Backyard Brains » Education

SpikerBox Manuscript Published in PLoS ONE, freely available to educators/scientists everywhere

Tim — Thu, 22 Mar 2012 21:27:55 +0000

We are pleased to announce that our manuscript formally describing the SpikerBox development, four experiments, and some classroom deployments, was released yesterday in PLoS ONE. Notably, this journal does not charge to view articles, so people anywhere around the world can download, read, use, and critique the work free of charge. How is this possible? The publication fees are supported by the scientific community. In our case, we subsidized the publication through a Kickstarter Project with the generous help of 53 backers. We champion open science hardware and public access to science, so it was especially rewarding for us to to publish, after peer review, this crowd-sourced, open-access, open-source hardware manuscript. Read away fellow colleagues!

Marzullo TC, Gage GJ (2012) The SpikerBox: A Low Cost, Open-Source BioAmplifier for Increasing Public Participation in Neuroscience Inquiry. PLoS ONE 7(3): e30837. doi:10.1371/journal.pone.0030837

First Production Manipulator Shipped, Hecho en Chile, Printed with MakerBot

Tim — Mon, 12 Mar 2012 18:11:46 +0000

If you’ve followed us over the past couple years, you’ll know we have been slowly working on a MicroManipulator to allow you to do more precise neural recordings instead of just “blindly” inserting electrodes in a cockroach leg, cricket, or earthworm. We’ve had prototypes of manipulators for about as long as we’ve been in existence, but the problem was that they took so dang long to build (about a week) and would break easily.

So, we’ve never worked beyond the working prototype stage of the manipulator as it was just too hard to produce reliably. Until today. Those “in the know” are familiar with a new technology that is taking over the hacker/Maker scene: The MakerBot! It’s a consumer grade 3D printer that allows you to design objects in programs in SketchupUp, Rhino, or AutoDesk 123 and print them on your tabletop device. Few technologies have we witnessed over the past few years that are as exciting as this one. With the MakerBot, we were able to reduce the number of pieces (not counting screws) from 21 to 5, and assembly time from a week to half a day and decreasing. Here’s what it looks like, with a video.

Click here to view the video on YouTube.

Compare it to one of our earlier prototypes from ~two years ago.

We shipped this first production unit to our friends Mohsen Omrani and Ethan Hemming at Queen’s University at Kinston, Ontario, who are testing it in their undergraduate neuroscience lab course. We have 1-2 more design tweaks to implement, and then we plan to begin offering it for sale in 2-4 weeks, first in preassembed form and eventually in kit form (both will be priced similarly to the SpikerBox). Stay tuned! And yes, as with our all inventions, this is open-source. We will post all our .stl files and schematics so you can print it on your own 3D printer if you like.

We want to thank our new colleague Tiburcio De La Carcova for helping tremendously with the design and production over the last intense two weeks as we raced to complete the unit in time for Mohsen. Tiburcio is a lifelong hardware freak and co-founder of videogame company Atakama Labs in Santiago, Chile.

Though we haven’t formally announced it yet, we are currently spending some time back-and-forth between Michigan and Chile on a “StartUp Chile” fellowship to bring neuroscience to the schools and students of South America. Notably, this manipulator was “Hecho en Chile” in a brand new hackerspace Tiburcio is building to encourage invention in Santiago. ¡Viva la NeuroRevolucion! Tú vas a ver más español en nuestro sitio web en breve……

“Cerebros del patio trasero” visita a Tejas del Oeste y lleva potenciales de acción al desierto

Tim — Wed, 25 Jan 2012 21:08:51 +0000

We are proud to have run many workshops in the Midwest, but co-founder Tim has longed to bring spikes to the Texas plains he recalls from his early years (he graduated from high school in El Paso and went to college in Austin). Thus, it was with great delight when Emily Verla Bovino, artist-in-residence with Fieldwork: Marfa and graduate researcher at UC-San Diego, invited Backyard Brains to come down and help run a workshop at Marfa Independent High School, deep in West Texas. To those not in the know, West Texas has the least light pollution in the lower 48 states, is terrific for astronomical observation, and is the “kind of Texas” you’d imagine if you’ve never visited.

___________________

______________

photos by Backyard Brains

The Marfa High School visit ran over two days the week before Christmas. The school is rather small with a total enrollment of ~100 students, so in a marathon session facilitated by Emily and both the arts and physics teachers, Tim lectured to all four classes: Freshman at 8 AM, Sophomores at 9 AM, Juniors at 10 AM, and Seniors at 11 AM! He presented principles of neurotechnology interspersed with neural recording and stimulation experiments, closing with a brief discussion of entrepreneurship.

