-use_gpu"
     """
-    linum_create_mosaic_grid_3d.py mosaic_grid_3d_z${slice_id}.ome.zarr --from_tiles_list $tiles --resolution ${params.resolution} --n_processes ${params.processes} --axial_resolution ${params.axial_resolution} --sharding_factor ${params.sharding_factor} ${options} ${gpu_opts}
+    linum_create_mosaic_grid_3d.py mosaic_grid_3d_z${slice_id}.ome.zarr --from_tiles_list ${tiles} --resolution ${params.resolution} --n_processes ${params.processes} --axial_resolution ${params.axial_resolution} --sharding_factor ${params.sharding_factor} ${options} ${gpu_opts}
     """
 
     stub:
@@ -38,11 +81,13 @@ process generate_aip {
     publishDir "${params.output}/aips", mode: 'copy'
 
     input:
-        tuple val(slice_id), path(mosaic_grid)
+    tuple val(slice_id), path(mosaic_grid)
+
     output:
-        tuple val(slice_id), path("aip_z${slice_id}.png")
+    tuple val(slice_id), path("aip_z${slice_id}.png")
+
     script:
-    String gpu_opts = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
+    def gpu_opts: String = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
     """
     linum_aip_png.py ${mosaic_grid} aip_z${slice_id}.png ${gpu_opts}
     """
@@ -58,9 +103,11 @@ process generate_mosaic_preview {
     publishDir "${params.output}/previews", mode: 'copy'
 
     input:
-        tuple val(slice_id), path(mosaic_grid)
+    tuple val(slice_id), path(mosaic_grid)
+
     output:
-        path("mosaic_grid_z${slice_id}_preview.png")
+    path "mosaic_grid_z${slice_id}_preview.png"
+
     script:
     """
     linum_screenshot_omezarr.py ${mosaic_grid} mosaic_grid_z${slice_id}_preview.png
@@ -75,10 +122,13 @@ process generate_mosaic_preview {
 process estimate_xy_shifts_from_metadata {
     cpus params.processes
     publishDir "${params.output}", mode: 'copy'
+
     input:
-        path(input_dir)
+    path input_dir
+
     output:
-        path("shifts_xy.csv")
+    path "shifts_xy.csv"
+
     script:
     """
     linum_estimate_xy_shift_from_metadata.py ${input_dir} shifts_xy.csv --n_processes ${params.processes}
@@ -92,16 +142,16 @@ process estimate_xy_shifts_from_metadata {
 
 process generate_slice_config {
     publishDir "${params.output}", mode: 'copy'
-    
+
     input:
-        tuple path(shifts_file), path(input_dir)
-    
+    tuple path(shifts_file), path(input_dir)
+
     output:
-        path("slice_config.csv")
-    
+    path "slice_config.csv"
+
     script:
-    String galvo_opts = params.detect_galvo ? "--detect_galvo --tiles_dir ${input_dir} --galvo_threshold ${params.galvo_confidence_threshold}" : ""
-    String exclude_first_opt = params.exclude_first_slices > 0 ? "--exclude_first ${params.exclude_first_slices}" : "--exclude_first 0"
+    def galvo_opts: String = params.detect_galvo ? "--detect_galvo --tiles_dir ${input_dir} --galvo_threshold ${params.galvo_confidence_threshold}" : ""
+    def exclude_first_opt: String = params.exclude_first_slices > 0 ? "--exclude_first ${params.exclude_first_slices}" : "--exclude_first 0"
     """
     linum_generate_slice_config.py ${shifts_file} slice_config.csv --from_shifts ${exclude_first_opt} ${galvo_opts}
     """
@@ -111,47 +161,3 @@ process generate_slice_config {
     printf 'slice_id,use\n' > slice_config.csv
     """
 }
-
-
-workflow {
-    if (params.use_old_folder_structure)
-    {
-        inputSlices = channel.fromPath("${params.input}/tile_x*_y*_z*/", type: 'dir')
-                            .map{path -> tuple(path.toString().substring(path.toString().length() - 2), path)}
-                            .groupTuple()
-    }
-    else
-    {
-        inputSlices = channel.fromPath("${params.input}/**/tile_x*_y*_z*/", type: 'dir')
-                            .map{path -> tuple(path.toString().substring(path.toString().length() - 2), path)}
-                            .groupTuple()
-    }
-    input_dir_channel = channel.fromPath("${params.input}", type: 'dir')
-
-    // Generate a 3D mosaic grid at full resolution
-    create_mosaic_grid(inputSlices)
-
-    // [Optional] Generate AIP images from mosaic grids for QC visualization
-    if (params.generate_aips) {
-        generate_aip(create_mosaic_grid.out)
-    }
-
-    // [Optional] Generate orthogonal view previews of mosaic grids.
-    // maxForks 1 on the process keeps screenshots sequential to avoid spawning
-    // 52 concurrent I/O-heavy jobs. Each task depends only on its own zarr
-    // being complete, which Nextflow already guarantees via channel ordering.
-    if (params.generate_previews) {
-        generate_mosaic_preview(create_mosaic_grid.out)
-    }
-
-    // Estimate XY shifts from metadata
-    estimate_xy_shifts_from_metadata(input_dir_channel)
-
-    // Generate slice configuration file (for controlling which slices to use in reconstruction)
-    if (params.generate_slice_config) {
-        // Combine shifts file with input directory for optional galvo detection
-        slice_config_input = estimate_xy_shifts_from_metadata.out
-            .combine(input_dir_channel)
-        generate_slice_config(slice_config_input)
-    }
-}
diff --git a/workflows/reconst_2.5d/soct_2.5d_reconst.nf b/workflows/reconst_2.5d/soct_2.5d_reconst.nf
index 6f0086b5..4eedeb16 100644
--- a/workflows/reconst_2.5d/soct_2.5d_reconst.nf
+++ b/workflows/reconst_2.5d/soct_2.5d_reconst.nf
@@ -1,5 +1,5 @@
 #!/usr/bin/env nextflow
-nextflow.enable.dsl=2
+nextflow.enable.dsl = 2
 
 /* S-OCT 2.5D Reconstruction */
 /*
@@ -15,179 +15,198 @@ Notes
 Add the -resume flag to resume the pipeline from the last successfully completed process.
 */
 
-params.directory = "."
-params.input_directory = params.directory + "/mosaicgrids"
-params.xy_shift_file = params.directory + "/shifts_xy.csv"
-params.output_directory = params.directory
+params.directory          = "."
+params.input_directory    = params.directory + "/mosaicgrids"
+params.xy_shift_file      = params.directory + "/shifts_xy.csv"
+params.output_directory   = params.directory
 
 // Tile shape
-params.tile_nx = 400
-params.tile_ny = 400
-params.spacing_xy = 1.875 // micron
-params.spacing_z = 200.0 // micron
+params.tile_nx            = 400
+params.tile_ny            = 400
+params.spacing_xy         = 1.875
+// micron
+params.spacing_z          = 200.0
+// micron
 
 // Tile cropping options
-params.xmin = 10
-params.xmax = 390
-params.ymin = 10
-params.ymax = 390
-params.nx = params.xmax - params.xmin
-params.ny = params.ymax - params.ymin
+params.xmin               = 10
+params.xmax               = 390
+params.ymin               = 10
+params.ymax               = 390
+params.nx                 = params.xmax - params.xmin
+params.ny                 = params.ymax - params.ymin
 
 // Illumination bias estimation options
-params.illum_n_samples = 512
-params.pos_n_samples = 512
-params.basic_working_size=128
+params.illum_n_samples    = 512
+params.pos_n_samples      = 512
+params.basic_working_size = 128
 
 // Position Estimation options
-params.initial_overlap = 0.2
+params.initial_overlap    = 0.2
 
 // Nifti resampled resolution in microns
-params.resolution_nifti = 10.0
+params.resolution_nifti   = 10.0
+
+workflow {
+    // Detect every tile directory
+    slices = channel.fromPath(params.input_directory + "/mosaic_grid_z*.tiff")
+    shifts = channel.fromPath(params.xy_shift_file)
+
+    // Remove compressed stripes caused by the raster scan
+    crop_tiles(slices.flatten())
+
+    // Per-slice illumination bias estimation
+    input_compensation = crop_tiles.out
+    estimate_illumination_bias(input_compensation)
+
+    // Illumination bias compensation
+    compensate_illumination_bias(input_compensation.combine(estimate_illumination_bias.out, by: 0))
+    mosaic_grids_compensated = compensate_illumination_bias.out
+
+    // Estimate the position the tile->position transform
+    estimate_position(mosaic_grids_compensated.map { item -> item[1] }.collect())
+
+    // Apply 2D stitching to all mosaic grids
+    stitch_mosaic(mosaic_grids_compensated.combine(estimate_position.out))
+
+    // Stack the mosaic to get an estimate of the 3D volume
+    stack_mosaic(stitch_mosaic.out.map { item -> item[1] }.collect(), shifts)
+
+    // Compress the stack to zip for transfer
+    compress_stack(stack_mosaic.out)
+
+    // Convert the stack to .ome_zarr format for visualization
+    // FIXME: this process is not working when running with a docker container
+    convert_to_omezarr(stack_mosaic.out)
+
+    // Resample the stack to 10 micron resolution
+    resample_stack(convert_to_omezarr.out)
+}
 
