zarrsmith 0.6.0__tar.gz

zarrsmith-0.6.0/.github/scripts/next_version.py

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+"""Compute the next zarrsmith release version for a merged pull request.
+
+Usage: python next_version.py <pr.json>
+
+``pr.json`` is the output of ``gh pr view <n> --json labels``. Existing tags are
+read from the local git repository. Prints the next version (``X.Y.Z``,
+without the leading ``v``), or nothing when the PR should not be released.
+
+Releases are opt-in: a PR is released only if it carries one of the labels
+``release:major``, ``release:minor`` or ``release:patch``. Without such a label
+nothing is tagged. If several are present the largest bump wins.
+"""
+
+from __future__ import annotations
+
+import json
+import re
+import subprocess
+import sys
+
+# Tags with a major at or above this are legacy calendar versions and are ignored.
+CALVER_MAJOR = 2000
+
+TAG_RE = re.compile(r"^v(\d+)\.(\d+)\.(\d+)$")
+KINDS = ("major", "minor", "patch")  # ordered by priority
+
+
+def latest_version(tags: list[str]) -> tuple[int, int, int] | None:
+    versions = []
+    for tag in tags:
+        m = TAG_RE.match(tag.strip())
+        if m:
+            v = tuple(int(x) for x in m.groups())
+            if v[0] < CALVER_MAJOR:
+                versions.append(v)
+    return max(versions) if versions else None
+
+
+def bump_kind(pr: dict) -> str | None:
+    labels = {label["name"].lower() for label in pr.get("labels") or []}
+    for kind in KINDS:
+        if f"release:{kind}" in labels:
+            return kind
+    return None
+
+
+def next_version(tags: list[str], pr: dict) -> str | None:
+    kind = bump_kind(pr)
+    if kind is None:
+        return None
+    major, minor, patch = latest_version(tags) or (0, 0, 0)
+    if kind == "major":
+        return f"{major + 1}.0.0"
+    if kind == "minor":
+        return f"{major}.{minor + 1}.0"
+    return f"{major}.{minor}.{patch + 1}"
+
+
+def main() -> None:
+    with open(sys.argv[1], encoding="utf-8") as fh:
+        pr = json.load(fh)
+    tags = subprocess.run(
+        ["git", "tag", "--list", "v*"], capture_output=True, text=True, check=True
+    ).stdout.splitlines()
+    print(next_version(tags, pr) or "")
+
+
+if __name__ == "__main__":
+    main()

zarrsmith-0.6.0/.github/workflows/docker-publish.yml

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+name: Build and Publish Docker Image
+
+on:
+  # Normal path: called by release.yml after a merged PR creates a new version tag.
+  workflow_call:
+    inputs:
+      version:
+        description: "Release version without the leading v (e.g. 0.10.1)"
+        required: true
+        type: string
+  # Tags pushed by hand (not by release.yml's GITHUB_TOKEN) still build an image.
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch: # Allows manual triggering
+
+env:
+  REGISTRY: ghcr.io
+  # Explicit, not github.repository: the images up to 0.5.5 stay at ghcr.io/embl-mif/pymif.
+  IMAGE_NAME: ${{ github.repository_owner }}/zarrsmith
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+
+    # Grants permissions to the GITHUB_TOKEN to upload packages to GHCR
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Resolve version
+        id: ver
+        env:
+          INPUT_VERSION: ${{ inputs.version }}
+        run: |
+          version="$INPUT_VERSION"
+          if [ -z "$version" ] && [ "$GITHUB_REF_TYPE" = "tag" ]; then
+            version="${GITHUB_REF_NAME#v}"
+          fi
+          echo "version=$version" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ steps.ver.outputs.version && format('v{0}', steps.ver.outputs.version) || '' }}
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            # Release version, e.g. 0.10.1, plus 'latest'
+            type=raw,value=${{ steps.ver.outputs.version }},enable=${{ steps.ver.outputs.version != '' }}
+            type=raw,value=latest,enable=${{ steps.ver.outputs.version != '' }}
+            # Manual runs on a branch are tagged with the branch name
+            type=ref,event=branch,enable=${{ steps.ver.outputs.version == '' }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            ZARRSMITH_VERSION=${{ steps.ver.outputs.version }}