Following the lectures/demos on neuroscience, the workshop began in the afternoon, where with the organization of art teacher Ellie Meyer, the sixteen students of teacher Benjie Rosaldo’s Robotics Class learned about analog electronics and built their own SpikerBoxes. This took place over two afternoons, and after we identified and fixed the usual errors of shorts and the occasional incorrectly-placed resistors, we concluded with the cricket drug experiments and demo’s of the RoboRoach. Some of the students learning the art of ranching part-time, we noted the comfort level with the bugs was higher than other workshops we have run…

photos by Emily Verla Bovino

During the second day of the workshop, we also had a live radio interview along with students Zach Madrid and Eileen Cordova. You can listen to our interview with station manager Tom Michael on KRTS Marfa Public Radio below:

Notably, our spikes in the studio were transmitted live across the land! A running joke from our graduate school days, and even today, is the question we often receive: “Have you ever thought of making your [insert invention/technique here] wireless?” For example, a “wireless” SpikerBox would interface with a computer or smartphone without the need of a cable. We hereby announce that “Yes We Can. The SpikerBox can go wireless!” By hooking up the SpikerBox to Marfa Public Radio’s 5,000 Watt radio tower, Spikes were broadcast over 15,000 square miles to listeners in the West Texas desert. Contact us if you are interested in purchasing your own 5,000 Watt Radio Tower to accompany your SpikerBox, but be aware of certain FCC regulations

photo by Backyard Brains

During our stay in Marfa, Emily’s three month residency at Fieldwork: Marfa was at its end. Her artistic “fieldwork” involved research for an episode in the epic life-log of a fictional character that Emily calls the “hyperthymestic RK”. In the episode, the second of a never-ending series (contact her if you would like a screening of the first installment online at rk-log.net) the character RK travels to a heterotopian West Texas of the near future to participate as a human subject in clinical studies. Emphasis in these studies is on neural engineering, specifically optogenetics and nanorobotics. The scenario for episode two, a scenography and audio-drama which Emily is now in the process of editing, was presented at the local Honky Tonk Bar “Padre’s”, an initiative owned and run by the multihyphenate David Beebe. We ran some demos of spikes to set the scene for a story of unmanned border check points patrolled remotely with battling transgenic beetles and cockroaches engineered in neurotech land yacht flexlabs.

Photo by Backyard Brains

The whole visit was quite fruitful on both the art and science fronts, and we are exploring how to make our visit to West Texas a yearly Fall tradition. West Texas, with it’s unique geography and open skies, has an expansive effect on the mind that many brain-workers, including the cosmologists Donald Judd and Carl Sagan, have been attracted to. Thus, with Emily, we are brainstorming ways to begin a “Looking Outward, Look Inward” yearly fall workshop. West Texas already has the famous McDonald Observatory to understand the universe beyond, so why not also make the borderlands a place to understand the universe within?

Unique work spaces are abundant in West Texas and should appeal to the numerous DIYbio groups that have cropped up across the country in recent years. As the trip wound down, Emily arranged for Tim to run experiments in Padre’s vintage airstream land yacht on ranch land just a few miles west of the landmark Marfa eateries Mando’s and Alice’s Cafe. Though Tim didn’t get the chance to taste Mando’s chile rellenos or Alice’s huevos rancheros, he did eat a “Marfa burrito”, went hunting for “fragile cockroaches”on the banks of the Rio Grande and even got to debug student boards with unidentified circuit shorts in the airstream.

Stay tuned. ¡Bienvenidos al futuro! ¿Que descubrimientos de los picos, nos esperan en el porvenir?

Photo by Backyard Brains

Photo by Emily Verla Bovino

Acknowledgements: We thank the Burns Family, Marfa Studio for the Arts, Fieldwork: Marfa, The Marfa National Bank, and Padre’s Marfa for sponsorship and support.

2-Channel SpikerBox Now Available. Measure Neuron Speed in Earthworms.

Tim — Tue, 10 Jan 2012 06:21:43 +0000

We hereby announce our 2-Channel SpikerBox. What can you do with it? Why, you can measure the speed of spikes as they travel down a nerve, in a truly “backyard” preparation using Earthworms. See our full experiment write up on how to do it! How fast is a spike? Faster than a car, faster than a plane, faster than a speeding bullet? Find out!

