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Merge pull request #4 from liuzhenqi77/enh
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‎.gitignore‎

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# Ruff
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.ruff_cache/
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uv.lock
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uv.lock
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# Claude code
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CLAUDE.local.md
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.claude/settings.local.json

‎docs/_static/theme_overrides.css‎

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/* https://stackoverflow.com/questions/56195758/different-maxdepth-for-specific-entries-in-toctree-sphinx */
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.rst-content .toctree-wrapper:not(:last-child) ul {
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margin-bottom: 12px;
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}
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/* Layout tweaks */
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.wy-nav-content {
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max-width: 1200px !important;
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}
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/* Make wide tables readable on desktop */
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@media screen and (min-width: 767px) {
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.wy-table-responsive table td {
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/* Prevent later stylesheets from re-wrapping cells */
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white-space: normal !important;
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}
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.wy-table-responsive {
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overflow: visible !important;
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}
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}
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/* Hide the hash icon that appears on hover in headings */
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.headerlink::after {
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font-size: 0;
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}
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/* Call attention to API signatures */
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dl.py.function dt,
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dl.py.class dt,
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dl.py.method dt {
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background: #f8f8f8;
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padding: 8px;
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}
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/* Paragraph readability */
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.wy-nav-content p {
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line-height: 1.5;
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}
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/* Cleaner parameter/field lists */
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.rst-content dl.field-list {
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display: grid;
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grid-template-columns: max-content 1fr;
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gap: 0 1em;
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align-items: baseline;
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}
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.rst-content dl.field-list > dd {
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align-self: center;
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}
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/* Emphasize parameter names */
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.rst-content dl.field-list dt {
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font-weight: 600;
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color: #555;
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}
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/* Signature parameter styling */
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.rst-content .sig-param .n {
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color: #333;
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}
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.rst-content .sig-param .default_value {
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color: #666;
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}
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/* Link styling */
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.rst-content a {
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color: #2980b9;
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}
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.rst-content a:hover {
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color: #1a5276;
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}
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/* Tighter list spacing inside field-list items */
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.rst-content dl.field-list dd ul li > p,
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.rst-content dl.field-list dd ul li > ul {
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margin-top: 0 !important;
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margin-bottom: 0 !important;
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}
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/* Highlight the current page in the sidebar */
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.wy-menu-vertical li.current > a {
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background: #fcfcfc;
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border-left: 3px solid #2980b9;
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}
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/* Inline code styling */
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.rst-content code.literal {
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background: #f0f0f0;
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padding: 2px 4px;
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border-radius: 3px;
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border: none;
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font-size: 85%;
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}
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/* Code block styling */
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.rst-content div[class^="highlight"] {
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background: #f8f8f8;
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border-radius: 4px;
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}
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.rst-content div[class^="highlight"] pre {
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font-size: 13px;
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line-height: 1.5;
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}

‎docs/api.rst‎

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.. _ref_images:
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:mod:`neuromaps_mouse.images` - Image and surface handling
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----------------------------------------------------------
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:mod:`neuromaps_mouse.images` - Image processing
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-------------------------------------------------
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.. automodule:: neuromaps_mouse.images
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:no-members:
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:no-inherited-members:
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.. currentmodule:: neuromaps_mouse.images
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.. autosummary::
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:template: function.rst
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:toctree: generated/
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parcellate_image
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register_image
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transform_image
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.. _ref_io:
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:mod:`neuromaps_mouse.io` - Image and surface handling
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------------------------------------------------------
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.. automodule:: neuromaps_mouse.io
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:no-members:
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:no-inherited-members:
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.. currentmodule:: neuromaps_mouse.io
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Functions to load the images and surfaces
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plot_allenccfv3_lightbox
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plot_allenccfv3_3d
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.. _ref_resampling:
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.. _ref_regions:
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:mod:`neuromaps_mouse.resampling` - Resampling workflows
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--------------------------------------------------------
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.. automodule:: neuromaps_mouse.resampling
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:mod:`neuromaps_mouse.regions` - Region queries and alignment
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-------------------------------------------------------------
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.. automodule:: neuromaps_mouse.regions
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.. currentmodule:: neuromaps_mouse.resampling
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.. currentmodule:: neuromaps_mouse.regions
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:toctree: generated/
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correlation
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moran
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.. _ref_transforms:
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:mod:`neuromaps_mouse.transforms` - Transformations between spaces
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------------------------------------------------------------------
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.. automodule:: neuromaps_mouse.transforms
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.. currentmodule:: neuromaps_mouse.transforms
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.. autosummary::
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:template: function.rst
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:toctree: generated/
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allenccfv3_to_allenccfv3

‎docs/installation.rst‎

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Requirements
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============
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TBD
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This package requires Python >= 3.8.
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.. _installation_basic:
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Basic installation
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==================
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Assuming you have the correct version of Python installed, you can install
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`neuromaps-mouse` by opening a terminal and running the following:
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.. code-block:: bash
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git clone https://github.com/netneurolab/neuromaps-mouse.git
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cd neuromaps-mouse
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pip install .
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.. _installation_optional:
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Optional dependencies
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=====================
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Some functionality in neuromaps-mouse requires additional dependencies.
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Pyvista
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-------
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Pyvista is the plotting library used in the package for 3D surface visualization.
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This will allow you to use functions like
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* :func:`neuromaps_mouse.plotting.plot_allenccfv3_3d`
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You will need a working Pyvista installation. We recommend using a clean conda
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environment and installing Pyvista using the following commands:
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.. code-block:: bash
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conda create -n plotting python=3.12
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conda activate plotting
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conda install -c conda-forge pyvista
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Pyvista is actively maintained and generally installs without issues. Please
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also check out their `detailed installation guide <https://docs.pyvista.org/getting-started/installation.html>`_.
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Pyvista is built on top of VTK, which supports multiple OpenGL window backends
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and you can choose one that fits your environment (see the `VTK runtime settings <https://docs.vtk.org/en/latest/advanced/runtime_settings.html>`_):
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* **X11**: standard Linux display server (requires an active X server)
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* **Win32**: native Windows OpenGL context
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* **EGL**: offscreen GPU context (good for headless servers with GPUs)
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* **OSMesa**: CPU-based software rendering (good for headless servers without GPUs)
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For example, on a headless Linux server without a GPU you can request OSMesa by
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setting the backend before importing PyVista/VTK:
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.. code-block:: python
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import os
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os.environ["VTK_DEFAULT_OPENGL_WINDOW"] = "vtkOSOpenGLRenderWindow"

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