Metadata-Version: 2.1
Name: NeuroR
Version: 1.1.2
Summary: A morphology repair tool
Home-page: https://github.com/bluebrain/neuror
Author: Blue Brain Project, EPFL
License: LGPLv3
Description: |banner|
        
        |build| |license| |docs| |doi|
        
        NeuroR
        ======
        
        Introduction
        ------------
        
        NeuroR is a collection of tools to repair morphologies.
        
        You can try NeuroR's functionality on MyBinder:
        
        - Cut-plane detection - |cutplane|
        - Morphology repair - |repair|
        
        Citation
        --------
        
        Cite NeuroR with the following DOI: |doi|
        
        NeuroR implements the methods discussed in the following paper:
        
           Anwar H., Riachi I., Schürmann F., Markram H. (2009). “An approach to capturing neuron morphological diversity,”
           in Computational Neuroscience: Realistic Modeling for Experimentalistsed. De Schutter E.,
           editor. (Cambridge: The MIT Press) 211–232
        
           `DOI: 10.7551/mitpress/9780262013277.003.0010 <https://doi.org/10.7551/mitpress/9780262013277.003.0010>`__
        
        Morphology repair with NeuroR
        -----------------------------
        
        There are presently three types of repair which are outlined below.
        
        Sanitization
        ~~~~~~~~~~~~
        
        This is the process of curating a morphological file. It currently:
        
        - removes zero-length segments
        - raises if the morphology has no soma
        - raises if the morphology has negative diameters
        
        Note: more functionality may be added in the future
        
        
        Cut plane repair
        ~~~~~~~~~~~~~~~~
        
        The cut plane repair aims at regrowing part of a morphologies that have been cut out
        when the cell has been experimentally sliced.
        
        ``neuror cut-plane repair`` contains the collection of CLIs to perform this repair.
        
        Additionally, there are CLIs for the cut plane detection and writing detected cut planes to
        JSON files:
        
        - If the cut plane is aligned with one of the X, Y or Z axes, the cut plane detection
          can be done automatically with the CLIs:
        
        .. code-block:: shell
        
           neuror cut-plane file
           neuror cut-plane folder
        
        - If the cut plane is not one the X, Y or Z axes, the detection has to be performed
          through the helper web application that can be launched with the following CLI:
        
        .. code-block:: shell
        
           neuror cut-plane hint
        
        Unravelling
        ~~~~~~~~~~~
        
        Unravelling is the action of "stretching" the cell that has been shrunk because of the dehydratation caused by the slicing.
        
        The unravelling CLI sub-group is:
        
        .. code-block:: shell
        
           neuror unravel
        
        .. admonition:: Info
           :class: info
        
           Unravelling is also part of the "full" process that performs unravelling and cut plane repair.
           The corresponding CLI is:
        
           .. code-block:: shell
        
              neuror cut-plane repair full
        
        The unravelling algorithm can be described as follows:
        
        * Segments are unravelled iteratively.
        * Each segment direction is replaced by the averaged direction in a sliding window around this segment.
        * The original segment length is preserved.
        * The start position of the new segment is the end of the latest unravelled segment.
        
        Installation
        ------------
        
        NeuroR is distributed as a Python package available on PyPi:
        
        .. code-block:: console
        
            $ pip install --pre neuror[plotly]
        
        Note: NeuroR relies on the experimental version 2 of NeuroM, hence the ``--pre`` option.
        
        Only Python 3.6 and above are supported.
        
        Prior to running ``pip install``, we recommend updating ``pip`` in your virtual environment unless you have a compelling reason not to do it:
        
        .. code:: console
        
            $ pip install --upgrade pip setuptools
        
        Contributing
        ------------
        
        If you want to improve the project or you see any issue, every contribution is welcome.
        Please check the `contribution guidelines <https://github.com/BlueBrain/NeuroR/blob/master/CONTRIBUTING.md>`__ for more information.
        
        License
        -------
        
        NeuroR is licensed under the terms of the GNU Lesser General Public License version 3.
        Refer to `COPYING.LESSER <https://github.com/BlueBrain/NeuroR/blob/master/COPYING.LESSER>`__
        and `COPYING <https://github.com/BlueBrain/NeuroR/blob/master/COPYING>`__ for details.
        
        .. |build| image:: https://travis-ci.com/BlueBrain/NeuroR.svg?branch=master
                      :target: https://travis-ci.com/BlueBrain/NeuroR
        
        .. |license| image:: https://img.shields.io/pypi/l/neuror
                        :target: https://github.com/BlueBrain/NeuroR/blob/master/COPYING.LESSER
        
        .. |docs| image:: https://readthedocs.org/projects/neuror/badge/?version=latest
                     :target: https://neuror.readthedocs.io/en/latest/?badge=latest
                     :alt: Documentation Status
        
        .. |doi| image:: https://zenodo.org/badge/244944511.svg
                    :target: https://zenodo.org/badge/latestdoi/244944511
        
        .. |cutplane| image:: https://mybinder.org/badge_logo.svg
                         :target: https://mybinder.org/v2/gh/BlueBrain/NeuroR/master?filepath=examples%2Fcut-plane-detection.ipynb
        
        .. |repair| image:: https://mybinder.org/badge_logo.svg
                       :target: https://mybinder.org/v2/gh/BlueBrain/NeuroR/master?filepath=examples%2Frepair.ipynb
        
        .. substitutions
        .. |banner| image:: doc/source/_images/BlueBrainNeuroR.png
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: plotly
Provides-Extra: docs