High School Students Hack Our RoboRoach Kit, Make it Better

Tim — Fri, 12 Aug 2011 00:43:27 +0000

We have been slowly rolling out our RoboRoach kits (we started shipping our beta units in late March 2011, and we have shipped 14 so far), and today we received some reports from the field. Robert Uglesich, a Professor at Cooper Union in Manhattan, used our RoboRoach kits this summer to teach high school students about microstimulation, analog electronics, and the neural basis of behavior. He reported today:

“I wanted to write to let you know that the summer program ended today and the students had a blast working with the RoboRoach kits. These last few weeks they were so enthused that they were getting to campus and starting to work before I even came in.”

There was a brief write-up today in the New York Times, but, more interestingly, the students made their own website summarizing their results. Their chief findings were:

1) The cerci nerves adapt more slowly to the stimulation than the antenna nerves. Also, stimulating cerci enables forward motion (our current antennal prep only allows right and left).

2) Randomizing the stimulation to the antenna nerves by using music patterns (instead of the constant 55 Hz stimulation we have set on the circuit) causes habituation to occur more slowly as well.

Thus, a three channel stimulator, with more heterogeneous stimulation patterns, would enable a RoboRoach system with forward, left, and right turning control that adapts more slowly. Nice work students! Impressive! Can we join your lab?

Our current efforts on the RoboRoach are to make the circuit lighter and reduce assembly time. Our current production version (gen3) weighs 6.25 g, an improvement from our first (9 g) and second (8 g) prototypes. It still takes about 6 hours to build however, so we are researching circuit configurations and interconnects that take less time to assemble and test.

“Circuits to Circuits II” workshop on June 24th. Teachers, sign up today!

Tim — Thu, 26 May 2011 19:40:24 +0000

It’s time for our second teacher workshop! In collaboration with the great folks at the SquareOne Education Network, we are hosting a teacher workshop on June 24th, 2011, whereby if you are a teacher within driving distance of the greater Detroit area, you can spend a day building your own SpikerBox amplifier and running experiments to take back to your classroom. You will also gain a wealth (the greatest wealth) of knowledge on how to do easy neuroscience with your students. Sign up is $25 and includes all the gear, materials, and lunch. To apply, fill out the very brief application and send to Barb Land at SquareOne! Space is limited (20 max), and yes, we do have SBCEU’s available! Welcome to the NeuroRevolution!

This workshop is subsidized by Backyard Brains, the SquareOne Network, and the Michigan Society for Neuroscience to give secondary school teachers access to tools to improve teaching about the brain. If you are a science professional (graduate student, professor, physician), you are welcome to come as well, but the fee is the normal $90 charge per attendee.

Date: Friday, June 24th at the Macomb Intermediate School District

Schedule:

8:30 – 8:45: Introductions

8:45 – 9:00: Brief lecture on electronics

9:00 – 10:00: SpikerBox Building Session I

10:00 – 10:30: Deeper Discussion on electronics

10:30 – 12:00: SpikerBox Building Continues

12:00 – 12:30: Lunch

12:30 – 1:15: SpikerBox Building Finish/ lecture on neuroscience

1:15 – 2:45: Experiments

2:45 – 3:30: Data Discussion/Feedback

Yes, this will make complete sense to you by the end of the day! Oh transistor, is there anything you cannot do?

Thanks to FundScience for Helping Us Sponsor an Optogenetics Design Project

Tim — Fri, 06 May 2011 18:32:09 +0000

Thanks to all who donated! The mission of FundScience is to get the public directly involved in funding scientific enterprise, so, of course, where did the $512.20 we raised actually go? Did it dump right into indirect costs? No way! Our organization develops low-cost neurotechnology, and the support of FundScience helped enable the building of an optogenetics prototype for a senior final design project we sponsored at the University of Michigan. What is optogenetics? It’s an exciting technology, developed in the early 2000′s, of stimulating neurons with light. The neurons in fruit flies and mice are modified using genetic engineering techniques, and the creatures have light-sensitive ion channels. It’s a rather useful technology (just ask any neuroscientist), but to date has only been available at advanced research institutions. But because of you, not anymore. We have made preliminary inroads towards making optogenetics a tool even high school students can use!

For our prototype to allow portable demonstrations of optogenetics in transgenic fruit flies, we needed a neuroamplifier, a micromanipulator, a microscope, and LED light controller. Backyard Brains has its own amplifier (the SpikerBox), and we decided to go with an off-the-shelf inexpensive microscope rather than design our own optics. Thus, our design efforts focused on the manipulator, the LED control, and the biological preparation. We worked with five seniors in biomedical engineering (Emily, Zack, Nick, John, and Sharon, all from Southeastern Michigan) over about 12 weeks. We are happy to report we were successful in building a functional prototype that we then tested with scientist Stefan Pulver of Cornell University/University of Cambridge.Here is a picture of the prototype.

