.. _tissues:

Tissues (dosma.tissues)

================================================================================

This page details the different tissues that are supported by DOSMA and briefly

explains the methods used for analysis and visualization.

Tissues are loosely defined as structures of interest in anatomical regions.

For example, both the femur and femoral cartilage are considered tissues are tissues

of the knee.

DOSMA currently supports 4 tissues:

1. Femoral cartilage (fc)

2. Tibial cartilage (tc)

3. Patellar cartilage (pc)

4. Meniscus (men)

Different tissues have different quantitative profiles, visualization methods, and

analysis techniques. The modules for the supported tissues implement and use these

differences for analysis of each tissue.

.. automodule::

   dosma.tissues

.. autosummary::

   :toctree: generated

   :nosignatures:

   dosma.tissues.FemoralCartilage

   dosma.tissues.TibialCartilage

   dosma.tissues.PatellarCartilage

   dosma.tissues.Meniscus

Femoral Cartilage

---------------------------------------------------------------------------------

Femoral cartilage has been closely studied for evaluating knee health. The structure

is often divided into sub-regions to evaluate the sensitivity of different regions of

the knee to chronic diseases such as osteoarthritis. These regions are identified by

three planes (12 regions):

1. **Sagittal**: Medial, Lateral

2. **Coronal**: Anterior, Central, Posterior

3. **Depth**: Deep, Superficial

For example, the deep-anterior-medial femoral cartilage tissue is one region.

To analyze differences in these regions, |T2| maps can be unrolled onto a 2D plane :cite:`monu2017cluster`.

DOSMA supports automatic division of femoral cartilage into these regions and unrolling of these regions.

Unrolled maps are produced for deep, superficial, and total (combined deep and superficial) layers as seen below.

.. figure:: figures/unrolled_fc.png

   :align: center

   :alt: Unrolled femoral cartilage |T2| maps

   :figclass: align-center

Tibial Cartilage

--------------------------------------------------------------------------------

Tibial cartilage is a flatter surface and is often divided across the three common

planes:

1. **Sagittal**: Medial, Lateral

2. **Coronal**: Anterior, Central, Posterior

3. **Axial**: Deep, Superficial

DOSMA automatically divides the tissue into these regions and produces corresponding

visualizations.

Patellar Cartilage

--------------------------------------------------------------------------------

Patellar cartilage is a thin, flat tissue. Because of this structure, it is not often

divided. However, there has been work that may suggest that deep/superficial differences

in the patellar cartilage may be insightful.

DOSMA divides patellar cartilage into deep/superficial layers across the coronal plane.

Meniscus

--------------------------------------------------------------------------------

DOSMA supports quantitative processing and segmentation of the mensiscus.

However, visualization for the meniscus is not yet supported.

.. Substitutions

.. |T2| replace:: T\ :sub:`2`

.. |T1| replace:: T\ :sub:`1`

.. |T1rho| replace:: T\ :sub:`1`:math:`{\rho}`

.. |T2star| replace:: T\ :sub:`2`:sup:`*`