 /* Processes */
 // Crop each tile within the mosaic grid.
 process crop_tiles {
     input:
-        path(mosaic_directory)
+    path mosaic_directory
+
     output:
-        tuple val(mosaic_directory.baseName), path("${mosaic_directory.baseName}_cropped.tiff")
+    tuple val(mosaic_directory.baseName), path("${mosaic_directory.baseName}_cropped.tiff")
+
     script:
     """
-    linum_crop_tiles.py $mosaic_directory ${mosaic_directory.baseName}_cropped.tiff --xmin ${params.xmin} --xmax ${params.xmax} --ymin ${params.ymin} --ymax ${params.ymax} --tile_shape ${params.tile_nx} ${params.tile_ny}
+    linum_crop_tiles.py ${mosaic_directory} ${mosaic_directory.baseName}_cropped.tiff --xmin ${params.xmin} --xmax ${params.xmax} --ymin ${params.ymin} --ymax ${params.ymax} --tile_shape ${params.tile_nx} ${params.tile_ny}
     """
 }
 
 // Estimate the illumination bias affecting each tile, using the BaSIC algorithm.
 process estimate_illumination_bias {
     input:
-        tuple val(key), path(mosaic_grid)
+    tuple val(key), path(mosaic_grid)
+
     output:
-        tuple val(key), path("${key}_flatfield.nii.gz"), path("${key}_darkfield.nii.gz")
+    tuple val(key), path("${key}_flatfield.nii.gz"), path("${key}_darkfield.nii.gz")
+
     script:
     """
-    linum_estimate_illumination.py $mosaic_grid ${key}_flatfield.nii.gz --tile_shape ${params.nx} ${params.ny} --output_darkfield ${key}_darkfield.nii.gz
+    linum_estimate_illumination.py ${mosaic_grid} ${key}_flatfield.nii.gz --tile_shape ${params.nx} ${params.ny} --output_darkfield ${key}_darkfield.nii.gz
     """
 }
 
 // Compensate the illumination bias affecting each tile, using the BaSIC algorithm.
 process compensate_illumination_bias {
     input:
-        tuple val(key), path(mosaic_grid), path(flatfield), path(darkfield)
+    tuple val(key), path(mosaic_grid), path(flatfield), path(darkfield)
+
     output:
-        tuple val(key), path("${key}_mosaic_grid_compensated.nii.gz")
+    tuple val(key), path("${key}_mosaic_grid_compensated.nii.gz")
+
     script:
     """
-    linum_compensate_illumination.py $mosaic_grid ${key}_mosaic_grid_compensated.nii.gz  --flatfield $flatfield --darkfield $darkfield --tile_shape ${params.nx} ${params.ny}
+    linum_compensate_illumination.py ${mosaic_grid} ${key}_mosaic_grid_compensated.nii.gz  --flatfield ${flatfield} --darkfield ${darkfield} --tile_shape ${params.nx} ${params.ny}
     """
 }
 
 // Estimate the tile positions within the mosaic grid.
 process estimate_position {
     input:
-        path mosaic_grids
+    path mosaic_grids
+
     output:
-        path "position_transform.npy"
+    path "position_transform.npy"
+
     script:
     """
-    linum_estimate_transform.py $mosaic_grids position_transform.npy --tile_shape ${params.nx} ${params.ny} --initial_overlap ${params.initial_overlap}
+    linum_estimate_transform.py ${mosaic_grids} position_transform.npy --tile_shape ${params.nx} ${params.ny} --initial_overlap ${params.initial_overlap}
     """
 }
 
 // Stitch each mosaic grid using the estimated tile positions.
 process stitch_mosaic {
     input:
-        tuple val(key), path(image), path(transform)
+    tuple val(key), path(image), path(transform)
+
     output:
-        tuple val(key), path("${key}_stitched.nii.gz")
+    tuple val(key), path("${key}_stitched.nii.gz")
+
     script:
     """
-    linum_stitch_2d.py $image $transform ${key}_stitched.nii.gz --blending_method diffusion --tile_shape ${params.nx} ${params.ny}
+    linum_stitch_2d.py ${image} ${transform} ${key}_stitched.nii.gz --blending_method diffusion --tile_shape ${params.nx} ${params.ny}
     """
 }
 
 // Stack the stitched mosaic grids to get a 2.5D reconstruction, using the input xy_shift between images
 process stack_mosaic {
     input:
-        path(images)
-        path(xy_shifts)
+    path images
+    path xy_shifts
+
     output:
-        path "stack.zarr"
+    path "stack.zarr"
+
     script:
     """
-    linum_stack_slices.py $images stack.zarr --xy_shifts $xy_shifts --resolution_xy ${params.spacing_xy} --resolution_z ${params.spacing_z}
+    linum_stack_slices.py ${images} stack.zarr --xy_shifts ${xy_shifts} --resolution_xy ${params.spacing_xy} --resolution_z ${params.spacing_z}
     """
 }
 
 // Convert the stack to nifti
 process resample_stack {
     input:
-        path stack
+    path stack
+
     output:
-        tuple path("stack_10um.nii.gz")
+    tuple path("stack_10um.nii.gz")
+
     script:
     """
-    linum_convert_omezarr_to_nifti.py $stack stack_10um.nii.gz --resolution ${params.resolution_nifti}
+    linum_convert_omezarr_to_nifti.py ${stack} stack_10um.nii.gz --resolution ${params.resolution_nifti}
     """
 }
 
 // Compress the zarr to zip for transfer
 process compress_stack {
     input:
-        path stack
+    path stack
+
     output:
-        path "stack.zarr.zip"
+    path "stack.zarr.zip"
+
     script:
     """
-    zip -r stack.zarr.zip $stack
+    zip -r stack.zarr.zip ${stack}
     """
 }
 
 // Convert the stack to .zarr format for visualization
 process convert_to_omezarr {
     input:
-        path stack
+    path stack
+
     output:
-        path "stack.ome_zarr"
+    path "stack.ome_zarr"
+
     script:
     """
-    linum_convert_zarr_to_omezarr.py $stack stack.ome_zarr -r ${params.spacing_z} ${params.spacing_xy} ${params.spacing_xy}
+    linum_convert_zarr_to_omezarr.py ${stack} stack.ome_zarr -r ${params.spacing_z} ${params.spacing_xy} ${params.spacing_xy}
     """
 }
-
-workflow{
-    // Detect every tile directory
-    slices = channel.fromPath(params.input_directory + "/mosaic_grid_z*.tiff")
-    shifts = channel.fromPath(params.xy_shift_file)
-
-    // Remove compressed stripes caused by the raster scan
-    crop_tiles(slices.flatten())
-
-    // Per-slice illumination bias estimation
-    input_compensation=crop_tiles.out
-    estimate_illumination_bias(input_compensation)
-
-    // Illumination bias compensation
-    compensate_illumination_bias(input_compensation.combine(estimate_illumination_bias.out, by:0))
-    mosaic_grids_compensated = compensate_illumination_bias.out
-
-    // Estimate the position the tile->position transform
-    estimate_position(mosaic_grids_compensated.map{ item -> item[1] }.collect())
-
-    // Apply 2D stitching to all mosaic grids
-    stitch_mosaic(mosaic_grids_compensated.combine(estimate_position.out))
-
-    // Stack the mosaic to get an estimate of the 3D volume
-    stack_mosaic(stitch_mosaic.out.map{ item -> item[1] }.collect(), shifts)
-
-    // Compress the stack to zip for transfer
-    compress_stack(stack_mosaic.out)
-
-    // Convert the stack to .ome_zarr format for visualization
-    // FIXME: this process is not working when running with a docker container
-    convert_to_omezarr(stack_mosaic.out)
-
-    // Resample the stack to 10 micron resolution
-    resample_stack(convert_to_omezarr.out)
-
-}
\ No newline at end of file
diff --git a/workflows/reconst_3d/diagnostics.nf b/workflows/reconst_3d/diagnostics.nf
index 8390562a..9f59c9b5 100644
--- a/workflows/reconst_3d/diagnostics.nf
+++ b/workflows/reconst_3d/diagnostics.nf
@@ -17,7 +17,7 @@ process analyze_rotation_drift {
     publishDir "${params.output}/diagnostics/rotation_analysis", mode: 'copy'
 
     input:
-    path("register_pairwise/*")
+    path "register_pairwise/*"
 
     output:
     path "rotation_analysis/*"
@@ -92,8 +92,8 @@ process stack_motor_only {
     publishDir "${params.output}/diagnostics/motor_only_stack", mode: 'copy'
 
     input:
-    path("slices/*")
-    path(shifts_file)
+    path "slices/*"
+    path shifts_file
 
     output:
     path "motor_only_stack.ome.zarr"
@@ -112,8 +112,8 @@ process analyze_acquisition_rotation {
     publishDir "${params.output}/diagnostics/acquisition_rotation", mode: 'copy'
 
     input:
-    path(shifts_file)
-    path("register_pairwise/*")
+    path shifts_file
+    path "register_pairwise/*"
 
     output:
     path "acquisition_rotation_analysis/*"
diff --git a/workflows/reconst_3d/soct_3d_reconst.nf b/workflows/reconst_3d/soct_3d_reconst.nf
index a58adb8e..d7b686f8 100644
--- a/workflows/reconst_3d/soct_3d_reconst.nf
+++ b/workflows/reconst_3d/soct_3d_reconst.nf
@@ -23,274 +23,663 @@ nextflow.enable.dsl = 2
 // ./diagnostics.nf and are gated below by `params.diagnostic_mode` and
 // per-stage flags.
 include {
-    analyze_rotation_drift;
-    stitch_motor_only;
-    stitch_refined;
-    compare_stitching;
-    stack_motor_only;
-    analyze_acquisition_rotation;
+    analyze_rotation_drift ;
+    stitch_motor_only ;
+    stitch_refined ;
+    compare_stitching ;
+    stack_motor_only ;
+    analyze_acquisition_rotation
 } from './diagnostics.nf'
 
