.. TauRecon documentation master file, created by
   sphinx-quickstart on Fri Dec 11 08:16:39 2020.
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Pipeline for 3D Reconstruction of Tau Burden Maps from MRI and Histology
========================================================================

.. toctree::
   :maxdepth: 2

    3D Printing Cutting Molds <make_molds.md>
    Data Organization <organize_data.md>
    Data Organization (PATCH|Lab PMACS cluster) <organize_data_pmacs.md>
    WildCat Training and Whole-Slide Analysis <wildcat_train.md>
    Whole-Slide Histology Processing <wsi_proc.md>
    Managing Histology Tasks with `svs_to_cloud.sh` <svs_to_cloud.md>
    Running 3D Reconstruction <recon.md>
    Tips and Tricks <tips_and_tricks.md>

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`