aind-lightsheet-registration 0.3.1__tar.gz

aind_lightsheet_registration-0.3.1/.copier-answers.yml

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+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 0.1.19
+_src_path: /home/galen.lynch/Documents/Code/aind-python-copier-template
+author_email: galen@galenlynch.com
+author_fullname: Galen Lynch
+auto_setup_repo: true
+current_year: '2026'
+github_org: AllenNeuralDynamics
+github_url: https://github.com/AllenNeuralDynamics/aind-lightsheet-registration
+include_claude_md: true
+include_cli: false
+include_commitizen: true
+include_docs: false
+include_notebooks: false
+include_type_hints: true
+institute_name: Allen Institute for Neural Dynamics
+license: MIT
+project_description: Register cleared light-sheet brains to a template and on to CCF
+project_name: AIND light-sheet registration
+project_slug: aind-lightsheet-registration
+publish_to_pypi: false
+python_package_import_name: aind_lightsheet_registration
+python_version: '3.11'
+target_python_version: '3.13'
+workflow_source: AllenNeuralDynamics/galen-uv-workflows
+workflow_version: v2

aind_lightsheet_registration-0.3.1/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

aind_lightsheet_registration-0.3.1/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

aind_lightsheet_registration-0.3.1/.github/ISSUE_TEMPLATE/user-story.md

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+---
+name: User story
+about: This template provides a basic structure for user story issues.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# User story
+As a ..., I want to ..., so I can ...
+
+*Ideally, this is in the issue title, but if not, you can put it here. If so, delete this section.*
+
+# Acceptance criteria
+- [ ] This is something that can be verified to show that this user story is satisfied.
+
+# Sprint Ready Checklist 
+- [ ] 1. Acceptance criteria defined 
+- [ ] 2. Team understands acceptance criteria 
+- [ ] 3. Team has defined solution / steps to satisfy acceptance criteria 
+- [ ] 4. Acceptance criteria is verifiable / testable 
+- [ ] 5. External / 3rd Party dependencies identified
+- [ ] 6. Ticket is prioritized and sized
+
+# Notes
+*Add any helpful notes here.*

aind_lightsheet_registration-0.3.1/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    # Workflow files stored in the default location of `.github/workflows`
+    # You don't need to specify `/.github/workflows` for `directory`. You can use `directory: "/"`.
+    directory: "/"
+    schedule:
+      interval: "weekly"
+  # Enable version updates for pip
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

aind_lightsheet_registration-0.3.1/.github/workflows/bump-call.yml

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+name: Bump Version
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    branches: [ main ]
+    types: [ completed ]
+  workflow_dispatch:
+    inputs:
+      increment:
+        description: "auto infers the bump from the commits; force one to release ci or chore changes"
+        type: choice
+        options: [auto, PATCH, MINOR, MAJOR]
+        default: auto
+
+permissions:
+  contents: write    # needed to push commits/tags
+  id-token: write    # needed if your reusable workflow exchanges OIDC tokens
+
+concurrency:
+  group: bump-${{ github.workflow }}-${{ github.event.workflow_run.head_branch || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  bump:
+    # Only run when:
+    #  • a CI run just succeeded (and the head commit message doesn't start with 'bump:')
+    #  • OR this is a manual dispatch
+    if: >
+      (github.event_name == 'workflow_run' &&
+       github.event.workflow_run.conclusion == 'success' &&
+       !startsWith(github.event.workflow_run.head_commit.message, 'bump:')) ||
+      (github.event_name == 'workflow_dispatch' &&
+      github.ref == 'refs/heads/main')
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/bump-version.yml@v2
+    with:
+      default-branch: main
+      increment: ${{ inputs.increment || 'auto' }}
+    secrets:
+      repo-token: ${{ secrets.SERVICE_TOKEN }}

aind_lightsheet_registration-0.3.1/.github/workflows/ci-call.yml

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+name: CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+  pull-requests: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-ci:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        # Floor and ceiling. They coincide when a project targets its own
+        # minimum, and a matrix must not then run the same version twice.
+        python-version: ["3.11", "3.13"]
+
+    if: >
+      (github.event_name != 'pull_request' || github.event.pull_request.draft == false) &&
+      github.actor != 'github-actions[bot]' &&
+      !(github.event_name == 'push' && startsWith(github.event.head_commit.message, 'bump:'))
+
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/ci.yml@v2
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      package-name: aind_lightsheet_registration
+      run-mypy: true
+    secrets:
+      # Passed on to `uv sync` as a git `url.insteadOf` credential, so
+      # internal or private git dependencies pinned in [tool.uv.sources]
+      # can be cloned. Harmless to leave in when all deps are public.
+      repo-token: ${{ secrets.GITHUB_TOKEN }}