 // =============================================================================
-// PROCESSES
+// MAIN WORKFLOW
 // =============================================================================
 
-// -----------------------------------------------------------------------------
-// Utility Processes
-// -----------------------------------------------------------------------------
-
-process README {
-    publishDir { "${params.output}/${task.process}" }, mode: 'move'
+workflow {
+    README()
 
-    output:
-    path "readme.txt"
+    def inputDir = Helpers.normalizePath(params.input)
+    def subject_name = Helpers.resolveSubjectName(inputDir, params.subject_name)
+    log.info("Subject: ${subject_name}")
+    log.info("GPU: ${params.use_gpu ? 'ENABLED' : 'DISABLED'}")
 
-    script:
-    """
-    echo "3D reconstruction pipeline" >> readme.txt
-    echo "" >> readme.txt
-    echo "[Params]" >> readme.txt
-    for p in ${params}; do echo " \$p" >> readme.txt; done
-    echo "" >> readme.txt
-    echo "[Command-line]" >> readme.txt
-    echo "${workflow.commandLine}" >> readme.txt
-    echo "" >> readme.txt
-    echo "[Configuration files]" >> readme.txt
-    for c in ${workflow.configFiles}; do echo " \$c" >> readme.txt; done
-    """
+    def debugSlices = Helpers.parseDebugSlices(params.debug_slices)
+    if (debugSlices) {
+        log.info("DEBUG MODE: Processing only slices ${debugSlices.sort().join(', ')}")
+    }
 
-    stub:
-    """
-    touch readme.txt
-    """
-}
+    // Shifts file
+    def shifts_xy_path = params.shifts_xy ?: "${inputDir}/shifts_xy.csv"
+    log.info("Shifts file: ${shifts_xy_path}")
 
-process analyze_shifts {
-    input:
-    path(shifts_file)
+    if (!file(shifts_xy_path).exists()) {
+        error(
+            """
+        Shifts file not found: ${shifts_xy_path}
 
-    output:
-    path "shifts_analysis/*"
+        Please ensure shifts_xy.csv exists in your input directory,
+        or specify the path with --shifts_xy /path/to/shifts_xy.csv
+        """
+        )
+    }
+    // Value channel — fans out to many consumers; see "Authoring Notes" in
+    // docs/NEXTFLOW_WORKFLOWS.md.
+    shifts_xy = channel.value(file(shifts_xy_path))
 
-    script:
-    """
-    linum_analyze_shifts.py ${shifts_file} shifts_analysis \
-        --resolution ${params.resolution} \
-        --iqr_multiplier ${params.outlier_iqr_multiplier}
-    """
+    // Slice config (optional)
+    def slice_config_path = params.slice_config ?: Helpers.joinPath(inputDir, "slice_config.csv")
+    def slicesToUse = null
+    if (file(slice_config_path).exists()) {
+        log.info("Slice config: ${slice_config_path}")
+        def parsed = Helpers.parseSliceConfig(slice_config_path)
+        slicesToUse = parsed.use
+        def total = slicesToUse.size() + parsed.excluded.size()
+        log.info("Slice config: ${total} entries (${slicesToUse.size()} included, ${parsed.excluded.size()} excluded)")
+    }
+    else if (params.slice_config) {
+        error("Slice config file not found: ${slice_config_path}")
+    }
 
-    stub:
-    """
-    mkdir -p shifts_analysis
-    touch shifts_analysis/placeholder.txt
-    """
-}
+    // Discover input mosaic grids
+    log.info("Looking for mosaic grids in: ${inputDir}")
 
-process generate_report {
-    publishDir "${params.output}", mode: 'copy'
+    def inputDirFile = file(inputDir)
+    def mosaicFiles = inputDirFile
+        .listFiles()
+        .findAll { f -> f.isDirectory() && f.name.startsWith('mosaic_grid') && f.name.endsWith('.ome.zarr') && f.name =~ /z\d+/ }
+        .sort { f -> f.name }
 
-    input:
-    tuple path(zarr), path(zip), path(png), path(annotated_png)
-    val subject_name
+    if (mosaicFiles.isEmpty()) {
+        error("No mosaic grids found in ${inputDir}. Expected: mosaic_grid*_z00.ome.zarr")
+    }
 
-    output:
-    path "${subject_name}_quality_report.${params.report_format ?: 'html'}"
+    def selectedIds = mosaicFiles
+        .collect { f -> Helpers.extractSliceId(f) }
+        .findAll { sid ->
+            if (debugSlices != null) {
+                return debugSlices.contains(sid)
+            }
+            if (slicesToUse != null) {
+                return slicesToUse.contains(sid)
+            }
+            return true
+        }
+    def skippedCount = mosaicFiles.size() - selectedIds.size()
+    if (skippedCount > 0) {
+        def reason = debugSlices != null ? "debug_slices filter" : "slice_config"
+        log.info("Found ${mosaicFiles.size()} mosaic grids; ${selectedIds.size()} selected, ${skippedCount} skipped (${reason})")
+    }
+    else {
+        log.info("Found ${mosaicFiles.size()} mosaic grids; all selected")
+    }
 
-    script:
-    def fmt          = params.report_format ?: 'html'
-    def verbose_flag = params.report_verbose ? "--verbose" : ""
-    def overview_arg = png          ? "--overview_png ${png}"          : ""
-    def annotated_arg = annotated_png ? "--annotated_png ${annotated_png}" : ""
-    """
-    linum_generate_pipeline_report.py ${params.output} ${subject_name}_quality_report.${fmt} \
-        --title "Quality Report: ${subject_name}" \
-        --format ${fmt} ${verbose_flag} ${overview_arg} ${annotated_arg}
-    """
+    inputSlices = channel.fromList(mosaicFiles)
+        .map { f -> Helpers.toSliceTuple(f) }
+        .filter { slice_id, _files ->
+            if (debugSlices != null) {
+                def included = debugSlices.contains(slice_id)
+                if (!included) {
+                    log.debug("Skipping slice ${slice_id} (not in debug_slices)")
+                }
+                return included
+            }
+            if (slicesToUse != null) {
+                return slicesToUse.contains(slice_id)
+            }
+            return true
+        }
 
-    stub:
-    """
-    touch ${subject_name}_quality_report.${params.report_format ?: 'html'}
-    """
-}
+    def has_slice_config = file(slice_config_path).exists() || params.auto_assess_quality
+    // Value channel — consumed by auto_assess, common_space, finalise, stack.
+    slice_config_channel = channel.value(
+        file(slice_config_path).exists() ? file(slice_config_path) : file('NO_SLICE_CONFIG')
+    )
 
-// -----------------------------------------------------------------------------
-// Preprocessing Processes
-// -----------------------------------------------------------------------------
+    if (params.analyze_shifts) {
+        analyze_shifts(shifts_xy)
+    }
 
-process resample_mosaic_grid {
-    input:
-    tuple val(slice_id), path(mosaic_grid)
+    // Stage 1: Preprocessing
+    resampled = params.resolution > 0 ? resample_mosaic_grid(inputSlices) : inputSlices
+    focal_fixed = params.fix_curvature_enabled ? fix_focal_curvature(resampled) : resampled
+    illum_fixed = params.fix_illum_enabled ? fix_illumination(focal_fixed) : focal_fixed
 
-    output:
-    tuple val(slice_id), path("mosaic_grid_z${slice_id}_resampled.ome.zarr")
+    // Stage 2: XY Stitching (image-registration-based blend refinement)
+    if (params.stitch_global_transform) {
+        pooled_mosaics = illum_fixed.map { _id, p -> p }.collect()
+        estimate_global_transform(pooled_mosaics, slice_config_channel)
+        stitch_inputs = illum_fixed.combine(estimate_global_transform.out.transform)
+    }
+    else {
+        // Value channel so the placeholder can fan out to every per-slice tuple.
+        no_transform = channel.value(file('NO_TRANSFORM'))
+        stitch_inputs = illum_fixed.combine(no_transform)
+    }
+    stitch_3d_with_refinement(stitch_inputs)
+    stitched_slices = stitch_3d_with_refinement.out.stitched
 
-    script:
-    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
-    def gpu_pin_block = Helpers.gpuPinBlock(params, "resample slice=${slice_id}")
-    """
-    ${gpu_pin_block}
-    linum_resample_mosaic_grid.py ${mosaic_grid} "mosaic_grid_z${slice_id}_resampled.ome.zarr" \
-        -r ${params.resolution} ${gpu_flag} --n_levels 0 -v
-    """
+    if (params.stitch_preview) {
+        generate_stitch_preview(stitched_slices)
+    }
 
-    stub:
-    """
-    mkdir -p mosaic_grid_z${slice_id}_resampled.ome.zarr
-    """
-}
+    // Stage 3: Corrections
+    beam_profile_correction(stitched_slices)
+    crop_interface(beam_profile_correction.out.corrected)
+    normalize(crop_interface.out.cropped)
 
-process fix_focal_curvature {
-    input:
-    tuple val(slice_id), path(mosaic_grid)
+    // Stage 3.5: Auto slice quality assessment (optional). Generates a
+    // slice_config.csv that marks degraded slices; an existing static
+    // slice_config.csv is merged so manually-excluded slices stay excluded.
+    // current_slice_config = the latest slice_config as it flows through the
+    // pipeline; rebound by auto_assess / detect_rehoming when each runs.
+    current_slice_config = slice_config_channel
+    if (params.auto_assess_quality) {
+        auto_assess_inputs = normalize.out.normalized
+            .map { _id, norm_path -> norm_path }
+            .collect()
+        auto_assess_quality(auto_assess_inputs, slice_config_channel)
+        current_slice_config = auto_assess_quality.out.slice_config
+    }
 
