I wanted to find a clean way to collect survey data online without dealing with surveymonkey. After looking around a bit, I stumbled upon google document’s form tool which can create any kind of survey you want. Even cooler, the data is published instantly to a secure spreadsheet in your google documents —which can be exported as a .txt or .csv file. In this example, I made a subject availability form (using the ‘Magazine’ theme) so I can schedule participants for an MEG/MRI study. Not bad eh?
And to illustrate how cool it is, I published the data to a website that updates with new data from the form. Check it out!
Graph visualization is a way to discover and visualize structures in complex relations. What sort of structures are people who do large scale computation studying? We can get a glimpse by visualizing the thousands of sparse matrices submitted to the University of Florida Sparse Matrix collection using sfdp algorithm . The resulting gallery contains the drawing of graphs as represented by 2328 sparse matrices in this collection. Each of these sparse matrices (a rectangular matrix is treated as a bipartite graph) is viewed as the adjacency matrix of an undirected graph, and is laid out by a multilevel graph drawing algorithm. If the graph is disconnected, then the largest connected component is drawn. The largest graph (Schenk@nlpkkt240) has 27,993,600 vertices and 366,327,376 edges. A simple coloring scheme is used: longer edges are colored with colder colors, and short ones warmer.
Although I am still recovering, I have to say that SFN was one of the coolest experiences I have ever had as a neurobio student. I met so many inspirational people as well as a few of my favorite scientists. Just the sheer mass of people (>36,000 attendees) and information (7 days of posters and symposia) illustrates how big the field is. Despite this, after the many conversations I had over these past few days and nights, I feel like I have more direction and focus than ever before. I am really looking forward to the upcoming year as perhaps my most productive. I have a lot to learn, but I can clearly see how it all fits together. Cheers to a great week!
Note: I was tempted to write about everything as it happened, however —despite being overwhelmed with information— I’m just not that fast! So, with a little time and redbull, more posts about SFN will come.
You are looking at a mouse fetus through an unbelievably expensive (~$120,000 USD) ‘Ultramicroscope’ made by ze German company, LaVision BioTec. In short, this scope is cool because will let you image a mouse’s brain in 3D in less than 10 minutes. It uses a thin sheet of laser light to excite the tissue while fluorescent light is detected from each slice. Reconstructing these slices will create a 3D volume at cellular resolution! Check out the video, then check out the site:
Electrophysiology recording systems are expensive and grant money needs to be maximized. What system should you purchase that will give the most accurate spike decoding for your money? Neural prosthesis have a size, power, and efficiency constraints. What is the optimal combination of sampling rate and bit resolution? Beyond anecdotal evidence, there here isn’t a whole lot of literature on the exact characteristics needed for a solid spike recording rig.
This is exactly why I was interested in Palmi Thorbergsson’s (PhD student at University of Lund, Sweden) poster talk entitled “Minimum Sampling Rate and Resolution for Detection and Classification of Neuronal Spikes in Extracellular Recordings.”
Palmi used data, a randomized collection of spiking acquired from celebellar neurons, that was collected at around 40Hz and resampled to different frequencies from 10kHz to 100kHz. The sampling rate (kHz) was plotted against spike detection accuracy in the form of type I and II errors. The error rate decreased exponentially between 0-20Hz, but flattened out after that. According to this data, a frugal scientist would stop spending after 25-30kHz. He also plotted resolution (bits) error rate. The biggest gains in performance were seen 1-8 bits. After that, the difference between 10 bits and 14 bits was fairly negligible.
Conclusion? A 25 kHz and 8 bit recording setup should provide all the power you need to make accurate inferences about spiking. The rest should be spent on other things!
Here is a photo of the results (used with permission). Sorry about the low resolution, I’m saving up for a new camera!
My first reaction was, “Wow, thats a lot of math for acupuncture…” But what promised to be the holy grail of acupuncture research, turned out less than stimulating (pun intended). I did like the idea of using a deeper analysis into the spatial locations of acupuncture points, however I feel like ICA and a Granger Causality model was a bit overkill…
Cognitive control (ie. how we start and stop actions) is central to the study of decision-making as well as certain psychiatric disorders. The most common experimental paradigms for measuring action inhibition are variations of a basic stop task, where the subject is told to stop just before performing some action, such as a button press, and the ‘stop-signal reaction time’ (SSRT) is measured. The talks today focused on this area of research.
Here is a brief overview of a talk that I found interesting:
Birte Forstmann (U. Amsterdam)
Neural basis of the speed/accuracy trade-off: model-based functional and structural studies in humans
Theres an accuracy vs. speed tradeoff in decision making that is governed by a cortico-striatal loop. Individual differences can be accounted for by differences in pre-SMA to stratal white matter tracts. Elderly people have lost strength along this track and are less flexible in adapting their speed vs. accuracy tradeoff.