aind_lightsheet_registration-0.3.1/.github/workflows/publish-call.yml

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+name: "Release"
+
+on:
+  push:
+    tags:
+      - 'v[0-9]*'          # semver tags
+  workflow_dispatch:
+
+permissions:
+  contents: write    # create release + upload assets
+
+concurrency:
+  group: release
+  cancel-in-progress: false   # let releases finish
+
+jobs:
+  run-release:
+    uses: AllenNeuralDynamics/galen-uv-workflows/.github/workflows/publish.yml@v2
+    with:
+      tag-name: ${{ github.ref_name }}
+      python-version: "3.13"
+      publish-to-pypi: true
+    secrets:
+      repo-token: ${{ secrets.GITHUB_TOKEN }}
+      pypi-token: ${{ secrets.AIND_PYPI_TOKEN }}

aind_lightsheet_registration-0.3.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# MacOs
+**/.DS_Store
+
+# VSCode
+.vscode/
+
+# Scratch / working directory
+scratch/
+
+# Claude
+.claude/
+
+# Repo setup scripts (generated by template, not meant to be committed)
+setup_repo.sh
+configure_repo.sh

aind_lightsheet_registration-0.3.1/.python-version

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+3.13

aind_lightsheet_registration-0.3.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## v0.3.1 (2026-10-21)
+
+## v0.3.0 (2026-10-21)
+
+### Feat
+
+- smooth the total SyN field by one voxel by default
+- refuse brains whose metadata names rotated axis directions
+- normalize brains to the convention their template declares
+- register at 50 um with the template-build schedule by default
+- store the seam profile as TSV with a JSON sidecar
+- add a calibrated tile-row seam profile
+- fit a brightness gain per tile in the sheet illumination model
+- skip illumination correction by default and stitch grids with empty tiles
+- correct, stitch and fuse raw SmartSPIM tiles before registration
+- prepare a brain from its zarr and register it to a template
+- threshold brain masks on log intensity by default
+
+### Fix
+
+- keep images alive while reading their arrays
+- start N4 from a coarse mesh so the bias field cannot follow anatomy
+
+## v0.2.0 (2026-10-16)
+
+### Feat
+
+- read a light-sheet pyramid level and prepare it for registration

aind_lightsheet_registration-0.3.1/CLAUDE.md

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+# CLAUDE.md
+
+Instructions for coding agents in this repository. [CONTRIBUTING.md](CONTRIBUTING.md) holds setup,
+checks, tests and conventions, and applies to agents as to people: read it before running or
+changing anything. [README.md](README.md) documents use.
+
+- Run every command through `uv`; never bare `pip` or `python`.
+- Before calling a change done, run `./scripts/run_linters_and_checks.sh -c`.
+- Keep this file to what only an agent needs; development practice belongs in CONTRIBUTING.md and
+  usage in README.md.