-    output:
-    tuple val(slice_id), path("mosaic_grid_z${slice_id}_focal_fix.ome.zarr")
+    // Stage 4: Common Space Alignment.
+    // detect_rehoming optionally corrects encoder-glitch spikes in the
+    // shifts file and (when a real slice_config exists) stamps
+    // rehomed/rehoming_reliable flags back into it.
+    if (params.detect_rehoming) {
+        detect_rehoming_input = shifts_xy.combine(current_slice_config)
+        detect_rehoming_events(detect_rehoming_input)
+        aligned_shifts = detect_rehoming_events.out.corrected_shifts
+        if (has_slice_config) {
+            current_slice_config = detect_rehoming_events.out.slice_config
+        }
+    }
+    else {
+        aligned_shifts = shifts_xy
+    }
 
-    script:
-    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
-    """
-    linum_detect_focal_curvature.py ${mosaic_grid} "mosaic_grid_z${slice_id}_focal_fix.ome.zarr" \\
-        --n_levels 0 ${gpu_flag}
-    """
+    common_space_input = normalize.out.normalized
+        .toSortedList { a, b -> a[0] <=> b[0] }
+        .flatten()
+        .collate(2)
+        .map { _meta, filename -> filename }
+        .collect()
+        .merge(aligned_shifts) { a, b -> tuple(a, b) }
+        .merge(current_slice_config) { a, b -> tuple(a[0], a[1], b) }
 
-    stub:
-    """
-    mkdir -p mosaic_grid_z${slice_id}_focal_fix.ome.zarr
-    """
-}
+    bring_to_common_space(common_space_input)
 
-process fix_illumination {
-    cpus params.processes
+    slices_common_space = bring_to_common_space.out
+        .flatten()
+        .toSortedList { a, b -> a.getName() <=> b.getName() }
 
-    input:
-    tuple val(slice_id), path(mosaic_grid)
+    if (params.common_space_preview) {
+        preview_input = bring_to_common_space.out
+            .flatten()
+            .map { f -> Helpers.toSliceTuple(f) }
+        generate_common_space_preview(preview_input)
+    }
 
-    output:
-    tuple val(slice_id), path("mosaic_grid_z${slice_id}_illum_fix.ome.zarr")
+    // Stage 5: Missing Slice Interpolation (optional).
+    // Single-slice gaps (use=false slices already filtered upstream) are
+    // interpolated with zmorph; per-slice diagnostics are merged into
+    // slice_config_final.csv. See docs/SLICE_INTERPOLATION_FEATURE.md.
+    if (params.interpolate_missing_slices) {
+        gaps_channel = slices_common_space
+            .map { sliceList -> [Helpers.detectSingleGaps(sliceList), sliceList] }
+            .flatMap { gapsAndSlices ->
+                def gaps = gapsAndSlices[0]
+                def sliceList = gapsAndSlices[1]
+                if (gaps.isEmpty()) {
+                    return []
+                }
+
+                gaps
+                    .collect { gap ->
+                        def (missingId, beforeId, afterId) = gap
+                        def sliceBefore = sliceList.find { f -> f.getName().contains("slice_z${beforeId}") }
+                        def sliceAfter = sliceList.find { f -> f.getName().contains("slice_z${afterId}") }
+                        (sliceBefore && sliceAfter) ? tuple(missingId, sliceBefore, sliceAfter) : null
+                    }
+                    .findAll { item -> item != null }
+            }
 
-    script:
-    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
-    """
-    linum_fix_illumination_3d.py ${mosaic_grid} "mosaic_grid_z${slice_id}_illum_fix.ome.zarr" \
-        --n_processes ${params.processes} \
-        --percentile_max ${params.clip_percentile_upper} ${gpu_flag} --n_levels 0
-    """
+        interpolate_missing_slice(gaps_channel)
 
-    stub:
-    """
-    mkdir -p mosaic_grid_z${slice_id}_illum_fix.ome.zarr
-    """
+        // Publish slice_config_final.csv as an artifact for the report.
+        // Intentionally NOT piped back into current_slice_config: when no
+        // gaps exist, interpolate_missing_slice does not run and finalise's
+        // output channel is empty, which would in turn empty out
+        // current_slice_config and silently skip stack. Stack only reads
+        // use/auto_excluded — neither column is modified here — so reading
+        // the upstream config is equivalent.
+        if (has_slice_config) {
+            finalise_interpolation(
+                current_slice_config,
+                interpolate_missing_slice.out.manifest.collect(),
+            )
+        }
+
+        all_slices = slices_common_space
+            .mix(interpolate_missing_slice.out.zarr.collect())
+            .flatten()
+            .toSortedList { a, b -> a.getName() <=> b.getName() }
+    }
+    else {
+        all_slices = slices_common_space
+    }
+
+    // Stage 6: Pairwise Registration
+    log.info("Registering slices pairwise")
+
+    fixed_slices = all_slices
+        .map { list -> list.size() > 1 ? list.subList(0, list.size() - 1) : [] }
+        .flatten()
+    moving_slices = all_slices
+        .map { list -> list.size() > 1 ? list.subList(1, list.size()) : [] }
+        .flatten()
+    pairs = fixed_slices.merge(moving_slices)
+
+    register_pairwise(pairs)
+
+    slices_collected = all_slices.flatten().collect()
+    transforms_collected = register_pairwise.out.collect()
+
+    // Stage 6.5: Export manual-alignment package (optional).
+    if (params.export_manual_align) {
+        export_input = slices_collected
+            .combine(transforms_collected)
+            .map { items -> Helpers.partitionSlicesAndTransforms(items) }
+        make_manual_align_package(export_input)
+    }
+
+    // Stage 6.75: Refine manual transforms (optional). Re-runs pairwise
+    // registration initialised from each manual transform; non-manual pairs
+    // are copied unchanged. Refined outputs replace automated transforms.
+    if (params.refine_manual_transforms && params.manual_transforms_dir) {
+        log.info("Refining manual transforms from: ${params.manual_transforms_dir}")
+        // Re-derive pairs from all_slices (value channel, safe to reuse)
+        refine_fixed = all_slices
+            .map { list -> list.size() > 1 ? list.subList(0, list.size() - 1) : [] }
+            .flatten()
+        refine_moving = all_slices
+            .map { list -> list.size() > 1 ? list.subList(1, list.size()) : [] }
+            .flatten()
+        // Key pairs by moving zarr basename (= transform dir name)
+        refine_pairs_keyed = refine_fixed
+            .merge(refine_moving)
+            .map { fixed, moving -> tuple(moving.getName().replace('.ome.zarr', ''), fixed, moving) }
+        // Key auto transform dirs by dir name
+        auto_transforms_keyed = register_pairwise.out
+            .flatten()
+            .filter { f -> !f.getName().endsWith('.ome.zarr') }
+            .map { dir -> tuple(dir.getName(), dir) }
+        // Join pairs with their corresponding auto transform dir
+        refine_input = refine_pairs_keyed
+            .join(auto_transforms_keyed)
+            .map { _id, fixed, moving, auto_tfm -> tuple(fixed, moving, auto_tfm) }
+        refine_manual_transforms(refine_input)
+        transforms_for_stack = refine_manual_transforms.out.collect()
+    }
+    else {
+        transforms_for_stack = transforms_collected
+    }
+
+    // Stage 7: Stacking
+    log.info("Stacking slices with registration refinements")
+
+    // Auto-exclude: detect clusters of consecutive low-quality registrations.
+    // Stamps auto_excluded/auto_exclude_reason into slice_config so stack
+    // sees them via --slice_config. Requires a real slice_config.
+    stack_slice_config = current_slice_config
+    if (params.auto_exclude_enabled && has_slice_config) {
+        auto_exclude_slices(transforms_for_stack, current_slice_config)
+        stack_slice_config = auto_exclude_slices.out.slice_config
+    }
+
+    // Build stack_input with `merge` (preserves list-vs-file structure of each
+    // input). Earlier versions used `combine`, which flattens lists into a
+    // single tuple and forced fragile filename-based dispatch in `.map`.
+    stack_input = slices_collected
+        .merge(shifts_xy) { s, x -> tuple(s, x) }
+        .merge(transforms_for_stack) { acc, t -> tuple(acc[0], acc[1], t) }
+        .merge(stack_slice_config) { acc, sc -> tuple(acc[0], acc[1], acc[2], sc) }
+        .map { slices, shifts, transforms, sc ->
+            tuple(slices, shifts, transforms, sc, subject_name, Helpers.extractSliceIdsString(slices))
+        }
+
+    stack(stack_input)
+    stack_output = stack.out.volume
+    stack_metadata = stack_input.map { _slices, _shifts, _transforms, _sc, name, ids_str ->
+        tuple(name, ids_str.split(',').size(), ids_str)
+    }
+
+    // Stage 8: Bias Field Correction (optional)
+    if (params.correct_bias_field) {
+        log.info("Running N4 bias field correction (mode=${params.bias_mode})")
+        znorm_input = stack_output
+            .combine(stack_metadata)
+            .map { zarr, _zip, _png, _annotated, name, n, ids_str -> tuple(zarr, name, n, ids_str) }
+        correct_bias_field(znorm_input)
+        final_stack_output = correct_bias_field.out
+    }
+    else {
+        final_stack_output = stack_output
+    }
+
+    // Stage 9: Report Generation (optional)
+    if (params.generate_report) {
+        generate_report(final_stack_output, subject_name)
+    }
+
+    // Stage 10: Atlas Registration (optional)
+    if (params.align_to_ras_enabled) {
+        log.info("Registering to Allen Mouse Brain Atlas (RAS alignment)")
+        align_to_ras(final_stack_output, subject_name)
+    }
+
+    // Stage 11: Diagnostics (optional). Toggle individually or via diagnostic_mode.
+    if (params.diagnostic_mode) {
+        log.info("DIAGNOSTIC MODE enabled (acq rotation, rotation drift, motor-only stitch/stack)")
+    }
+
+    if (Helpers.diagEnabled(params, 'analyze_acquisition_rotation')) {
+        analyze_acquisition_rotation(shifts_xy, register_pairwise.out.collect())
+    }
+
+    if (Helpers.diagEnabled(params, 'analyze_rotation_drift')) {
+        analyze_rotation_drift(register_pairwise.out.collect())
+    }
+
+    if (Helpers.diagEnabled(params, 'motor_only_stack')) {
+        motor_only_stack_input = normalize.out.normalized
+            .map { _id, slice_file -> slice_file }
+            .collect()
+        stack_motor_only(motor_only_stack_input, shifts_xy)
+    }
+
+    // motor_only_stitch is also a prerequisite for compare_stitching, so run it
+    // whenever either is requested. A second `stitch_motor_only(illum_fixed)`
+    // call would emit the same channel twice, which Nextflow forbids.
+    def runMotorStitch = Helpers.diagEnabled(params, 'motor_only_stitch')
+    def runComparison = params.compare_stitching || params.diagnostic_mode
+    if (runMotorStitch || runComparison) {
+        stitch_motor_only(illum_fixed)
+    }
+
+    if (runComparison) {
+        log.info("Running stitching comparison (motor-only vs refined)...")
+
+        stitch_refined(illum_fixed)
+
+        motor_stitch_with_id = stitch_motor_only.out.map { f -> Helpers.toSliceTuple(f) }
+        refined_stitch_with_id = stitch_refined.out[0].map { f -> Helpers.toSliceTuple(f) }
+
+        comparison_input = motor_stitch_with_id.combine(refined_stitch_with_id, by: 0)
+
+        compare_stitching(comparison_input)
+    }
 }
 
