Tag: behavior

Open source animal behaviour monitoring

In the last issue of the Journal of Neuroscience Methods (impact factor: 1.5), 3 papers deal with animal behaviour monitoring and 2 of them introduce open source software.

Roseanna Ramazani and her colleagues “designed an automated system for the collection and analysis of locomotor behavior data, using the IEEE 1394 acquisition program dvgrab, the image toolkit ImageMagick and the programming language Perl” [1]. What is interesting is that they highlight the longevity and reliability of open source software, leaving behing the simplistic view “open source = free as in free beer”:

Some of these previous methods might have been able to meet our needs. Unfortunately, these previous programs are no longer available and all use proprietary software and/or hardware that no longer exists. The methods that we describe use only open source software tools and run interchangeably on different hardware platforms (we have used Mac OSX, Windows XP and Linux, although the data in this paper was all analyzed with a computer running Linux). Open source tools tend to have greater permanence than closed source since they are maintained by communities and they can be modified by the end user. It also is not limited to a single camera system or computer platform. It is readily available to the public, and can be modified by future users, provided that they have a general understanding of the programming language Perl.

In a second paper, Ganea and colleagues describe “a novel home cage activity counter for the recording of basal activity in rodents” [2]. It is not open source but they describe a system similar to Gemvid (my system) and they even don’t cite it! They submitted their paper after mine was published and they even cite Pasquali’s paper which describe a similar method and was published in the same journal as Gemvid. But maybe, if they would have cited my paper, their discussion about cost, limitation to light phase of circadian phase and special hardware would fizzle out 😉

In a third paper, Jonathan Peirce introduce a “Psychophysics software in Python” [3]. I must admit I didn’t know what is a “psychophysics software” until I read the paper and visited the website: http://www.psychopy.org.

So, it seems open source software slowly gain more and more attention in biomedical science … (when I started my Ph.D., nearly no one spoke about open source software, open access to scientific litterature neither, btw).

[1] R.B. Ramazani, H.R. Krishnan, S.E. Bergeson and N.S. Atkinson, “Computer automated movement detection for the analysis of behavior” Journal of Neuroscience Methods 162 (1-2): 171-179
[2] K. Ganea, C. Liebl, V. Sterlemann, M.B. Müller and M.V. Schmidt, “Pharmacological validation of a novel home cage activity counter in mice” Journal of Neuroscience Methods 162 (1-2): 180-186
[3] J.W. Peirce, “PsychoPy—Psychophysics software in Python” Journal of Neuroscience Methods 162 (1-2): 8-13