Amazing visualization
Generative artworks by Elijah Porter Title: Seth Lloyd
Backyard Brains is a small company that sells $100 single-neuron recording kits, complete with live cockroaches to test it out on. Thats right, I said cockroaches. You just pluck off a leg —don’t worry they grow back— and record from the nerves inside, or, as shown in this video, stimulate them.
Why? Because Greg Gage and Tim Marzullo, two neuroscience graduate alumni from the University of Michigan, were clever and crazy enough to design a very engaging tool for teaching neuroscience to elementary school students.
Check out their flagship product, the Spikerbox, which is driven by a simple op-amp circuit, a few filters, an A/D, and a speaker —so you can hear the neurons fire! This is probably the coolest DIY neuroscience kit I have seen, and although I am too poor to have a backyard, I will probably order the ‘el cheapo’ pcb and try this one out at a Starbucks near you!
California Senator Dianne Feinstein (wiki) has written a lengthy response to my letter about the “Combating Online Infringement and Counterfeits Act” (COICA). It is extremely rare for a Senator to write a detailed and personalized response letter, and I think her words are worth sharing. Here’s the dialogue:
Dear Senator Feinstein,
The language of the Combating Online Infringement and Counterfeits Act (COICA) is far too loose and will be exploited to the detriment of our constitutional rights. It allows companies to censor sites without offering due process to the defendant through the Attorney General’s blacklist (Section j.1). Additionally, it strips the ability of smaller groups to defend their work by allowing the prosecution to place the burden of evidence on their lack of “technical means” (Section 2324.g).
Please do not allow the COICA to progress. This act is pure censorship and works agains the freedoms our country has fought for while degrading our international image as defenders of such liberties. We have no business investing in freedom abroad if we cannot do so at home.
I implore you to see the unconstitutionality of such an act and represent your constituents best interest of keeping the internet a place of freedom.
Sincerely, David Deriso
Dear Mr. Deriso:
Thank you for writing to express your opposition to the “Combating Online Infringement and Counterfeits Act.” I appreciate knowing your views on this matter.
America’s copyright industry is one of our most important economic engines, and giving artists and inventors the incentive to produce cutting edge works is vital to the country. The protection of intellectual property is particularly important to California, which is home to thriving film, music, and high-technology industries. I am strongly opposed to theft of copyrighted works, and I believe copyright owners should be able to prevent their works from being illegally duplicated.
On September 20, 2010, Senator Patrick Leahy (D-VT) introduced the “Combating Online Infringement and Counterfeits Act” (S. 3804), of which I am an original cosponsor. This legislation is carefully crafted to address the growing problem of online piracy and copyright infringement, and would allow the U.S. Department of Justice to shut down websites which are “dedicated to infringing activities.” These are sites that, in the bill’s language, are “primarily designed or have no demonstrable commercially significant purpose or use other than…” selling infringing or counterfeit goods.
Please know that I have been working with California high-technology businesses and Senator Leahy to improve the bill’s language and address the concerns of legitimate high-tech businesses, public interest groups, and others. This legislation is currently awaiting action in the Senate Judiciary Committee, of which I am a member.
Again, thank you for taking the time to share your concerns with me. Should you have additional questions or concerns, please do not hesitate to contact my staff in Washington, D.C. at (202) 224-xxxx.
Sincerely yours, Dianne Feinstein United States Senator
Her letter seems genuine although she avoids certain points. Paragraph two struck me as her way of saying that the “thriving film, music, and high-technology industries” that compose her constituency are pressuring her to pass the bill. She also argues that copyrights are among our “most important economic engines,” suggesting that the bill may nourish the famished California economy. I see where she is coming from.
Despite her political pressures, she has indicated a desire to “improve the bill’s language and address the concerns of legitimate high-tech businesses.” Let’s hope that she will follow through.
My main criticism is that she (strategically?) neglects to address the DA’s blacklist that seems to circumvent the right to a fair trial. Also, I’d like to know what a “demonstrable commercially significant purpose or use” is. Does this mean that if sites like wiki-leaks started selling t-shirts, they would be spared? I’m not convinced that this resolves the grayness of the bill’s jurisdiction.
For the moment, I am glad that my voice was heard and can only hope that the bill’s language improves.
What do you think?
Read more of my analysis on the “Combating Online Infringement and Counterfeits Act” (COICA). (Part 1, Part 2, Part 3)
Implantable electrodes for neural recordings have come a long way from their predecessors, but most still have the properties of being bulky and stiff. Jonathan Viventi, PhD, a bioengineer from the University of Pennsylvania, has developed a new generation of ultra-thin and flexible silicone active electrodes that use silk to mold to the convolutions of soft neural tissue.