On April 17th, we successfully recorded EMG’s (electromyograms) from channelrhodopsin-2 expressing fruit flies using the prototype we built. These flies have ChR expressed in their glutamatergic neurons, and when blue light is flashed upon them, the muscles in their body wall contract. Using the manipulator to place the electrode on the exposed muscle, the microscope to view the dissection, the amplifier to record EMGs, and the LED controller to flash light, we had a fully contained optogenetics rig. Below you can listen to an audio recording of light-evoked EMG. It’s noisy, but you can hear the response!

Here are the students posing with their invention!

For our second prototype, which we are currently working on, we will increase the stability of the manipulator by combining the y and x-axis with the z-axis of the manipulator. We also need to improve the iPhone application that controls the LED. The biggest weakness of our design is more biological than mechanical; the Drosophila dissection takes expertise to do well. Once the stability improves, we will begin demoing this unit to high schools. We have actually already begun demonstrations of the behavioral responses of transgenic fruit flies to blue light. See below for some investigation by students at Winans Academy in Detroit.

We thank all the donators who contributed to this project, the hard working senior design students, and our colleague Stefan Pulver for providing the fruit flies, time, and expertise. We are bootstrapping the continued development; the work continues! Below is the exact cost breakdown of the use of the funds.

“Circuits to Circuits” Teacher Workshop on March 23rd. Build your own!

Tim — Mon, 07 Mar 2011 21:17:49 +0000

We have run workshops for students, but now it’s time for the teachers!In collaboration with the great folks at the SquareOne Education Network, we are hosting a teacher workshop on March 23rd, 2011 whereby, if you are a teacher within driving distance of the greater Detroit area, you can spend a day building your own SpikerBox amplifier and running experiments to take back to your classroom. You will also gain a wealth (the greatest wealth) of knowledge on how to do easy neuroscience with your students. This is our first teacher workshop, help us help you! Sign up is $25 and includes all the gear, materials, and lunch. To apply, fill out the very brief application here and send to Barb Land at SquareOne! Space is limited (20 max). Welcome to the NeuroRevolution!

Date: Wednesday, March 23 at the Macomb Intermediate School District

Schedule:

9:00 -9:15: Introductions

9:15 – 10:00: Brief lecture on neuroscience and electronics

10:00 – 10:15: Break

10:15 – 12:30: Spiker Box Building Session

12:30 – 1:00 Lunch

1:00 – 2:00: Experiments

2:00 – 2:30: Discussion, feedback and pooling of results

2:30 – 2:45: Break

2:45 – 4:00: Lesson plan and new experiment design.

Note: For this workshop, we do not have SBCEU’s available, but we plan to for all future workshops.

Yes, this will make complete sense to you by the end of the day! Oh transistor, is there anything you cannot do?

Congrats to Connor and Michael, first high school students to build SpikerBoxes unsupervised

Tim — Thu, 10 Feb 2011 19:10:30 +0000

We have been slowly distributing ourSpikerBoxes to high schools (nine so far), in efforts to bring the sound of spikes to physics and biology labs around the country. Letizia Judd, biology teacher atSt. Mary’s Preparatory School in Orchard Lake, MI, recently purchased a fullDIY classroom kit, where even (off-menu) the stimulation and iPhone cables were built by the students. Mike and Connor, both seniors at the school, built fully working SpikerBoxes with zero, repeat zero!, help from us. They now join the ranks of neuroscience professors, post-docs, and graduate students who have built their own neuro-amplifiers. Congrats!The iPhone cables required minor repairs, which they fixed. St. Mary’s was also our first Michigan high school customer. Thanks for believing in us!

We announce our “build a better SpikerBox” competition

Tim — Mon, 07 Feb 2011 20:43:45 +0000

The SpikerBox has gone through 7 development cycles, but we know it can be better. Designing electronics and experiments is one of the most fun things we do here at Backyard Brains, and we now announce our Penaeidae Prize! Can you design a better SpikerBox? Deadline is May 15th, and the winner will have their name stenciled on the next run of SpikerBoxes, as well as a sponsored abstract at the 2011 Society for Neuroscience meeting in Washington, D.C.! Oh nascent Engineers of the world, design! Let forth your creative fury!