+// =============================================================================
+// PROCESSES
+// =============================================================================
+
 // -----------------------------------------------------------------------------
-// Stitching Processes
+// Utility Processes
 // -----------------------------------------------------------------------------
 
-process estimate_global_transform {
-    input:
-    path("pool_input/*")
-    path(slice_config)
+process README {
+    publishDir { "${params.output}/${task.process}" }, mode: 'move'
 
     output:
-    path("global_affine.npy"), emit: transform
-    path("global_affine.json"), optional: true, emit: diagnostics
+    path "readme.txt"
 
     script:
-    def slice_config_arg = slice_config.name != 'NO_SLICE_CONFIG' ? "--slice_config ${slice_config}" : ""
-    def histogram_arg = params.stitch_global_transform_histogram_match ? "--histogram_match" : ""
-    def empty_arg = params.stitch_global_transform_max_empty_fraction != null
-        ? "--max_empty_fraction ${params.stitch_global_transform_max_empty_fraction}"
-        : ""
-    def n_samples_arg = (params.stitch_global_transform_n_samples as int) > 0
-        ? "--n_samples ${params.stitch_global_transform_n_samples as int}"
-        : ""
-    def include_arg = params.stitch_global_transform_slices?.trim()
-        ? "--include_slice " + params.stitch_global_transform_slices.toString().split('[,\\s]+').join(' ')
-        : ""
-    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
     """
-    linum_estimate_global_transform.py pool_input global_affine.npy \
-        --overlap_fraction ${params.stitch_overlap_fraction} \
-        ${slice_config_arg} \
-        ${include_arg} \
-        ${histogram_arg} \
-        ${empty_arg} \
-        ${n_samples_arg} \
-        --seed ${params.stitch_global_transform_seed} \
-        --diagnostics_json global_affine.json \
-        -f ${gpu_flag}
+    echo "3D reconstruction pipeline" >> readme.txt
+    echo "" >> readme.txt
+    echo "[Params]" >> readme.txt
+    for p in ${params}; do echo " \$p" >> readme.txt; done
+    echo "" >> readme.txt
+    echo "[Command-line]" >> readme.txt
+    echo "${workflow.commandLine}" >> readme.txt
+    echo "" >> readme.txt
+    echo "[Configuration files]" >> readme.txt
+    for c in ${workflow.configFiles}; do echo " \$c" >> readme.txt; done
     """
 
     stub:
     """
-    touch global_affine.npy
-    touch global_affine.json
+    touch readme.txt
     """
 }
 
-process stitch_3d_with_refinement {
-    publishDir { "${params.output}/${task.process}" }, mode: 'copy', pattern: "*_metrics.json"
-
+process analyze_shifts {
     input:
-    tuple val(slice_id), path(mosaic_grid), path(input_transform)
+    path shifts_file
 
     output:
-    tuple val(slice_id), path("slice_z${slice_id}_stitch_3d.ome.zarr"), emit: stitched
-    path("*_metrics.json"), optional: true, emit: metrics
+    path "shifts_analysis/*"
 
     script:
-    def transform_arg = input_transform.name != 'NO_TRANSFORM' ? "--input_transform ${input_transform}" : ""
     """
-    linum_stitch_3d_refined.py ${mosaic_grid} "slice_z${slice_id}_stitch_3d.ome.zarr" \
-        --overlap_fraction ${params.stitch_overlap_fraction} \
-        --blending_method ${params.stitch_blending_method} \
-        --refinement_mode blend_shift \
-        --max_refinement_px ${params.max_blend_refinement_px} \
-        ${transform_arg} \
-        --n_levels 0 \
-        -f
+    linum_analyze_shifts.py ${shifts_file} shifts_analysis \
+        --resolution ${params.resolution} \
+        --iqr_multiplier ${params.outlier_iqr_multiplier}
     """
 
     stub:
     """
-    mkdir -p slice_z${slice_id}_stitch_3d.ome.zarr
+    mkdir -p shifts_analysis
+    touch shifts_analysis/placeholder.txt
     """
 }
 
-process generate_stitch_preview {
-    publishDir "${params.output}/previews/stitched_slices", mode: 'copy'
+process generate_report {
+    publishDir "${params.output}", mode: 'copy'
 
     input:
-    tuple val(slice_id), path(stitched_slice)
+    tuple path(zarr), path(zip), path(png), path(annotated_png)
+    val subject_name
 
     output:
-    path "slice_z${slice_id}_stitched.png"
+    path "${subject_name}_quality_report.${params.report_format ?: 'html'}"
 
     script:
+    def fmt = params.report_format ?: 'html'
+    def verbose_flag = params.report_verbose ? "--verbose" : ""
+    def overview_arg = png ? "--overview_png ${png}" : ""
+    def annotated_arg = annotated_png ? "--annotated_png ${annotated_png}" : ""
     """
-    linum_screenshot_omezarr.py ${stitched_slice} "slice_z${slice_id}_stitched.png" \
-        --z_slice 0
+    linum_generate_pipeline_report.py ${params.output} ${subject_name}_quality_report.${fmt} \
+        --title "Quality Report: ${subject_name}" \
+        --format ${fmt} ${verbose_flag} ${overview_arg} ${annotated_arg}
     """
 
     stub:
     """
-    touch slice_z${slice_id}_stitched.png
+    touch ${subject_name}_quality_report.${params.report_format ?: 'html'}
     """
 }
 
 // -----------------------------------------------------------------------------
-// Correction Processes
+// Preprocessing Processes
 // -----------------------------------------------------------------------------
 