zarrsmith-0.6.0/.github/workflows/documentation.yml

@@ -0,0 +1,38 @@
+name: documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0  # tags are needed to derive the version shown in the docs
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+      - name: Install package and docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[docs]"
+      - name: Sphinx build
+        run: |
+          sphinx-build documentation _build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build
+          force_orphan: true

zarrsmith-0.6.0/.github/workflows/release.yml

@@ -0,0 +1,116 @@
+name: release
+
+# Releases are opt-in: only a merged PR into main labelled release:major, release:minor or
+# release:patch creates a vX.Y.Z tag, a GitHub Release, a PyPI release and a Docker image. All other merged
+# PRs skip this workflow (the job-level `if` means no runner is started).
+# The version is computed by .github/scripts/next_version.py.
+# pull_request_target is used so merges of PRs from forks also get a write token; the
+# job only checks out the merge commit, i.e. code that is already on main.
+on:
+  pull_request_target:
+    types: [closed]
+    branches: [main]
+
+jobs:
+  tag:
+    if: >-
+      github.event.pull_request.merged == true && (
+      contains(github.event.pull_request.labels.*.name, 'release:major') ||
+      contains(github.event.pull_request.labels.*.name, 'release:minor') ||
+      contains(github.event.pull_request.labels.*.name, 'release:patch'))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: read
+    # Serialize releases so two quick merges never compute the same version.
+    concurrency:
+      group: release
+      cancel-in-progress: false
+    outputs:
+      version: ${{ steps.version.outputs.version }}
+
+    steps:
+      - name: Check out merge commit
+        uses: actions/checkout@v5
+        with:
+          ref: ${{ github.event.pull_request.merge_commit_sha }}
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - name: Compute next version
+        id: version
+        env:
+          GH_TOKEN: ${{ github.token }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          gh pr view "$PR_NUMBER" --repo "$GITHUB_REPOSITORY" \
+            --json labels > "$RUNNER_TEMP/pr.json"
+          version=$(python .github/scripts/next_version.py "$RUNNER_TEMP/pr.json")
+          echo "version=$version" >> "$GITHUB_OUTPUT"
+          if [ -z "$version" ]; then
+            echo "No release for this PR."
+          else
+            echo "Next version: $version"
+          fi
+
+      - name: Create tag and GitHub Release
+        if: steps.version.outputs.version != ''
+        env:
+          GH_TOKEN: ${{ github.token }}
+          VERSION: ${{ steps.version.outputs.version }}
+          SHA: ${{ github.event.pull_request.merge_commit_sha }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git tag -a "v$VERSION" -m "zarrsmith $VERSION" "$SHA"
+          git push origin "v$VERSION"
+          gh release create "v$VERSION" --repo "$GITHUB_REPOSITORY" \
+            --title "v$VERSION" --generate-notes --verify-tag
+
+  # Trusted publishing: PyPI accepts this repository's release.yml in the `pypi` environment,
+  # so no token is stored. It must run in this top-level workflow (PyPI rejects reusable ones).
+  pypi:
+    needs: tag
+    if: needs.tag.outputs.version != ''
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/zarrsmith
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Check out release tag
+        uses: actions/checkout@v5
+        with:
+          ref: v${{ needs.tag.outputs.version }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - name: Build sdist and wheel
+        env:
+          SETUPTOOLS_SCM_PRETEND_VERSION: ${{ needs.tag.outputs.version }}
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  # Tags pushed with GITHUB_TOKEN do not trigger other workflows, so call the image build directly.
+  docker:
+    needs: tag
+    if: needs.tag.outputs.version != ''
+    uses: ./.github/workflows/docker-publish.yml
+    with:
+      version: ${{ needs.tag.outputs.version }}
+    permissions:
+      contents: read
+      packages: write

zarrsmith-0.6.0/.github/workflows/tests.yml

@@ -0,0 +1,34 @@
+name: tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests
+        run: |
+          pytest -q

