Tag Archives: open source hardware

Open source neurophysiology kit

TED, a conference famous for freely sharing their talks, launched an initiative this year to share online lessons: TedEd. The idea of TedEd is to pair gifted educators with inspiring animators to produce short lessons on subjects designed to engage school-children.

As with all TED videos, these are free to share under the Creative Commons license.

The first TedEd talk introduced the SpikerBox, an open source neural recording kit, specifically designed to give students a hands-on experience with neural recording. In this case, recording the neural activity in the legs of cockroaches:


The SpikerBox is a product of BackyardBrains, founded by Greg Gage and Tim Marzullo, joined by an enthusiastic group of fellow developers.

The SpikerBox comes either pre-assembled, or in kit form, and allows for easy recording of neural activity using Audacity (open source software for recording audio). The SpikerBox can also be hooked up to a free iPhone/iPod app, and there is also an android version. The newer EMG SpikerBox (EMG=ElectroMyoGram) enables users to measure the electrical activity of their own muscles.

The Backyard Brains wiki includes a number of experiments that can be conducted with the SpikerBox, as well as a library of raw spike recordings that you can analyse, plus tools for data analysis. Intriguingly, they have also opened up their finances for all to inspect.

Three other Backyard Brains devices are in beta: a platform to turn a smartphone into a microscope (SmartScope), a device to (briefly) control the left right movements of a cockroach (RoboRoach), and a Micromanipulator for precisely placing electrodes in a cockroach brain.

BackyardBrains are currently developing a module for the EMG Spikerbox which will measure reaction time in humans using muscle contractions.

What other intriguing hardware have you seen emerging in the DIY cognitive experiment space?

(For instance, Chip Epstein makes an interesting entry into the open source neuroscience space, with a set of plans for Homebrew Do-it-yourself EEG, EKG, and EMG.)

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Tools for Psychology and Neuroscience

Open source tools make new options available for designing experiments, doing analysis, and writing papers. Already, we can see hardware becoming available for low-cost experimentation. There is an OpenEEG project. There are open source eye tracking tools for webcams. Stimulus packages like VisionEgg can be used to collect reaction times or to send precise timing signals to fMRI scanners. Neurolens is a free functional neuroimage analysis tool.

Cheaper hardware and software make it easier for students to practice techniques in undergraduate labs, and easier for graduate students to try new ideas that might otherwise be cost-prohibitive.

Results can be collected and annotated using personal wiki lab notebook programs like Garrett Lisi’s deferentialgeometry.org. Although some people, like Lisi, share their notebooks on the web (a practice known as open notebook science), it is not necessary to share wiki notebooks with anyone to receive substantial benefit from them. Wiki notebooks are an aid to the working researcher because they can be used to record methods, references and stimuli in much more detail than the published paper can afford. Lab notebooks, significantly, can include pointers to all of the raw data, together with each transformation along the chain of data provenance. This inspires trust in the analysis, and makes replication easier. Lab notebooks can also be a place to make a record of the commands that were used to generate tables and graphs in languages like R.

R is an open source statistics package. It scriptable, and can be used in place of SPSS (Revelle (2008), Baron & Li (2007)). It is multi-platform, can be freely shared with collaborators, and can import and export data in a CSV form that is readable by other statistics packages, spreadsheets, and graphing packages.

R code can be embedded directly into a LaTeX or OpenOffice document using a utility called Sweave. Sweave can be used with LaTeX to automatically format documents in APA style (Zahn, 2008). With Sweave, when you see a graph or table in a paper, it’s always up to date, generated on the fly from the original R code when the PDF is generated. Including the LaTeX along with the PDF becomes a form of reproducible research, rooted in Donald Knuth’s idea of literate programming. When you want to know in detail how the analysis was done, you need look no further than the source text of the paper itself.

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Baron, J. & Li, Y. (9 Nov 2007). ‘Notes on the use of R for psychology experiments and questionnaires.’
http://www.psych.upenn.edu/~baron/rpsych/rpsych.html

Revelle, W. (25 May 2008). ‘Using R for Psychological Research. A simple guide to an elegant package.’ http://www.personality-project.org/R/

Zahn, Ista. (2008). ‘Learning to Sweave in APA Style.’ The PracTeX Journal. http://www.tug.org/pracjourn/2008-1/zahn/