Anatomical Structure Collection (ASC)
======================================

Summary
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``AnatomicalStructureCollection`` (ASC) holds anatomical structures (e.g., vertebrae, ribs, organs) and their associated data. Use ASC as the primary data model for Anatomy workflows (registration, projection, deformation).

Contents
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- Structures: collection of ``AnatomicalStructure`` objects.
- Key-value stores: images, meshes, keypoints, planes, point clouds, splines.
- Properties and display options (e.g., style sheets, alpha).
- See :doc:`Algorithms/ASCViewer` for how to access and export the data stored in the ASC.

.. image:: images/Anatomical-Structures.png

Generic ASC
-----------
A "Generic ASC" is a flexible ASC without anatomy-specific subclasses. It lets you:

- Represent arbitrary anatomical structures by identifier (no predefined class required).
- Attach the same kinds of data as any ASC (meshes, images, keypoints, splines, planes, point clouds).
- Use general-purpose algorithms (e.g., ASC Registration, ASC Projection) without needing a dedicated type.

Typical use cases: quick prototyping, importing data from external sources that don’t map to a built-in structure, or building composite scenes. It saves/loads exactly like any other ASC.


ASC Sets
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An ``ASCSet`` is a container that holds multiple ``AnatomicalStructureCollection`` objects together as a single data item. ASC Sets can be saved/loaded as single files and work with algorithms like :doc:`Algorithms/ASCIo` for import/export operations. Individual ASCs within a set remain independently accessible while benefiting from unified data management.

Anatomical Structures
---------------------
Each entry in an ASC is an ``AnatomicalStructure`` identified by a stable string (e.g., "L3", "Sacrum"). Structures expose the same standard data containers:

- Images, meshes, keypoints, planes, point clouds, splines
- Attributes/properties and per-element display options

Subclasses may exist for specific anatomies (e.g., ``Sacrum``), but ASCs work uniformly with generic structures where no subclass is required.

Style Sheets
------------
.. image:: images/AnatomyStyleSheets.png

The AnatomyPlugin uses a CSS-inspired style sheet system to control the visual appearance of anatomical structures and their associated data (meshes, keypoints, planes, etc.). Style sheets provide flexible, rule-based styling that can:

- Target specific structures: Use selectors to match anatomical structures by identifier (e.g., "L3", "liver"), content type (mesh, keypoint, plane), or custom attributes.
- Apply visual properties: Set colors, transparency, visibility, line width, point size, and other display properties.
- Apply conditional styling based on states like ":focus", ":selected", or ":highlighted".
- Enable/disable dynamically: Toggle entire style sheets on/off to switch between different visualization modes.

Style sheets use a selector-declaration syntax similar to CSS. For example, a rule might target all meshes with or specific structures. The system supports wildcards, attribute matching, and complex selectors for fine-grained control over anatomical visualizations.

Use the `Anatomy -> Inspect Style Sheets` controller to browse, edit, and preview style changes in real-time.

Save and load
-------------
- Save/load ASC and ASC sets using right-click menu `Export -> ASC File` as `.imf` (recommended) or as `.zip` file to export the contents of the ASCs using industry-standard formats.

See also
--------
- :doc:`Algorithms/ASCViewer` for inspecting and editing structures.
- :doc:`Algorithms/ASCRegistration` for aligning two ASCs.
- :doc:`Algorithms/ASCProjection` for rendering projections.