-process beam_profile_correction {
-    publishDir { "${params.output}/${task.process}" }, mode: 'copy', pattern: "*_metrics.json"
+process resample_mosaic_grid {
+    input:
+    tuple val(slice_id), path(mosaic_grid)
+
+    output:
+    tuple val(slice_id), path("mosaic_grid_z${slice_id}_resampled.ome.zarr")
+
+    script:
+    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
+    def gpu_pin_block = Helpers.gpuPinBlock(params, "resample slice=${slice_id}")
+    """
+    ${gpu_pin_block}
+    linum_resample_mosaic_grid.py ${mosaic_grid} "mosaic_grid_z${slice_id}_resampled.ome.zarr" \
+        -r ${params.resolution} ${gpu_flag} --n_levels 0 -v
+    """
+
+    stub:
+    """
+    mkdir -p mosaic_grid_z${slice_id}_resampled.ome.zarr
+    """
+}
+
+process fix_focal_curvature {
+    input:
+    tuple val(slice_id), path(mosaic_grid)
+
+    output:
+    tuple val(slice_id), path("mosaic_grid_z${slice_id}_focal_fix.ome.zarr")
+
+    script:
+    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
+    """
+    linum_detect_focal_curvature.py ${mosaic_grid} "mosaic_grid_z${slice_id}_focal_fix.ome.zarr" \\
+        --n_levels 0 ${gpu_flag}
+    """
+
+    stub:
+    """
+    mkdir -p mosaic_grid_z${slice_id}_focal_fix.ome.zarr
+    """
+}
+
+process fix_illumination {
+    cpus params.processes
+
+    input:
+    tuple val(slice_id), path(mosaic_grid)
+
+    output:
+    tuple val(slice_id), path("mosaic_grid_z${slice_id}_illum_fix.ome.zarr")
+
+    script:
+    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
+    """
+    linum_fix_illumination_3d.py ${mosaic_grid} "mosaic_grid_z${slice_id}_illum_fix.ome.zarr" \
+        --n_processes ${params.processes} \
+        --percentile_max ${params.clip_percentile_upper} ${gpu_flag} --n_levels 0
+    """
+
+    stub:
+    """
+    mkdir -p mosaic_grid_z${slice_id}_illum_fix.ome.zarr
+    """
+}
+
+// -----------------------------------------------------------------------------
+// Stitching Processes
+// -----------------------------------------------------------------------------
+
+process estimate_global_transform {
+    input:
+    path "pool_input/*"
+    path slice_config
+
+    output:
+    path ("global_affine.npy"), emit: transform
+    path ("global_affine.json"), optional: true, emit: diagnostics
+
+    script:
+    def slice_config_arg = slice_config.name != 'NO_SLICE_CONFIG' ? "--slice_config ${slice_config}" : ""
+    def histogram_arg = params.stitch_global_transform_histogram_match ? "--histogram_match" : ""
+    def empty_arg = params.stitch_global_transform_max_empty_fraction != null
+        ? "--max_empty_fraction ${params.stitch_global_transform_max_empty_fraction}"
+        : ""
+    def n_samples_arg = (params.stitch_global_transform_n_samples as int) > 0
+        ? "--n_samples ${params.stitch_global_transform_n_samples as int}"
+        : ""
+    def include_arg = params.stitch_global_transform_slices?.trim()
+        ? "--include_slice " + params.stitch_global_transform_slices.toString().split('[,\\s]+').join(' ')
+        : ""
+    def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
+    """
+    linum_estimate_global_transform.py pool_input global_affine.npy \
+        --overlap_fraction ${params.stitch_overlap_fraction} \
+        ${slice_config_arg} \
+        ${include_arg} \
+        ${histogram_arg} \
+        ${empty_arg} \
+        ${n_samples_arg} \
+        --seed ${params.stitch_global_transform_seed} \
+        --diagnostics_json global_affine.json \
+        -f ${gpu_flag}
+    """
+
+    stub:
+    """
+    touch global_affine.npy
+    touch global_affine.json
+    """
+}
+
+process stitch_3d_with_refinement {
+    publishDir { "${params.output}/${task.process}" }, mode: 'copy', pattern: "*_metrics.json"
+
+    input:
+    tuple val(slice_id), path(mosaic_grid), path(input_transform)
+
+    output:
+    tuple val(slice_id), path("slice_z${slice_id}_stitch_3d.ome.zarr"), emit: stitched
+    path ("*_metrics.json"), optional: true, emit: metrics
+
+    script:
+    def transform_arg = input_transform.name != 'NO_TRANSFORM' ? "--input_transform ${input_transform}" : ""
+    """
+    linum_stitch_3d_refined.py ${mosaic_grid} "slice_z${slice_id}_stitch_3d.ome.zarr" \
+        --overlap_fraction ${params.stitch_overlap_fraction} \
+        --blending_method ${params.stitch_blending_method} \
+        --refinement_mode blend_shift \
+        --max_refinement_px ${params.max_blend_refinement_px} \
+        ${transform_arg} \
+        --n_levels 0 \
+        -f
+    """
+
+    stub:
+    """
+    mkdir -p slice_z${slice_id}_stitch_3d.ome.zarr
+    """
+}
+
+process generate_stitch_preview {
+    publishDir "${params.output}/previews/stitched_slices", mode: 'copy'
+
+    input:
+    tuple val(slice_id), path(stitched_slice)
+
+    output:
+    path "slice_z${slice_id}_stitched.png"
+
+    script:
+    """
+    linum_screenshot_omezarr.py ${stitched_slice} "slice_z${slice_id}_stitched.png" \
+        --z_slice 0
+    """
+
+    stub:
+    """
+    touch slice_z${slice_id}_stitched.png
+    """
+}
+
+// -----------------------------------------------------------------------------
+// Correction Processes
+// -----------------------------------------------------------------------------
+
+process beam_profile_correction {
+    publishDir { "${params.output}/${task.process}" }, mode: 'copy', pattern: "*_metrics.json"
 
     input:
     tuple val(slice_id), path(slice_3d)
 
     output:
     tuple val(slice_id), path("slice_z${slice_id}_axial_corr.ome.zarr"), emit: corrected
-    path("*_metrics.json"), optional: true, emit: metrics
+    path ("*_metrics.json"), optional: true, emit: metrics
 
     script:
     """
@@ -312,7 +701,7 @@ process crop_interface {
 
     output:
     tuple val(slice_id), path("slice_z${slice_id}_crop_interface.ome.zarr"), emit: cropped
-    path("*_metrics.json"), optional: true, emit: metrics
+    path ("*_metrics.json"), optional: true, emit: metrics
 
     script:
     """
@@ -336,7 +725,7 @@ process normalize {
 
     output:
     tuple val(slice_id), path("slice_z${slice_id}_normalize.ome.zarr"), emit: normalized
-    path("*_metrics.json"), optional: true, emit: metrics
+    path ("*_metrics.json"), optional: true, emit: metrics
 
     script:
     def gpu_flag = params.use_gpu ? "--use_gpu" : "--no-use_gpu"
@@ -360,9 +749,9 @@ process detect_rehoming_events {
     tuple path(shifts_csv), path(slice_config_in)
 
     output:
-    path "shifts_xy_clean.csv",           emit: corrected_shifts
-    path "slice_config.csv",              optional: true, emit: slice_config
-    path "diagnostics/*",                 optional: true, emit: diagnostics
+    path "shifts_xy_clean.csv", emit: corrected_shifts
+    path "slice_config.csv", optional: true, emit: slice_config
+    path "diagnostics/*", optional: true, emit: diagnostics
 
     script:
     def diag_arg = params.rehoming_diagnostics ? "--diagnostics diagnostics" : ""
@@ -426,14 +815,17 @@ process bring_to_common_space {
     script:
     def slice_config_arg = slice_config.name != 'NO_SLICE_CONFIG' ? "--slice_config ${slice_config}" : ""
 
-    def excluded_args = params.common_space_excluded_slice_mode ?
-        "--excluded_slice_mode ${params.common_space_excluded_slice_mode} --excluded_slice_window ${params.common_space_excluded_slice_window}" : ""
+    def excluded_args = params.common_space_excluded_slice_mode
+        ? "--excluded_slice_mode ${params.common_space_excluded_slice_mode} --excluded_slice_window ${params.common_space_excluded_slice_window}"
+        : ""
 
     def refine_arg = params.common_space_refine_unreliable ? "--refine_unreliable" : ""
-    def discrepancy_arg = (params.common_space_refine_unreliable && params.common_space_refine_max_discrepancy_px > 0) ?
-        "--refine_max_discrepancy_px ${params.common_space_refine_max_discrepancy_px}" : ""
-    def min_corr_arg = (params.common_space_refine_unreliable && params.common_space_refine_min_correlation > 0) ?
-        "--refine_min_correlation ${params.common_space_refine_min_correlation}" : ""
+    def discrepancy_arg = (params.common_space_refine_unreliable && params.common_space_refine_max_discrepancy_px > 0)
+        ? "--refine_max_discrepancy_px ${params.common_space_refine_max_discrepancy_px}"
+        : ""
+    def min_corr_arg = (params.common_space_refine_unreliable && params.common_space_refine_min_correlation > 0)
+        ? "--refine_min_correlation ${params.common_space_refine_min_correlation}"
+        : ""
 
     """
     linum_align_mosaics_3d_from_shifts.py inputs shifts_xy.csv common_space \
@@ -639,14 +1031,15 @@ process make_manual_align_package {
     tuple path("slices/*"), path("transforms/*")
 
     output:
-    path("manual_align_package"), emit: pkg
+    path ("manual_align_package"), emit: pkg
 
     script:
     // When interpolation is enabled, interpolated slices live in a separate
     // publish dir (interpolate_missing_slice/) rather than bring_to_common_space/.
     // Pass that directory so the plugin's SSH reader can locate them.
-    def interp_dir_opt = params.interpolate_missing_slices ?
-        "--interpolated_slices_remote_dir ${params.output}/interpolate_missing_slice" : ""
+    def interp_dir_opt = params.interpolate_missing_slices
+        ? "--interpolated_slices_remote_dir ${params.output}/interpolate_missing_slice"
+        : ""
     """
     linum_export_manual_align.py slices transforms manual_align_package \
         --level ${params.manual_align_level} \
@@ -666,31 +1059,20 @@ process make_manual_align_package {
 // publishDir mode is conditional: 'symlink' when a downstream step will produce
 // the final output (preserves work-dir files for -resume); 'move' when this is last.
 process stack {
-    publishDir { "${params.output}/${task.process}" },
-        mode: (params.correct_bias_field || params.align_to_ras_enabled) ? 'symlink' : 'move',
-        saveAs: { fn -> fn.endsWith('.ome.zarr') ? null : fn }
+    publishDir { "${params.output}/${task.process}" }, mode: (params.correct_bias_field || params.align_to_ras_enabled) ? 'symlink' : 'move', saveAs: { fn -> fn.endsWith('.ome.zarr') ? null : fn }
 
     input:
     tuple path("slices/*"), path(shifts_file), path("transforms/*"), path(slice_config), val(subject_name), val(slice_ids_str)
 