zarrsmith-0.6.0/.gitignore

@@ -0,0 +1,15 @@
+__pycache__/
+_build/
+*.py[cod]
+*.zarr
+*.egg-info/
+.env
+.ipynb_checkpoints
+.vscode*
+pymif_old/
+documentation/demonstration_open_zarr.avi
+documentation/demonstration_open_zarr.mp4
+documentation/demonstration_open_zarr.gif
+documentation/Thumbs.db
+*build/
+zarrsmith/_version.py

zarrsmith-0.6.0/Dockerfile

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+# Base image
+FROM python:3.12-slim
+
+# Avoid interactive prompts
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies (same as your original)
+RUN apt-get update && apt-get install -y \
+    libfontconfig1 \
+    libgl1 \
+    libglx0 \
+    libglib2.0-0 \
+    procps \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set workdir
+WORKDIR /app
+
+# Copy project files
+COPY . /app
+
+# Optional: choose extras at build time (default = base)
+ARG ZARRSMITH_EXTRAS=""
+# Package version (set by CI); the image has no git, so setuptools-scm cannot read tags
+ARG ZARRSMITH_VERSION=""
+
+# Upgrade pip and install package
+RUN pip install --upgrade pip && \
+    if [ -n "$ZARRSMITH_VERSION" ]; then \
+        export SETUPTOOLS_SCM_PRETEND_VERSION="$ZARRSMITH_VERSION"; \
+    fi && \
+    if [ -z "$ZARRSMITH_EXTRAS" ]; then \
+        pip install .; \
+    else \
+        pip install ".[${ZARRSMITH_EXTRAS}]"; \
+    fi
+
+# Default shell
+CMD ["/bin/bash"]

zarrsmith-0.6.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 European Molecular Biology Laboratory (EMBL)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

zarrsmith-0.6.0/MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include zarrsmith/napari *.yaml
+recursive-include zarrsmith/napari/resources *.svg

