.. include:: modules/header.rst

Preprocessing pipeline documentation
====================================
These pages contain documentation for the Kleinfeld lab's brain preprocessing pipeline.
Specifically, the documentation includes:

* A description of all necessary modules, classes and methods.
* A high level description of the pipeline (non technical documentation).
* A description of all the steps in the process (technical documentation).
* Instructions on installing the necessary software.
* A HOWTO set of instructions to run the actual steps of the pipeline.


Use the side navigation panel to view different documentation topics within this topic.

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.. toctree::
   :titlesonly:
   :maxdepth: 4
   :caption: Preprocessing pipeline
   :hidden:

   modules/data_ingestion.rst
   modules/masking_scripts.rst
   modules/pipeline_scripts.rst
   modules/registration_scripts.rst
   modules/pipeline_utilities.rst
   modules/high_level_description_of_preprocessing_pipeline.rst
   modules/description_czi_2_neuroglancer.rst
   modules/software_installation.rst
   modules/running_czi_2_neuroglancer.rst
   modules/database_models.rst
   modules/controllers.rst
   modules/image_manipulation.rst
   modules/cell_labeling.rst


   
Indices and modules
~~~~~~~~~~~~~~~~~~~

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