PyMICE

PyMICE is a Python® library for mice behavioural data analysis.

The library can be used for loading and analysing of data obtained from IntelliCage™ system in an intuitive way in Python programming language.

The library provides user with an object oriented application programming interface (API) and a data abstraction layer. It also comes with auxiliary tools supporting development of analysis workflows, like data validators and a tool for workflow configuration.

We do recommend to use the PyMICE library with the Anaconda Python distribution (available at http://continuum.io/downloads website).


Citation

We ask that PyMICE resource identifier (RRID:nlx_158570) is provided in any published research making use of PyMICE.


Installation

PyPI badge
The library is available as a package from the Python Package Index (PyPI). You can install it with pip command:
$ pip install PyMICE
or
$ easy_install PyMICE

build badge
You can also download a bleeding edge version of PyMICE from GitHub: https://github.com/Neuroinflab/PyMICE

In case you use Windows™ operating system and get the following error message on installation:
error: Unable to find vcvarsall.bat
try to install the Microsoft Visual C++ Compiler for Python 2.7:
https://www.microsoft.com/en-us/download/details.aspx?id=44266
This blog entry might be also helpful for users of Python 3:
http://blog.ionelmc.ro/2014/12/21/compiling-python-extensions-on-windows/


Online documentation

Online documentation is available at the PyMICE GitHub documentation page.


Tutorials

For Python 2.7:

For Python 3.3+:

 

You can also download the tutorials via Dropbox: https://www.dropbox.com/s/hscyf6db4nb0c30/PyMICEtutorial.zip?dl=1 in a form of Jupyter notebooks. You can start working with them just by typing

$ jupyter notebook

command in the directory they were extracted to.

For more details about working with Jupyter notebooks please see the http://jupyter.org/ website.


Security

Since PyMICE 0.2.1 the packages available in Python Package Index are PGP signed, however it seems that neither pip nor easy_install checks the signature.

Feel free to download the packages and their signatures from the PyPI website and verify their integrity with the following public key:

PGP public key

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Authors

  • The library
    • Jakub Mateusz Dzik a.k.a. Kowalski
    • Szymon Łęski
  • Tutorial data
    • Alicja Puścian (Laboratory of Emotions Neurobiology)

Acknowledgement

JD and SŁ supported by Symfonia NCN grant: UMO-2013/08/W/NZ4/00691.

AP supported by a grant from Switzerland through the Swiss Contribution to the
enlarged European Union (PSPB-210/2010 to Ewelina Knapska and Hans-Peter Lipp).