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AllenInstitute / mouse_connectivity_models

Python package providing mesoscale connectivity models for mouse.
http://mouse-connectivity-models.readthedocs.io/en/latest/
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neuroscience open-science python scikit-learn

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mouse_connectivity_models

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.. image:: cortical_projection.gif

mouse_connectivitymodels is a Python module for constructing and testing mesoscale connectivity models using data from the Allen Institute for Brain Science <https://brain-map.org>.

It provides models written in Scikit-Learn <http://scikit-learn.org>_ estimator style, and has been used in the following publications:

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 <https://git-scm.com/> for our version control and Github <https://github.com/> for hosting our main repository.

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

$ git clone git@github.com: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 <https://github.com/AllenInstitute/ mouse_connectivity_models/blob/master/CONTRIBUTING.md>_, then refer to the contributing guide <http://AllenInstitute.github.io/mouse_connectivity_models/ contributing.html>_.

Installing the dev requirements

Use `pipenv <https://github.com/pypa/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 <https://pytest.org>_ ::

$ pytest mcmodels

Help and Support

Documentation


The documentation that supports mouse_connectivity_models can be found at the
`Website <http://mouse-connectivity-models.readthedocs.io/en/latest/>`_.