zarrsmith-0.6.0/PKG-INFO

@@ -0,0 +1,177 @@
+Metadata-Version: 2.4
+Name: zarrsmith
+Version: 0.6.0
+Summary: Microscopy I/O, OME-Zarr forging and NGFF utilities: read vendor datasets, write multiscale OME-Zarr, fuse mosaics, from Python, the command line and napari.
+Author-email: Nicola Gritti <nicola.gritti@embl.es>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/embl-mif/zarrsmith
+Project-URL: Documentation, https://embl-mif.github.io/zarrsmith/
+Project-URL: Issues, https://github.com/embl-mif/zarrsmith/issues
+Project-URL: Changelog, https://github.com/embl-mif/zarrsmith/releases
+Keywords: microscopy,zarr,ome-zarr,ngff,napari
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: async-lru>=2.3.0
+Requires-Dist: bioio>=3.3.0
+Requires-Dist: bioio-czi>=2.6.0
+Requires-Dist: dask>=2026.3.0
+Requires-Dist: dask-image>=2025.11.0
+Requires-Dist: h5py>=3.16.0
+Requires-Dist: imagecodecs>=2026.10.10
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: natsort
+Requires-Dist: numba>=0.64.0
+Requires-Dist: numcodecs>=0.16.5
+Requires-Dist: numpy>=2.4.3
+Requires-Dist: ome-zarr>=0.16.0
+Requires-Dist: pandas>=3.0.1
+Requires-Dist: readlif>=0.6.6
+Requires-Dist: scikit-image>=0.26.0
+Requires-Dist: scikit-learn>=1.8.0
+Requires-Dist: scipy>=1.17.1
+Requires-Dist: slideio>=2.10.0
+Requires-Dist: tifffile>=2026.3.3
+Requires-Dist: tqdm>=4.67.3
+Requires-Dist: typer>=0.24.1
+Requires-Dist: xlsxwriter>=3.2.9
+Requires-Dist: xyzservices>=2025.11.0
+Requires-Dist: zarr>=3.1.6
+Requires-Dist: zict>=3.0.0
+Provides-Extra: napari
+Requires-Dist: magicgui>=0.10.1; extra == "napari"
+Requires-Dist: napari; extra == "napari"
+Requires-Dist: napari-animation; extra == "napari"
+Requires-Dist: napari-clusters-plotter>=0.11; extra == "napari"
+Requires-Dist: napari-metadata; extra == "napari"
+Requires-Dist: napari-ome-zarr>=0.8.2; extra == "napari"
+Requires-Dist: pyconify>=0.2.1; extra == "napari"
+Requires-Dist: PyQt6; extra == "napari"
+Requires-Dist: QtPy>=2.4.3; extra == "napari"
+Provides-Extra: notebooks
+Requires-Dist: notebook>=7.5.5; extra == "notebooks"
+Provides-Extra: dev
+Requires-Dist: pytest>=9.0.2; extra == "dev"
+Requires-Dist: build>=1.4.1; extra == "dev"
+Requires-Dist: wheel>=0.46.3; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: Sphinx>=9.1.0; extra == "docs"
+Requires-Dist: sphinx-autoapi>=3.8.0; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=3.9.11; extra == "docs"
+Requires-Dist: sphinx_rtd_theme>=3.1.0; extra == "docs"
+Requires-Dist: myst-parser>=5.0.0; extra == "docs"
+Provides-Extra: all
+Requires-Dist: zarrsmith[dev,docs,napari,notebooks]; extra == "all"
+Dynamic: license-file
+
+<h1>
+  <img src="https://raw.githubusercontent.com/embl-mif/zarrsmith/main/zarrsmith/napari/resources/zarrsmith-icon.svg" alt="ZarrSmith logo" width="120" align="left">
+  ZarrSmith — microscopy I/O, OME-Zarr forging, and NGFF utilities
+  <br clear="left">
+</h1>
+<!-- The logo has an absolute URL so that it also shows on PyPI.
+documentation/index.md repeats this header in Markdown (Sphinx needs a Markdown title and does not
+rewrite HTML paths) and includes this README from here. -->
+
+![Python](https://img.shields.io/badge/python-3.12-green)
+[![License](https://img.shields.io/github/license/embl-mif/zarrsmith.svg)](https://github.com/embl-mif/zarrsmith/blob/main/LICENSE)
+[![Tests](https://github.com/embl-mif/zarrsmith/actions/workflows/tests.yml/badge.svg)](https://github.com/embl-mif/zarrsmith/actions/workflows/tests.yml)
+[![codecov](https://codecov.io/gh/embl-mif/zarrsmith/graph/badge.svg)](https://codecov.io/gh/embl-mif/zarrsmith)
+[![Documentation](https://github.com/embl-mif/zarrsmith/actions/workflows/documentation.yml/badge.svg)](https://github.com/embl-mif/zarrsmith/actions/workflows/documentation.yml)
+[![Docker](https://github.com/embl-mif/zarrsmith/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/embl-mif/zarrsmith/actions/workflows/docker-publish.yml)
+[![GitHub release](https://img.shields.io/github/v/release/embl-mif/zarrsmith.svg)](https://github.com/embl-mif/zarrsmith/releases)
+[![GitHub stars](https://img.shields.io/github/stars/embl-mif/zarrsmith.svg?style=social)](https://github.com/embl-mif/zarrsmith/stargazers)
+
+**ZarrSmith** is a Python package for reading microscopy datasets from multiple acquisition systems, building multiscale pyramids, writing **OME-NGFF / OME-Zarr**, and working with those datasets from Python, the command line and napari.
+
+The rendered documentation is at **[embl-mif.github.io/zarrsmith](https://embl-mif.github.io/zarrsmith/)**.
