regrender 0.1.0__tar.gz

regrender-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,29 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      - run: uvx ruff check .
+      - run: uvx mypy regrender/
+
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          python-version: "3.12"
+      # napari import needs a display + Qt/OpenGL system libs
+      - uses: pyvista/setup-headless-display-action@v3
+      - run: uv sync --extra test
+      - run: uv run pytest -q
+        env:
+          QT_QPA_PLATFORM: offscreen

regrender-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,27 @@
+name: Publish to PyPI
+
+# Publishes on a version tag push (e.g. `git push origin v0.1.0`).
+# The tag must match the version in pyproject.toml (checked below).
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # trusted publishing (OIDC) — no API token needed
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+      # fail early if the release tag (e.g. v0.1.0) doesn't match pyproject's version
+      - name: Check tag matches version
+        run: |
+          tag="${GITHUB_REF_NAME#v}"
+          pkg=$(grep '^version = ' pyproject.toml | cut -d'"' -f2)
+          echo "tag=$tag pkg=$pkg"
+          [ "$tag" = "$pkg" ] || { echo "tag $tag != pyproject version $pkg"; exit 1; }
+      - run: uv build
+      - uses: pypa/gh-action-pypi-publish@release/v1

regrender-0.1.0/.gitignore

@@ -0,0 +1,195 @@
+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the enitre vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+.DS_Store

regrender-0.1.0/.idea/.gitignore

@@ -0,0 +1,8 @@
+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml

regrender-0.1.0/.idea/2dccf.iml

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$/../neuralib2">
+      <excludeFolder url="file://$MODULE_DIR$/../neuralib2/.venv" />
+      <excludeFolder url="file://$MODULE_DIR$/../neuralib2/packages/neuralib-imaging/.venv" />
+    </content>
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/.venv" />
+    </content>
+    <orderEntry type="jdk" jdkName="uv (regrender)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

regrender-0.1.0/.idea/deployment.xml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="PublishConfigData" remoteFilesAllowedToDisappearOnAutoupload="false">
+    <serverData>
+      <paths name="yuting@172.18.1.31:22 password">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$/../neuralib2" web="/" />
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+      <paths name="yuting@172.18.1.31:22 password (2)">
+        <serverdata>
+          <mappings>
+            <mapping local="$PROJECT_DIR$/../neuralib2" web="/" />
+            <mapping local="$PROJECT_DIR$" web="/" />
+          </mappings>
+        </serverdata>
+      </paths>
+    </serverData>
+  </component>
+</project>

regrender-0.1.0/.idea/dictionaries/project.xml

@@ -0,0 +1,7 @@
+<component name="ProjectDictionaryState">
+  <dictionary name="project">
+    <words>
+      <w>allenccf</w>
+    </words>
+  </dictionary>
+</component>

regrender-0.1.0/.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,8 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="DuplicatedCode" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
+    <inspection_tool class="Eslint" enabled="true" level="WARNING" enabled_by_default="true" />
+    <inspection_tool class="PyInterpreterInspection" enabled="false" level="WARNING" enabled_by_default="false" />
+  </profile>
+</component>

regrender-0.1.0/.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

regrender-0.1.0/.idea/misc.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="uv (pycams)" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="uv (regrender)" project-jdk-type="Python SDK" />
+</project>

regrender-0.1.0/.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/2dccf.iml" filepath="$PROJECT_DIR$/.idea/2dccf.iml" />
+    </modules>
+  </component>
+</project>

regrender-0.1.0/.idea/regrender.iml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module external.system.id="pyproject.toml" type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

regrender-0.1.0/.idea/vcs.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/../neuralib2" vcs="Git" />
+  </component>
+</project>

regrender-0.1.0/.python-version

@@ -0,0 +1 @@
+3.12

regrender-0.1.0/.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: "2"
+
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc
+
+sphinx:
+  configuration: docs/source/conf.py

regrender-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Yu-Ting Wei
+
+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.