Photo: (left) Conformal, neural electrode array wrapped onto a model of the brain. The wrapping process occurs spontaneously, driven by capillary forces associated with dissolution of a thin, supporting substrate of silk. Photo credit: Dae-Hyeong Kim, University of Illinois at Urbana-Champaign (right) Traditional electrode array currently used in epilepsy recordings for patients with intractable seizures. Source: Children’s Memorial Hospital, Chicago (link)
During surgery for epileptic seizures, neurosurgeons determine which areas to resect by looking for specific neural signals recorded from an electrode array placed on subdural tissue. However, the poor spatial resolution of these electrode arrays make it difficult to determine exactly where the problematic neurons are located. Each electrode in the array sits above tens of millions of neurons, and can can even be spaced over 1 centimeter apart (see picture above). Dr. Viventi says that using such broadly spaced electrodes for predicting where seizures are most likely to occur is like “flying over Manhattan with a single microphone and trying to predict if a riot is about to break out.” However, neurosurgeons still rely on these low spatial resolution electrodes to make critical decisions.
To address this inaccuracy, Dr. Viventi has combined several technologies used in microchip manufacturing to literally print 750 electrodes spaced at a mere 250 μM apart onto a silicon sheet. Each of these electrodes are amplified and multiplexed on the sheet itself, and unlike traditional high density electrode arrays, which require a large amount of wires, Dr. Viventi’s system only has 36 traces printed onto a flat tape! This means that the system can fit into smaller spaces, making future procedures more accurate and less invasive.
If the electrode design is not amazing enough, the silicone can be bound to a layer of silk that dissolves away when exposed to cerebrospinal fluid (CSF), during which the thin silicone traces melt over the curvatures of the sulci and gyri forming a tight contact with the neural tissue.
Photo: Flexible, multiplexed electrophysiology mapping device composed of high-performance silicon nanomembrane transistors. Photo credit: Dae-Hyeong Kim, University of Illinois at Urbana-Champaign
As you can imagine, the computational load is significant and indeed pushes the power/size needs for prosthetic applications. The current A/D measurement device had to be custom built to scream through the 750 channels at the 200kHz to give each channel a usable frequency of 12.5kHz. The SNR was around ~34dB, but improved when the multiplexing rates decreased. While the SNR is great considering the newness of the technology, it also indicates a need for more research or better manufacturing to decrease the noise from the multiplexing system.
Dr. Viventi’s electrodes have already found applications in neural and cardiac electrophysiology recordings. The videos below are from the supplementary materials of Dr. Vivent’s article in 2010 Science Translational Medicine and show the array at work for cardiology recordings. I look forward to the next generation of neural implantable devices implementing this new electrode design.
Video: The video above shows in-vivo cardiac monitoring of a pig. Notice the contrast between the silicone array’s slim design and the medieval-looking electrode system currently accepted as the standard. If a surgeon was operating on your heart or brain, which electrode would you rather have them use? (Can’t see video? Try here)
Video: The video above shows what the analysis of voltage data received from the electrode array looks like. It’s an incredible view of voltage data across time and space, as if we have been given a detailed window into the activity of these local field potentials. (Can’t see video? Try here)
References:
Kim, D. H., Viventi, J., Amsden, J. J., Xiao, J., Vigeland, L., Kim, Y. S., et al. (2010). Dissolvable films of silk fibroin for ultrathin conformal bio-integrated electronics. Nature Materials. 9(6), 511-517.
Viventi, J., Kim, D. H., Moss, J. D., Kim, Y. S., Blanco, J. A., Annetta, N., et al. (2010). A conformal, bio-interfaced class of silicon electronics for mapping cardiac electrophysiology. Science Translational Medicine. 2(24), 1-4.
Dr. V.S. Ramachandran’s newest book, The Tell-Tale Brain: A Neuroscientist’s Quest for What Makes Us Human, is slated to hit store shelves early 2011. In his usual style, Dr. Ramachandran dismantles unique neurological disorders that first estrange us from our own introspections before illuminating the idiosyncratic existence of the of the human mind. The lab has been buzzing with excitement about it’s release, although not many of us (including myself) have been able to get a glimpse of it. I find that reading Dr. Ramachandran’s writings is just like reading a novel, and I can’t wait to get lost in this one!
Thank you to the Society for Neuroscience (SFN) 2010 conference organizers for featuring my blog. I hope that my writing will meet the standards of such a diverse and intelligent audience.
For students on a budget, my couch in La Jolla is open to you! Please feel free to message me if you need a place to stay. I know hotels are filling up. (Update: My couch is now full. If you’re in a pinch, try couchsurfing.org.)
Also, when you’re in San Diego, you will probably want to explore the nightlife. Here are my suggestions:
Nightclubs: Fluxx, Ivy Hotel, Stingaree (avoid paying a cover and use the guestlists)
Sushi: Harney Sushi, Ra Sushi, Sushi Deli 1 & 2
The gaslamp quarter is packed with restaurants, just walk around 5th and 6th Ave near Market St and enjoy! PS. There’s over 30,000 scientists coming. Wow.
Hi, my name is Dave. I try to combine art, engineering, and medicine in my work and research. I am currently part of an applied machine learning laboratory at the UCSD Institute of Neural Computation (Machine Perception Laboratory).
