.. toctree::
   :maxdepth: 3
   :caption: Home

   index.rst

.. toctree::
   :maxdepth: 3
   :caption: Installation

   installation/installation

.. toctree::
   :maxdepth: 2
   :caption: Getting started

   getting_started/first_registration.md

.. toctree::
   :maxdepth: 2
   :caption: User guide

   guide/prepare_qupath_project.md
   guide/start_and_import.md
   guide/abba_window.md
   guide/select_display_slices.md
   guide/orient_slices.md
   guide/position_along_atlas.md
   guide/inplane_registration.md
   guide/save_load_share.md
   guide/export_results.md
   guide/qupath_analysis.md

.. toctree::
   :caption: See also

   Whole-brain analysis with BraiAn <https://silvalab.codeberg.page/BraiAn/>

.. toctree::
   :maxdepth: 2
   :caption: Reference

   reference/menu_reference.md
   reference/shortcuts.md
   reference/file_formats.md
   reference/state_files.md

.. toctree::
   :maxdepth: 2
   :caption: Cite

   cite.md

.. toctree::
   :maxdepth: 2
   :caption: Help

   frequently_asked_questions.md

.. toctree::
   :maxdepth: 2
   :caption: Other resources

   resources/demo_dataset.md
   resources/video_tuto.md
   resources/slides_tuto.md