PyMICE

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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 that reference to our paper as well as to the library itself is
provided in any published research making use of PyMICE.

The recommended in-text citation format is: PyMICE (Dzik, Puścian, et al. 2017) v. 1.2.0 (Dzik, Łęski, & Puścian 2017)

and the recommended bibliography entry format:

Dzik J. M., Łęski S., Puścian A. (July 21, 2017) “PyMICE” computer software
(v. 1.2.0; RRID:nlx_158570) doi: 10.5281/zenodo.832982

Dzik J. M., Puścian A., Mijakowska Z., Radwanska K., Łęski S. (June 22, 2017)
“PyMICE: A Python library for analysis of IntelliCage data” Behavior Research
Methods doi: 10.3758/s13428-017-0907-5

If the journal does not allow for inclusion of the resource identifier (RRID:nlx_158570) in the bibliography, we ask to provide it in-text:

PyMICE (RRID:nlx_158570) [1] v. 1.2.0 [2]

1. Dzik JM, Puścian A, Mijakowska Z, Radwanska K, Łęski S. PyMICE: A Python library for analysis of IntelliCage data. Behav Res Methods. 2017. DOI: 10.3758/s13428-017-0907-5
2. Dzik JM, Łęski S, Puścian A. PyMICE [computer software]. Version 1.2.0. Warsaw: Nencki Institute – PAS; 2017. DOI: 10.5281/zenodo.832982

We have provided a solution to facilitate referencing to the library. Please
run:

>>> help(pm.Citation)

for more information (given that the library is imported as pm).


Installation

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

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

PyMICE tutorials

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).