     output:
     tuple path("${subject_name}.ome.zarr"), path("${subject_name}.ome.zarr.zip"), path("${subject_name}.png"), path("${subject_name}_annotated.png"), emit: volume
-    path("*_metrics.json"), optional: true, emit: metrics
-    path("z_matches.csv"), optional: true, emit: z_matches
-    path("stacking_decisions.csv"), optional: true, emit: stacking_decisions
+    path ("*_metrics.json"), optional: true, emit: metrics
+    path ("z_matches.csv"), optional: true, emit: z_matches
+    path ("stacking_decisions.csv"), optional: true, emit: stacking_decisions
 
     script:
     def gpu_flag = params.use_gpu ? " --use_gpu" : " --no-use_gpu"
-    def options = Helpers.stackBlendingArgs(params) +
-                  Helpers.stackZMatchingArgs(params) +
-                  Helpers.stackPairwiseTransformArgs(params) +
-                  Helpers.stackSliceConfigArg(slice_config) +
-                  Helpers.stackManualOverrideArg(params) +
-                  Helpers.stackCumulativeArgs(params) +
-                  Helpers.stackSmoothingArgs(params) +
-                  " --no_xy_shift" +  // slices are already in common space
-                  gpu_flag +
-                  Helpers.pyramidArgs(params)
+    def options = Helpers.stackBlendingArgs(params) + Helpers.stackZMatchingArgs(params) + Helpers.stackPairwiseTransformArgs(params) + Helpers.stackSliceConfigArg(slice_config) + Helpers.stackManualOverrideArg(params) + Helpers.stackCumulativeArgs(params) + Helpers.stackSmoothingArgs(params) + " --no_xy_shift" + gpu_flag + Helpers.pyramidArgs(params)
 
     def annotated_args = Helpers.annotatedScreenshotArgs(params, slice_ids_str)
     """
@@ -714,9 +1096,7 @@ process stack {
 process correct_bias_field {
     cpus params.processes
 
-    publishDir { "${params.output}/${task.process}" },
-        mode: params.align_to_ras_enabled ? 'symlink' : 'move',
-        saveAs: { fn -> fn.endsWith('.ome.zarr') ? null : fn }
+    publishDir { "${params.output}/${task.process}" }, mode: params.align_to_ras_enabled ? 'symlink' : 'move', saveAs: { fn -> fn.endsWith('.ome.zarr') ? null : fn }
 