aind_lightsheet_registration-0.3.1/CONTRIBUTING.md

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+# Contributing to AIND light-sheet registration
+
+This document is for people changing aind-lightsheet-registration: setting up, running the checks and tests,
+and the conventions a change follows. Using the package is documented in [README.md](README.md).
+
+## Setup
+
+```bash
+uv sync
+```
+
+`uv sync` creates `.venv` holding the package and the dev group. `uv` manages the environment and
+the lockfile, `uv.lock`: run commands with `uv run`, add a dependency with `uv add <package>` and a
+development tool with `uv add --group dev <package>`, and never install with bare `pip`. The
+jupyter group adds a kernel (`uv sync --group jupyter`).
+
+## Checks
+
+```bash
+./scripts/run_linters_and_checks.sh -c
+```
+
+Without `-c` the script only formats. With it, the script also runs ruff's linter, mypy, interrogate,
+codespell and pytest with coverage, passing any arguments after `--` to pytest. It runs in the
+existing `.venv` and does not sync it.
+
+The same checks, one at a time:
+
+```bash
+uv run --frozen ruff format
+uv run --frozen ruff check
+uv run --frozen mypy
+uv run --frozen interrogate -v src
+uv run --frozen codespell --check-filenames
+uv run --frozen pytest --cov aind_lightsheet_registration
+```
+
+## Tests
+
+```bash
+uv run pytest                          # the whole suite
+uv run pytest tests/test_example.py    # one file
+uv run pytest -k "version"             # tests whose names match
+```
+
+## Conventions
+
+- Source lives in `src/aind_lightsheet_registration/` and tests in `tests/`; hatchling builds the
+  wheel.
+- ruff sets a line length of 120 and numpy-style docstrings, and exempts tests from the
+  docstring and annotation rules. interrogate fails below 30%
+  docstring coverage of `src`.
+- mypy checks `src/aind_lightsheet_registration` in strict mode.
+- Comments and docstrings say what the code does not: why it is written this way, and what breaks
+  otherwise. They carry no history; the reason for a change belongs in its commit message.
+- `scratch/` is gitignored and excluded from the linters, for work that is not kept.
+- Commit messages follow [Conventional Commits](https://www.conventionalcommits.org/) (`feat:`,
+  `fix:`, `docs:`, `chore:`): an imperative title, and a body giving what changed and why. After CI
+  passes on `main`, the bump workflow uses commitizen to bump the version from them and update
+  `CHANGELOG.md`.
+- A change a user would notice updates README.md in the same commit.

aind_lightsheet_registration-0.3.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Allen Institute for Neural Dynamics
+
+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.
+

aind_lightsheet_registration-0.3.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: aind-lightsheet-registration
+Version: 0.3.1
+Summary: Register cleared light-sheet brains to a template and on to CCF
+Project-URL: Repository, https://github.com/AllenNeuralDynamics/aind-lightsheet-registration/
+Project-URL: Issues, https://github.com/AllenNeuralDynamics/aind-lightsheet-registration/issues
+Project-URL: Changelog, https://github.com/AllenNeuralDynamics/aind-lightsheet-registration/blob/main/CHANGELOG.md
+Author: Allen Institute for Neural Dynamics
+Author-email: Galen Lynch <galen@galenlynch.com>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.11
+Requires-Dist: aind-registration-utils<0.6,>=0.5
+Requires-Dist: aind-zarr-utils<0.18,>=0.17.2
+Requires-Dist: fsspec>=2024.6
+Requires-Dist: numpy<3,>=2
+Requires-Dist: ome-zarr>=0.7
+Requires-Dist: pywavelets>=1.6
+Requires-Dist: s3fs>=2024.6
+Requires-Dist: scikit-image>=0.24
+Requires-Dist: scipy>=1.13
+Requires-Dist: simpleitk<3,>=2
+Requires-Dist: tyro>=0.9
+Requires-Dist: zarr>=3.1
+Description-Content-Type: text/markdown
+
+# AIND light-sheet registration
+
+![CI](https://github.com/AllenNeuralDynamics/aind-lightsheet-registration/actions/workflows/ci-call.yml/badge.svg)
+[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border.json)](https://github.com/copier-org/copier)
+
+Register cleared light-sheet brains to a template and on to CCF
+
+## Installation
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+## Usage
+
+<!-- What a user imports or runs, with a short example. Setup for changing the code belongs in CONTRIBUTING.md. -->
+
+## Contributing
+
+Setup, checks, tests and conventions are in [CONTRIBUTING.md](CONTRIBUTING.md).
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

aind_lightsheet_registration-0.3.1/README.md

@@ -0,0 +1,30 @@
+# AIND light-sheet registration
+
+![CI](https://github.com/AllenNeuralDynamics/aind-lightsheet-registration/actions/workflows/ci-call.yml/badge.svg)
+[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
+[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
+[![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border.json)](https://github.com/copier-org/copier)
+
+Register cleared light-sheet brains to a template and on to CCF
+
+## Installation
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+## Usage
+
+<!-- What a user imports or runs, with a short example. Setup for changing the code belongs in CONTRIBUTING.md. -->
+
+## Contributing
+
+Setup, checks, tests and conventions are in [CONTRIBUTING.md](CONTRIBUTING.md).
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.