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ByB Acquires New Microscope

We have good versions of our Ganglionizer (micromanipulator) and SpikerBox (amplifier), but the missing component for in vivo ganglia experiments is an inexpensive microscope. ByB saved its lunch money and recently purchased a 30X dissection scope for $60 from Benz Microscopy. Having no background in optics, ByB is rolling up its sleeves and reverse engineering a dissection scope. First step, take one apart and see how it works.

microscope

Michael Benz, the third generation owner of Benz Microscope (a very cool business in south Ann Arbor), is enthusiastically helping us design our own microscopes by letting us purchase some raw optics components from his massive workshop. Thanks Michael!


Call for Audacity to build Digital Oscilloscope Function?

ByB has had magnificent success using Audacity to view and record their neural data, and Tim has begun thinking about modifying Audacity to contain a digital oscilloscope mode. Here is what he wrote to the Audacity team:

Hi folks,

I just sent an e-mail regarding getting Audacity to work on the OLPC (one labtop per child) project, but I want to suggest/discuss a larger idea.

My colleague Greg Gage and I founded “Backyard Brains” as a startup to deliver low cost neuroscience to high schools, universities, and amateur scientists by building tools to record from the nervous system of insects.

www.backyardbrains.com

We have developed our own electronics, and we are using “Audacity” to view and record the data on labtops. This all works wonderfully on the PC and Mac, and we are currently trying to get it to work on the OLPC (re: previous discussions).

You folks at Audacity have built a very powerful audio processing tool, but you have inadvertently (or maybe intentionally) also created a very valuable scientific tool! By accessing the microphone input of any standard labtop, we can feed almost any analog signal we want from any scientific instrument we build into your very easy to use and intuitive program (with a huge array of post-processing built in). And, If we need to, we simply save our data as wav files and then do any further post-processing in Matlab.

The only thing Audacity needs to make it a killer scientific tool is a sort of “digital oscilloscope” mode with a trigger function. The youtube link below shows what neural data looks like in triggering mode.

http://en.wikipedia.org/wiki/Oscilloscope#Triggered_sweeps

http://www.youtube.com/watch?v=rXRALyENrB0

To do this would be a modification of the viewing options in Audacity. I do not know how difficult this is, but I wanted to throw it out there. We have been attempting to modify other programs to do this, but Audacity is just a much more mature program. Let me know what you think!

Sincerely,

Tim


First Recorded Spikes on the OLPC

While Greg and Evan have been working on modifying the Measure program on the OLPC (one laptop per child) in order to view and store neural data (the current build can’t store data, and it needs a trigger function and better visualization), Tim has been experimenting with the Audacity program. This is the same program we use on our PCs and Macs to view the neural data; the program is open source and has excellent signal processing capabilities (Tim has even written songs using this program).

Audacity is in its first OLPC build (you have to launch it from the terminal), but it works!

OLPC-SpikeBox-Audacity

In the picture above, you can see the SpikerBox (with a cockroach leg on it) going to the microphone input of the OLPC, and Audacity displaying the neural data. The three bursts in the center of the display are when I blew on the barbs of the cockroach leg, causing an evoked discharge in the nerves. The software works well enough for demos, but there are three things we would like to see:

1) Fixing the play-through function during monitoring and recording. Listening to the output through the computer speakers while Audacity is recording is important for our teaching purposes. Turning on “Software Playthrough” causes Audacity to only record 1/2 second then crash.

2) Saving the recorded data in the journal of the OLPC. From the save menu of Audacity, you cannot navigate to the

/home/olpc/.,sugar/default/datastore/store

directory (which is the journal directory), as the .sugar folder is invisible in Audacity. Right now we are saving to the Audacity applications folder.

3) This is a minor thing, but wrapping the Audacity program so that it can be loaded from the main OLPC application page (rather than the terminal) would be nice.

Stayed tuned. We continue our labor of love…

Audacity Output

Above is a screenshot from the OLPC. You can see the spontaneous discharge nicely (as well as when I blew on the leg on the right side of the display). Having received my chops in Mammalian Extracellular Neurophysiology, I am amazed at the signal to noise ratio of invertebrate neurons. Cockroaches have it going on!