     input:
     tuple path(stacked_zarr), val(subject_name), val(n_slices), val(slice_ids_str)
@@ -799,370 +1179,3 @@ process align_to_ras {
     touch ${subject_name}_ras.ome.zarr.zip
     """
 }
-
-// =============================================================================
-// MAIN WORKFLOW
-// =============================================================================
-
-workflow {
-    README()
-
-    def inputDir = Helpers.normalizePath(params.input)
-    def subject_name = Helpers.resolveSubjectName(inputDir, params.subject_name)
-    log.info "Subject: ${subject_name}"
-    log.info "GPU: ${params.use_gpu ? 'ENABLED' : 'DISABLED'}"
-
-    def debugSlices = Helpers.parseDebugSlices(params.debug_slices)
-    if (debugSlices) {
-        log.info "DEBUG MODE: Processing only slices ${debugSlices.sort().join(', ')}"
-    }
-
-    // Shifts file
-    def shifts_xy_path = params.shifts_xy ?: "${inputDir}/shifts_xy.csv"
-    log.info "Shifts file: ${shifts_xy_path}"
-
-    if (!file(shifts_xy_path).exists()) {
-        error """
-        Shifts file not found: ${shifts_xy_path}
-
-        Please ensure shifts_xy.csv exists in your input directory,
-        or specify the path with --shifts_xy /path/to/shifts_xy.csv
-        """
-    }
-    // Value channel — fans out to many consumers; see "Authoring Notes" in
-    // docs/NEXTFLOW_WORKFLOWS.md.
-    shifts_xy = channel.value(file(shifts_xy_path))
-
-    // Slice config (optional)
-    def slice_config_path = params.slice_config ?: Helpers.joinPath(inputDir, "slice_config.csv")
-    def slicesToUse = null
-    if (file(slice_config_path).exists()) {
-        log.info "Slice config: ${slice_config_path}"
-        def parsed = Helpers.parseSliceConfig(slice_config_path)
-        slicesToUse = parsed.use
-        def total = slicesToUse.size() + parsed.excluded.size()
-        log.info "Slice config: ${total} entries (${slicesToUse.size()} included, ${parsed.excluded.size()} excluded)"
-    } else if (params.slice_config) {
-        error("Slice config file not found: ${slice_config_path}")
-    }
-
-    // Discover input mosaic grids
-    log.info "Looking for mosaic grids in: ${inputDir}"
-
-    def inputDirFile = file(inputDir)
-    def mosaicFiles = inputDirFile.listFiles()
-        .findAll { f -> f.isDirectory() && f.name.startsWith('mosaic_grid') && f.name.endsWith('.ome.zarr') && f.name =~ /z\d+/ }
-        .sort { f -> f.name }
-
-    if (mosaicFiles.isEmpty()) {
-        error("No mosaic grids found in ${inputDir}. Expected: mosaic_grid*_z00.ome.zarr")
-    }
-
-    def selectedIds = mosaicFiles.collect { f -> Helpers.extractSliceId(f) }.findAll { sid ->
-        if (debugSlices != null) return debugSlices.contains(sid)
-        if (slicesToUse != null) return slicesToUse.contains(sid)
-        return true
-    }
-    def skippedCount = mosaicFiles.size() - selectedIds.size()
-    if (skippedCount > 0) {
-        def reason = debugSlices != null ? "debug_slices filter" : "slice_config"
-        log.info "Found ${mosaicFiles.size()} mosaic grids; ${selectedIds.size()} selected, ${skippedCount} skipped (${reason})"
-    } else {
-        log.info "Found ${mosaicFiles.size()} mosaic grids; all selected"
-    }
-
-    inputSlices = channel
-        .fromList(mosaicFiles)
-        .map { f -> Helpers.toSliceTuple(f) }
-        .filter { slice_id, _files ->
-            if (debugSlices != null) {
-                def included = debugSlices.contains(slice_id)
-                if (!included) log.debug "Skipping slice ${slice_id} (not in debug_slices)"
-                return included
-            }
-            if (slicesToUse != null) return slicesToUse.contains(slice_id)
-            return true
-        }
-
-    def has_slice_config = file(slice_config_path).exists() || params.auto_assess_quality
-    // Value channel — consumed by auto_assess, common_space, finalise, stack.
-    slice_config_channel = channel.value(
-        file(slice_config_path).exists() ? file(slice_config_path) : file('NO_SLICE_CONFIG')
-    )
-
-    if (params.analyze_shifts) {
-        analyze_shifts(shifts_xy)
-    }
-
-    // Stage 1: Preprocessing
-    resampled = params.resolution > 0 ? resample_mosaic_grid(inputSlices) : inputSlices
-    focal_fixed = params.fix_curvature_enabled ? fix_focal_curvature(resampled) : resampled
-    illum_fixed = params.fix_illum_enabled ? fix_illumination(focal_fixed) : focal_fixed
-
-    // Stage 2: XY Stitching (image-registration-based blend refinement)
-    if (params.stitch_global_transform) {
-        pooled_mosaics = illum_fixed.map { _id, p -> p }.collect()
-        estimate_global_transform(pooled_mosaics, slice_config_channel)
-        stitch_inputs = illum_fixed.combine(estimate_global_transform.out.transform)
-    } else {
-        // Value channel so the placeholder can fan out to every per-slice tuple.
-        no_transform = channel.value(file('NO_TRANSFORM'))
-        stitch_inputs = illum_fixed.combine(no_transform)
-    }
-    stitch_3d_with_refinement(stitch_inputs)
-    stitched_slices = stitch_3d_with_refinement.out.stitched
-
-    if (params.stitch_preview) {
-        generate_stitch_preview(stitched_slices)
-    }
-
-    // Stage 3: Corrections
-    beam_profile_correction(stitched_slices)
-    crop_interface(beam_profile_correction.out.corrected)
-    normalize(crop_interface.out.cropped)
-
-    // Stage 3.5: Auto slice quality assessment (optional). Generates a
-    // slice_config.csv that marks degraded slices; an existing static
-    // slice_config.csv is merged so manually-excluded slices stay excluded.
-    // current_slice_config = the latest slice_config as it flows through the
-    // pipeline; rebound by auto_assess / detect_rehoming when each runs.
-    current_slice_config = slice_config_channel
-    if (params.auto_assess_quality) {
-        auto_assess_inputs = normalize.out.normalized
-            .map { _id, norm_path -> norm_path }
-            .collect()
-        auto_assess_quality(auto_assess_inputs, slice_config_channel)
-        current_slice_config = auto_assess_quality.out.slice_config
-    }
-
-    // Stage 4: Common Space Alignment.
-    // detect_rehoming optionally corrects encoder-glitch spikes in the
-    // shifts file and (when a real slice_config exists) stamps
-    // rehomed/rehoming_reliable flags back into it.
-    if (params.detect_rehoming) {
-        detect_rehoming_input = shifts_xy.combine(current_slice_config)
-        detect_rehoming_events(detect_rehoming_input)
-        aligned_shifts = detect_rehoming_events.out.corrected_shifts
-        if (has_slice_config) {
-            current_slice_config = detect_rehoming_events.out.slice_config
-        }
-    } else {
-        aligned_shifts = shifts_xy
-    }
-
-    common_space_input = normalize.out.normalized
-        .toSortedList { a, b -> a[0] <=> b[0] }
-        .flatten()
-        .collate(2)
-        .map { _meta, filename -> filename }
-        .collect()
-        .merge(aligned_shifts) { a, b -> tuple(a, b) }
-        .merge(current_slice_config) { a, b -> tuple(a[0], a[1], b) }
-
-    bring_to_common_space(common_space_input)
-
-    slices_common_space = bring_to_common_space.out
-        .flatten()
-        .toSortedList { a, b -> a.getName() <=> b.getName() }
-
-    if (params.common_space_preview) {
-        preview_input = bring_to_common_space.out
-            .flatten()
-            .map { f -> Helpers.toSliceTuple(f) }
-        generate_common_space_preview(preview_input)
-    }
-
-    // Stage 5: Missing Slice Interpolation (optional).
-    // Single-slice gaps (use=false slices already filtered upstream) are
-    // interpolated with zmorph; per-slice diagnostics are merged into
-    // slice_config_final.csv. See docs/SLICE_INTERPOLATION_FEATURE.md.
-    if (params.interpolate_missing_slices) {
-        gaps_channel = slices_common_space
-            .map { sliceList -> [Helpers.detectSingleGaps(sliceList), sliceList] }
-            .flatMap { gapsAndSlices ->
-                def gaps = gapsAndSlices[0]
-                def sliceList = gapsAndSlices[1]
-                if (gaps.isEmpty()) return []
-
-                gaps.collect { gap ->
-                    def (missingId, beforeId, afterId) = gap
-                    def sliceBefore = sliceList.find { f -> f.getName().contains("slice_z${beforeId}") }
-                    def sliceAfter = sliceList.find { f -> f.getName().contains("slice_z${afterId}") }
-                    (sliceBefore && sliceAfter) ? tuple(missingId, sliceBefore, sliceAfter) : null
-                }.findAll { item -> item != null }
-            }
-
-        interpolate_missing_slice(gaps_channel)
-
-        // Publish slice_config_final.csv as an artifact for the report.
-        // Intentionally NOT piped back into current_slice_config: when no
-        // gaps exist, interpolate_missing_slice does not run and finalise's
-        // output channel is empty, which would in turn empty out
-        // current_slice_config and silently skip stack. Stack only reads
-        // use/auto_excluded — neither column is modified here — so reading
-        // the upstream config is equivalent.
-        if (has_slice_config) {
-            finalise_interpolation(
-                current_slice_config,
-                interpolate_missing_slice.out.manifest.collect(),
-            )
-        }
-
-        all_slices = slices_common_space
-            .mix(interpolate_missing_slice.out.zarr.collect())
-            .flatten()
-            .toSortedList { a, b -> a.getName() <=> b.getName() }
-    } else {
-        all_slices = slices_common_space
-    }
-
-    // Stage 6: Pairwise Registration
-    log.info "Registering slices pairwise"
-
-    fixed_slices = all_slices
-        .map { list -> list.size() > 1 ? list.subList(0, list.size() - 1) : [] }
-        .flatten()
-    moving_slices = all_slices
-        .map { list -> list.size() > 1 ? list.subList(1, list.size()) : [] }
-        .flatten()
-    pairs = fixed_slices.merge(moving_slices)
-
-    register_pairwise(pairs)
-
-    slices_collected = all_slices.flatten().collect()
-    transforms_collected = register_pairwise.out.collect()
-
-    // Stage 6.5: Export manual-alignment package (optional).
-    if (params.export_manual_align) {
-        export_input = slices_collected
-            .combine(transforms_collected)
-            .map { items -> Helpers.partitionSlicesAndTransforms(items) }
-        make_manual_align_package(export_input)
-    }
-
-    // Stage 6.75: Refine manual transforms (optional). Re-runs pairwise
-    // registration initialised from each manual transform; non-manual pairs
-    // are copied unchanged. Refined outputs replace automated transforms.
-    if (params.refine_manual_transforms && params.manual_transforms_dir) {
-        log.info "Refining manual transforms from: ${params.manual_transforms_dir}"
-        // Re-derive pairs from all_slices (value channel, safe to reuse)
-        refine_fixed = all_slices
-            .map { list -> list.size() > 1 ? list.subList(0, list.size() - 1) : [] }
-            .flatten()
-        refine_moving = all_slices
-            .map { list -> list.size() > 1 ? list.subList(1, list.size()) : [] }
-            .flatten()
-        // Key pairs by moving zarr basename (= transform dir name)
-        refine_pairs_keyed = refine_fixed
-            .merge(refine_moving)
-            .map { fixed, moving -> tuple(moving.getName().replace('.ome.zarr', ''), fixed, moving) }
-        // Key auto transform dirs by dir name
-        auto_transforms_keyed = register_pairwise.out
-            .flatten()
-            .filter { f -> !f.getName().endsWith('.ome.zarr') }
-            .map { dir -> tuple(dir.getName(), dir) }
-        // Join pairs with their corresponding auto transform dir
-        refine_input = refine_pairs_keyed
-            .join(auto_transforms_keyed)
-            .map { _id, fixed, moving, auto_tfm -> tuple(fixed, moving, auto_tfm) }
-        refine_manual_transforms(refine_input)
-        transforms_for_stack = refine_manual_transforms.out.collect()
-    } else {
-        transforms_for_stack = transforms_collected
-    }
-
-    // Stage 7: Stacking
-    log.info "Stacking slices with registration refinements"
-
-    // Auto-exclude: detect clusters of consecutive low-quality registrations.
-    // Stamps auto_excluded/auto_exclude_reason into slice_config so stack
-    // sees them via --slice_config. Requires a real slice_config.
-    stack_slice_config = current_slice_config
-    if (params.auto_exclude_enabled && has_slice_config) {
-        auto_exclude_slices(transforms_for_stack, current_slice_config)
-        stack_slice_config = auto_exclude_slices.out.slice_config
-    }
-
-    // Build stack_input with `merge` (preserves list-vs-file structure of each
-    // input). Earlier versions used `combine`, which flattens lists into a
-    // single tuple and forced fragile filename-based dispatch in `.map`.
-    stack_input = slices_collected
-        .merge(shifts_xy) { s, x -> tuple(s, x) }
-        .merge(transforms_for_stack) { acc, t -> tuple(acc[0], acc[1], t) }
-        .merge(stack_slice_config) { acc, sc -> tuple(acc[0], acc[1], acc[2], sc) }
-        .map { slices, shifts, transforms, sc ->
-            tuple(slices, shifts, transforms, sc, subject_name, Helpers.extractSliceIdsString(slices))
-        }
-
-    stack(stack_input)
-    stack_output = stack.out.volume
-    stack_metadata = stack_input.map { _slices, _shifts, _transforms, _sc, name, ids_str ->
-        tuple(name, ids_str.split(',').size(), ids_str)
-    }
-
-    // Stage 8: Bias Field Correction (optional)
-    if (params.correct_bias_field) {
-        log.info "Running N4 bias field correction (mode=${params.bias_mode})"
-        znorm_input = stack_output
-            .combine(stack_metadata)
-            .map { zarr, _zip, _png, _annotated, name, n, ids_str -> tuple(zarr, name, n, ids_str) }
-        correct_bias_field(znorm_input)
-        final_stack_output = correct_bias_field.out
-    } else {
-        final_stack_output = stack_output
-    }
-
-    // Stage 9: Report Generation (optional)
-    if (params.generate_report) {
-        generate_report(final_stack_output, subject_name)
-    }
-
-    // Stage 10: Atlas Registration (optional)
-    if (params.align_to_ras_enabled) {
-        log.info "Registering to Allen Mouse Brain Atlas (RAS alignment)"
-        align_to_ras(final_stack_output, subject_name)
-    }
-
-    // Stage 11: Diagnostics (optional). Toggle individually or via diagnostic_mode.
-    if (params.diagnostic_mode) {
-        log.info "DIAGNOSTIC MODE enabled (acq rotation, rotation drift, motor-only stitch/stack)"
-    }
-
-    if (Helpers.diagEnabled(params, 'analyze_acquisition_rotation')) {
-        analyze_acquisition_rotation(shifts_xy, register_pairwise.out.collect())
-    }
-
-    if (Helpers.diagEnabled(params, 'analyze_rotation_drift')) {
-        analyze_rotation_drift(register_pairwise.out.collect())
-    }
-
-    if (Helpers.diagEnabled(params, 'motor_only_stack')) {
-        motor_only_stack_input = normalize.out.normalized
-            .map { _id, slice_file -> slice_file }
-            .collect()
-        stack_motor_only(motor_only_stack_input, shifts_xy)
-    }
-
-    // motor_only_stitch is also a prerequisite for compare_stitching, so run it
-    // whenever either is requested. A second `stitch_motor_only(illum_fixed)`
-    // call would emit the same channel twice, which Nextflow forbids.
-    def runMotorStitch = Helpers.diagEnabled(params, 'motor_only_stitch')
-    def runComparison = params.compare_stitching || params.diagnostic_mode
-    if (runMotorStitch || runComparison) {
-        stitch_motor_only(illum_fixed)
-    }
-
-    if (runComparison) {
-        log.info "Running stitching comparison (motor-only vs refined)..."
-
-        stitch_refined(illum_fixed)
-
-        motor_stitch_with_id = stitch_motor_only.out.map { f -> Helpers.toSliceTuple(f) }
-        refined_stitch_with_id = stitch_refined.out[0].map { f -> Helpers.toSliceTuple(f) }
-
-        comparison_input = motor_stitch_with_id
-            .combine(refined_stitch_with_id, by: 0)
-
-        compare_stitching(comparison_input)
-    }
-}