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https://github.com/alleninstitute/mouse_connectivity_models

Python package providing mesoscale connectivity models for mouse.
https://github.com/alleninstitute/mouse_connectivity_models

neuroscience open-science python scikit-learn

Last synced: 17 days ago
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Python package providing mesoscale connectivity models for mouse.

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README 

        
.. -*- mode: rst -*-



mouse_connectivity_models

=========================



|Travis|_ |Codecov|_ |Readthedocs|_



.. |Travis| image:: https://travis-ci.org/AllenInstitute/mouse_connectivity_models.svg?branch=master

.. _Travis: https://travis-ci.org/AllenInstitute/mouse_connectivity_models



.. |Codecov| image:: https://codecov.io/gh/AllenInstitute/mouse_connectivity_models/branch/master/graph/badge.svg

.. _Codecov: https://codecov.io/gh/AllenInstitute/mouse_connectivity_models

.. |Readthedocs| image:: https://readthedocs.org/projects/mouse-connectivity-models/badge/?version=latest

.. _Readthedocs: http://mouse-connectivity-models.readthedocs.io/en/latest/?badge=latest



.. image:: cortical_projection.gif



mouse_connectivity_models is a Python module for constructing and testing

mesoscale connectivity models using data from the `Allen Institute for Brain

Science `_.



It provides models written in `Scikit-Learn `_

``estimator`` style, and has been used in the following publications:



- `High resolution data-driven model of the mouse connectome

  `_



**Download**: http://download.alleninstitute.org/publications/A_high_resolution_data-driven_model_of_the_mouse_connectome/



**Website**: http://mouse-connectivity-models.readthedocs.io/en/latest/



Installation

------------



Dependencies

~~~~~~~~~~~~



mouse_connectivity_models requires:



- Python (>=2.7 or >= 3.4)

- scikit-learn (>= 0.22.1)

- allensdk (>= 2.10.1)



For running the examples Matplotlib >= 1.3.1 is required.



We have only tested and used this package on Linux.



User installation

~~~~~~~~~~~~~~~~~



We use `Git `_ for our version control and `Github

`_ for hosting our main repository.



You can check out the latest sources and install using ``pip``::



    $ git clone [email protected]:AllenInstitute/mouse_connectivity_models.git

    $ cd mouse_connectivity_models

    $ pip install .



Level of Support

----------------

We are not currently supporting this code, but simply releasing it to the

community AS IS but are not able to provide any guarantees of support. The

community is welcome to submit issues, but you should not expect an active

response.



Contributing

------------

We encourage the community to contribute! Please first review the `Allen

Institute Contributing Agreement `_, then refer to the

`contributing guide `_.



Installing the ``dev`` requirements

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Use `pipenv `_ to install the ``dev``

dependencies. If you do not have ``pipenv`` currently installed ::



   $ pip install pipenv



Then install ``dev`` dependencies ::



   $ pipenv install --dev



This will create a virtual environment on your machine for this project. To

activate the virtual environment (to develop) ::



   $ pipenv shell



Testing

~~~~~~~



After installation, you can launch the test suite from outside the source

directory (``mcmodels``) using `pytest `_ ::



   $ pytest mcmodels



Help and Support

----------------



Documentation

~~~~~~~~~~~~~

The documentation that supports mouse_connectivity_models can be found at the

`Website `_.