Rata Julia

Rata Julia

Rata Julia is an application for behavioural neuroscience open field studies, fully developed using Julia[1]:

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

Rata Julia’s main function is to track rodents’s 2D position in an open field, based on video data. It performs image processing to provides other features such as a stable displacement count and a posture classification. The posture classification defines if the animal is standing or roaring. This algorithm was design for open field experiments, widely used in behavioral neuroscience, which help characterizing several domains of activity, such as displacament, exploration, and stereotypy [2]. The routine analyses one image per video frame, size 320 x 240. Each image has its contrast and rightness enhanced. Then, the pixels related to tail and head are deleted for defining the image equivalent of the animal’s center of mass. Several checkpoints were previewed to warn the user about unexpected errors. The code counts with parallel computation, using all cores a machine has.

Rata Julia is developed as part of the postdoctoral work of Carolina Brum Medeiros, PhD. for the Edmond and Lily Safra International Institute of Neuroscience. Rata Julia will soon be release under MIT License.

======== Quick facts:

* system requirements:
– cross platform: Linux, Mac OS, Windows (tested on Windows 7, Debian);
– Julia Language installed (tested on version 0.4.1)
– required packages for Julia: Images.jl, Distributions.jl, DistributedArrays.jl, FileIO.jl

* benchmark example: for 24 cores, the running time was 1 h 30 min for 144000 frames

* thanks to Dr. Mariana Araujo, Kellyn Costa, and Julia Dev Community

======== References:

[1] http://www.julialang.org (access date: January 15th, 2016).
[2] Shoji Tanaka, Jared W. Young, Adam L. Halberstadt, Virginia L. Masten, Mark A. Geyer.
“Four factors underlying mouse behavior in an open field”.
Behav Brain Research Journal. Published in final edited form as: Behav Brain Res.
2012 July 15; 233(1): 10.1016/j.bbr.2012.04.045.