+
+> [!NOTE]
+> ZarrSmith was called **PyMIF** up to version 0.5.5. From 0.6.0, import `zarrsmith` and run the `zarrsmith` command instead of `pymif`. The Docker images of PyMIF stay available at `ghcr.io/embl-mif/pymif:<version>`; newer images are at `ghcr.io/embl-mif/zarrsmith`.
+
+---
+
+## What ZarrSmith does
+
+- **Microscope managers** read Luxendo, Opera, SCAPE, Viventis, Zeiss, Evident (Olympus VSI) and OME-Zarr datasets into one lazy (Dask) API with a shared metadata schema. → [Readers and conventions](documentation/readers.md)
+- **OME-Zarr writing**: full export, empty datasets and groups, image and label region updates, any subset of the `tczyx` axes. → [Python API](documentation/python-api.md)
+- **Pyramids and subsetting**: multiscale generation, cropping, channel reordering, metadata updates. → [Python API](documentation/python-api.md)
+- **Mosaics**: raw tiles shown at their stage position and fused into one OME-Zarr image (3D or projection). → [Mosaics](documentation/mosaic.md)
+- **Chromatic shift correction**: the Z offset between channels measured on the sample itself, and a corrected copy with the same layout as the input. → [Chromatic shift correction](documentation/chromatic-shift.md)
+- **Command line**: one-off and CSV-batch conversion, mosaic fusion and chromatic shift correction. → [Command line](documentation/cli.md)
+- **Napari widgets**: conversion with ROI selection, mosaic fusion, exploration of segmented objects (features plot linked with the viewer). → [Napari plugin](documentation/napari-plugin.md)
+- **Output tuning**: sharding, singleton axes, parallel writing, progress bars. → [Advanced writing options](documentation/advanced.md)
+
+## Installation
+
+```console
+conda create -n zarrsmith python=3.12
+conda activate zarrsmith
+git clone https://github.com/embl-mif/zarrsmith.git
+cd zarrsmith
+pip install .            # or: pip install -e .[napari] for development with the napari widgets
+```
+
+Versioning, releases and development installs: [Installation and versioning](documentation/installation.md).
+
+## Quick start
+
+```python
+import zarrsmith.microscope_manager as mm
+
+source = mm.ViventisManager("path/to/Position_1")   # any microscope manager
+source.build_pyramid(num_levels=3)
+source.to_zarr("output.zarr")                       # NGFF v0.5 / Zarr v3
+
+z = mm.ZarrManager("output.zarr")
+z.visualize()                                       # open in napari
+```
+
+```console
+zarrsmith convert -i INPUT_PATH -m MICROSCOPE -z OUTPUT_ZARR
+zarrsmith fuse -i ACQUISITION_FOLDER -z OUTPUT_ZARR -rds 4 8 8   # fuse raw tiles
+zarrsmith chromatic-shift -i INPUT_ZARR -z OUTPUT_ZARR -r shift.json   # align channels in Z
+```
+
+## Documentation
+
+**Getting started**
+
+| Page | Contents |
+|---|---|
+| [Installation and versioning](documentation/installation.md) | environments, extras, release labels |
+| [Readers and conventions](documentation/readers.md) | supported microscopes, shared reader behaviour, logging |
+
+**Working with data**
+
+| Page | Contents |
+|---|---|
+| [Python API](documentation/python-api.md) | export, empty datasets, axis-aware metadata, labels, region writes |
+| [Mosaics](documentation/mosaic.md) | raw tiles, placement check, fusion options |
+| [Chromatic shift correction](documentation/chromatic-shift.md) | measuring the Z offset between channels, the corrected dataset, checking the result, `zarrsmith chromatic-shift` |
+| [Advanced writing options](documentation/advanced.md) | sharding, singleton axes, parallel writing, progress bar |
+
+**Interfaces**
+
+| Page | Contents |
+|---|---|
+| [Command line](documentation/cli.md) | `zarrsmith convert`, `zarrsmith fuse`, `zarrsmith chromatic-shift` (one dataset or a CSV batch) |
+| [Napari plugin](documentation/napari-plugin.md) | converter, mosaic fusion and objects explorer widgets |
+
+**Reference**
+
+| Page | Contents |
+|---|---|
+| [API reference](https://embl-mif.github.io/zarrsmith/autoapi/zarrsmith/index.html) | generated from the docstrings |
+| [Contributing](documentation/contributing.md) | package layout, adding a microscope manager or a mosaic manager, `zarrsmith.utils`, documentation |
+
+## Help
+
+For questions or bug reports, open an
+[issue](https://github.com/embl-mif/zarrsmith/issues) on GitHub, or contact the current maintainers.
+
+> [!IMPORTANT]
+> If ZarrSmith contributes to your work, please acknowledge ZarrSmith and the EMBL Mesoscopic Imaging Facility in your publications.