regrender-0.1.0/PKG-INFO

@@ -0,0 +1,102 @@
+Metadata-Version: 2.4
+Name: regrender
+Version: 0.1.0
+Summary: 2D mouse brain registration, ROI/Probe annotation, and brainrender reconstruction
+Project-URL: Homepage, https://github.com/ytsimon2004/regrender
+Project-URL: Repository, https://github.com/ytsimon2004/regrender
+Project-URL: Documentation, https://regrender.readthedocs.io
+Author-email: Yu-Ting Wei <ytsimon2004@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: allen-ccf,brain-atlas,brainrender,napari,neuroscience,registration
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Requires-Dist: argclz>=1.0.1
+Requires-Dist: imageio
+Requires-Dist: napari[pyqt5]
+Requires-Dist: neuralib-atlas[brainrender]>=0.7.3
+Requires-Dist: rich
+Provides-Extra: doc
+Requires-Dist: pydata-sphinx-theme; extra == 'doc'
+Requires-Dist: sphinx; extra == 'doc'
+Requires-Dist: sphinx-copybutton; extra == 'doc'
+Provides-Extra: lint
+Requires-Dist: mypy; extra == 'lint'
+Requires-Dist: ruff; extra == 'lint'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Description-Content-Type: text/markdown
+
+# regrender
+
+**Tools for 2D mouse brain registration to the Allen Common Coordinate Framework (CCF)**
+
+A napari-based Python toolkit
+For registering histological brain slices to the Allen Brain Atlas, annotating cells/ROIs,
+reconstructing probe tracks, and rendering the results with brainrender.
+
+## Features
+
+- **Interactive slice→CCF registration** (`regrender register`) — pick landmark pairs in napari, estimate a homography/affine transform.
+- **ROI annotation** (`regrender roi`) — label cells on raw images, project them into CCF space, and render.
+- **Probe-track reconstruction** (`regrender probe`) — reconstruct electrode shanks from dye labels across serial sections.
+- **brainrender rendering** of ROIs and probes in 3D atlas space.
+
+## Demo
+
+**`regrender register`** — match landmark pairs between the atlas plane (left) and histology (right):
+
+<img src="docs/source/_static/register.png" alt="register" width="800">
+
+**`regrender roi`** — label cells per channel, then project + render in 3D with brainrender:
+
+<img src="docs/source/_static/roi.png" alt="roi" width="800">
+
+**`regrender probe`** — pick dye points per shank and reconstruct the tracks in 3D:
+
+<img src="docs/source/_static/probe.png" alt="probe" width="800">
+
+
+## Installation
+
+```bash
+# Option 1 — one-shot CLI install, no clone or env needed (recommended for users)
+uv tool install git+https://github.com/ytsimon2004/regrender.git
+
+# Option 2 — uv virtual environment (development)
+git clone https://github.com/ytsimon2004/regrender.git && cd regrender
+uv venv && source .venv/bin/activate
+uv pip install -e .
+
+# Option 3 — conda environment (development)
+git clone https://github.com/ytsimon2004/regrender.git && cd regrender
+conda create -n regrender python=3.12 -y && conda activate regrender
+pip install -e .
+```
+
+See the [installation docs](https://regrender.readthedocs.io/en/latest/get_start/installation.html) for details.
+
+## Quick Start
+
+```bash
+# 1. label ROIs on raw slices
+regrender roi -D <slices_dir>
+
+# 2. register each slice to the CCF
+regrender register -D <slices_dir>
+
+# 3. project ROIs to CCF + render  (or use the GUI "Project + Render" button)
+regrender roi --project --render -D <slices_dir>
+
+# probe tracks
+regrender probe -D <slices_dir>
+```
+
+See the [full documentation](https://regrender.readthedocs.io) for the complete workflow.
+
+## Contact
+
+**Yu-Ting Wei** - ytsimon2004@gmail.com

regrender-0.1.0/README.md

@@ -0,0 +1,70 @@
+# regrender
+
+**Tools for 2D mouse brain registration to the Allen Common Coordinate Framework (CCF)**
+
+A napari-based Python toolkit
+For registering histological brain slices to the Allen Brain Atlas, annotating cells/ROIs,
+reconstructing probe tracks, and rendering the results with brainrender.
+
+## Features
+
+- **Interactive slice→CCF registration** (`regrender register`) — pick landmark pairs in napari, estimate a homography/affine transform.
+- **ROI annotation** (`regrender roi`) — label cells on raw images, project them into CCF space, and render.
+- **Probe-track reconstruction** (`regrender probe`) — reconstruct electrode shanks from dye labels across serial sections.
+- **brainrender rendering** of ROIs and probes in 3D atlas space.
+
+## Demo
+
+**`regrender register`** — match landmark pairs between the atlas plane (left) and histology (right):
+
+<img src="docs/source/_static/register.png" alt="register" width="800">
+
+**`regrender roi`** — label cells per channel, then project + render in 3D with brainrender:
+
+<img src="docs/source/_static/roi.png" alt="roi" width="800">
+
+**`regrender probe`** — pick dye points per shank and reconstruct the tracks in 3D:
+
+<img src="docs/source/_static/probe.png" alt="probe" width="800">
+
+
+## Installation
+
+```bash
+# Option 1 — one-shot CLI install, no clone or env needed (recommended for users)
+uv tool install git+https://github.com/ytsimon2004/regrender.git
+
+# Option 2 — uv virtual environment (development)
+git clone https://github.com/ytsimon2004/regrender.git && cd regrender
+uv venv && source .venv/bin/activate
+uv pip install -e .
+
+# Option 3 — conda environment (development)
+git clone https://github.com/ytsimon2004/regrender.git && cd regrender
+conda create -n regrender python=3.12 -y && conda activate regrender
+pip install -e .
+```
+
+See the [installation docs](https://regrender.readthedocs.io/en/latest/get_start/installation.html) for details.
+
+## Quick Start
+
+```bash
+# 1. label ROIs on raw slices
+regrender roi -D <slices_dir>
+
+# 2. register each slice to the CCF
+regrender register -D <slices_dir>
+
+# 3. project ROIs to CCF + render  (or use the GUI "Project + Render" button)
+regrender roi --project --render -D <slices_dir>
+
+# probe tracks
+regrender probe -D <slices_dir>
+```
+
+See the [full documentation](https://regrender.readthedocs.io) for the complete workflow.
+
+## Contact
+
+**Yu-Ting Wei** - ytsimon2004@gmail.com

regrender-0.1.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

regrender-0.1.0/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd