.. neurd documentation master file, created by
   sphinx-quickstart on Mon Jul 17 18:29:53 2023.
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Welcome to NEURD's documentation!
=================================

.. toctree::
    :maxdepth: 2
    :caption: Contents:
    
    modules.rst

Getting Started with NEURD
==========================
* Tutorial 1: Decomposing neuron and autoproofreading pipeline `Excitatory notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Auto_Proof_Pipeline/Single_Soma_Exc/neuron_pipeline_vp5_single_demo_exc.ipynb>`_ , `Inhibitory notebook <https://github.com/reimerlab/NEURD/tree/main/Applications/Tutorials/Auto_Proof_Pipeline/Single_Soma_Inh>`_
* Tutorial 2: Splitting multi-somas `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Auto_Proof_Pipeline/Double_Soma/neuron_pipeline_vp5_double_soma.ipynb>`_
* Tutorial 3: Exploring NEURD precomputed features: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Neuron_Features/Neuron_Features_Tutorial.ipynb>`_
* Tutorial 4: Exploring NEURD hierarchical graph representation: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Neuron_Features/Neuron_Limb_Branch_Hierarchical_Data_Structure.ipynb>`_
* Tutorial 5: Spine detection and tuning: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Spine_Detection_On_Mesh_Branch/Tuning_Spine_Detection_Parameters.ipynb>`_
* Tutorial 6: Volume Data Interface override example: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/VDI_override/Tutorial_Making_Vdi_Override_Whale.ipynb>`_
* Tutorial 7: Volume Data Interface Override CAVE client example: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/VDI_microns_caveclient/vdi_microns_caveclient_demo.ipynb>`_
* Tutorial 8: Computing Proximities: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Proximities/Tutorial_Proximities_vp2.ipynb>`_
* Tutorial 9: Computing Conversion Ratios: `notebook <https://github.com/reimerlab/NEURD/blob/main/Applications/Tutorials/Connectivity_Analysis/Connectivity_Tutorial_1_Conversion_Rate_of_Downstream_Groups.ipynb>`_





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

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