.. _spinelocalization:

Spine Localization and Classification
=====================================

.. image:: SpineLocalizationAndClassification.png

Summary
-------
Detects, segments and classifies vertebrae in a calibrated CT or MRI volume. Use this to obtain a :doc:`SpineData <../SpineData>` with vertebra positions, anatomical types (e.g., cervical/thoracic/lumbar) and levels, label maps and / or surface meshes of vertebrae, illium, sacrum and vertebral discs (MRI only).

Input
-----
- Single-volume ``SharedImageSet`` (CT/MRI), multi-volume inputs are not supported. Ensure the modality is correctly set for the input; otherwise modality can be set manually.
- Optionally a label image or existing :doc:`SpineData <../SpineData>` can be provided.

Output
------
- :doc:`SpineData <../SpineData>` with vertebra entries containing surface mesh, body center and pedicle keypoints, and vertebra label maps.

Controller capabilities
-----------------------
- Model selection: choose model set/version if needed. This can be used to select the preferred Machine Learning engine and the set (version) of machine learning models.
- Export: save state (including current :doc:`SpineData <../SpineData>`), export label maps and segmentation images after segmentation.

Workflow
--------
1) Load a CT or MRI image and (optionally) define a region of interest/bounds.
2) Localize Vertebrae: predict bounds, set bounds, detect vertebra landmarks, and classify types to create initial :doc:`SpineData <../SpineData>` entries.
3) (Optional) Edit vertebrae:
   - Add Vertebra: place body/left/right keypoints to add a vertebra.
   - Remove Vertebra: delete selected vertebra; classification updates accordingly.
   - Pin/Correct Types: pin type for selected vertebra; re-run classification.
4) (Optional) Segment structures:
   - Segment Vertebrae: segment all vertebrae; review meshes.
   - Segment Sacrum and Ilium: segment pelvis structures where supported.
   - Segment Discs (MRI only): run disc segmentation for MRI inputs.
   - Export Label Map: export a multi-label volume assembled from current segmentations.
5) (Optional) Context and masking:
   - Run Context Model: compute anatomical context predictions and add them to the data model when available. This aids the classification model in the assignment of anatomical types.
   - Apply Mask: create/apply a spine mask to the original source image.
6) (Optional) Save/Load: persist or restore the algorithm state (includes :doc:`SpineData <../SpineData>`). See :ref:`spinedata-save-load`.