Neuron News

The Open Source Virtual Brain

A screenshot view of The Whole Brain Catalog software; from the WBC Wiki

The Open Source movement has been an integral part of software development for many years now, and it is starting to explode into the science world. The latest project might even transform brain science communication and understanding to a new level as the new Whole Brain Catalog is now available for anyone to access.

The brain is complicated. The brain is designed with a biological network of connected cells so intricate that a complete visualization or map of the system has yet to be developed. Neuroscientists have been trying to determine a way to create this map for many years, and advances in brain imaging has helped inch us closer toward this realization. The Whole Brain Catalog, from researchers at UC San Diego, is the latest attempt at constructing this map, and they are taking a little inspiration from Google.

The software integrates imaging data and models from anyone who is able to contribute. There is still so much to discover about the structure and function of the brain, and amassing this sort of information from everyone in an organized and visually integrated way could really bring about a revolution in the fundamental understanding of the human brain.

Researchers generating data can provide 2D images, 3D reconstructions, cellular morphologies, and even functional simulations that will all be integrated into the system’s catalog. Users, which may be anyone from other neuroscience professionals to the interested citizen scientists, can explore through actual imagery of slices of the brain and wander around 3D models of brain regions all the way down to molecular structures.

A future goal of the WBC is to integrate their extensive data with the National Institute of Health’s Neuroscience Information Framework (NIF), which currently is a growing online database of all web-based neuroscience resources. Anyone can register today with this open-source program through Neuinfo and search the extensive collection of neuroscience information.

Although the WBC sounds wonderful and exciting, the software is very much in an early, beta-testing stage. We have been trying to install the program here at Neuron News on a Dell laptop running an Intel Celeron 2 GHz, 2 GB RAM, which is just below the minimum computing system for the software (view system requirements). So, the software has loaded up, but quickly took everything this little computer had to offer and crashed it down hard.

If you have the computing resources to try out the latest release of The Whole Brain Catalog (download now), please comment here to let us know about what interesting images and simulations you discover. And, we would also appreciate if you could share your screenshots with Neuron News.

What this sort of software and world-wide open collaboration could also foster is a Zooniverse-inspired citizen science project. The team that started the Galaxy Zoo interface is continuing to help citizen scientists look “upward” with new projects to look at the Moon, Mars, galaxies, solar storms, and more. It would be also exciting to offer the opportunity for people to look “inward,” and enable citizen scientists to help identify and discover new things out of the deluge of data coming from the neuroinformatics and neuroimaging fields. In fact, the interest in participation might exponentially increase from the Zooniverse’s current 300,000-plus world-wide volunteers, since it might be more broadly considered that trying to figure out more about ourselves is paramount to watching for a dark black hole so many light years away.

It is likely that some group has already begun the initial considerations for developing a citizen science-lead, at home discovery interface for the human brain. If not, then we would like to formally propose the idea here on Neuron News, and find out what you think about the possibility of creating an open platform allowing anyone to explore the human mind and help make scientific observations and discoveries by sifting through the increasing collection of brain images and models.

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“3-D brain model could revolutionize neurology” :: :: July 30, 2010 :: [ READ ]

Mice Walk Again

Stained motor neuron from human spinal cord; Courtesy Wikimedia Commons.

Historically, the medical approach to curing the incurable effects of tragic spinal cord injuries–such as the case made famous by America’s classic super hero, Christopher Reeve–has been to affect regeneration of damaged nerves through stem cell therapy or by introducing growth factor proteins, like BDNF. Success with these applications has yet to be realized, as apparently the adult body’s resistance to re-growing its nerve centers is stronger than expected.

Recently, however, a team at Children’s Hospital Boston lead by Zhigang He, has been developing an alternate approach to the problem. Instead of trying to force existing nerve fibers to regrow, or by introducing new cells to take their place, the group manipulates the communication in the cells to “turn off” an apparent gene that tells the neuron to stop growing. With the gene shut down, then neuron is free to generate and flourish as it sees fit.

They have found at least three proteins involved with the critical myelin coating of neuronal axons, which actively work together to inhibit myelin growth. Blocking the proteins either genetically or chemically is being shown to promote the sprouting and re-generation of local structures in neuron networks.

The process is being tested in mice with spinal cord injuries by removing a special enzyme, called PTEN, that is activated in mature systems to limit cell growth. With the enzyme out of the picture, the cells think they are young again, and start to grow. No controversial stems cells, and no introduction of unnatural chemicals… just removing a little key that is in the way. Of course, it would likely be important to be able to replace the key once the damaged cells have rejuvenated, otherwise a cancer-like state might be a drastic side effect.

Although this new therapy is not near to human trials, it is a wonderfully positive example of how significant advances in human improvement might come from looking at problems at a little different angle. These experimental mice are just paving the way for the coming acceleration into reversing such devastating human experiences that include wide-spread nervous system damage and degradation.

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“Mice regain movement after spinal cord injury” :: Scientific American Observations :: August 8, 2010 :: [ READ ]

“PTEN deletion enhances the regenerative ability of adult corticospinal neurons”, Kai Lui, et al., Nature Neuroscience, August 8, 2010 [ READ full article :: Download PDF ]

“Spinal cord regeneration success in mice” :: BBC News Health :: August 8, 2010 [ READ ]

Conscious Learning in the Unconscious

Sitting at the bed side of a loved one who has slipped into a coma and simply reading a story, talking about the day, or just holding hands most likely feels like a pointless and endless effort for the recovery of the vegetative patient. There can only be the glimmer of hope that maybe they can sense your presence, but there is no definitive way to know for sure if your interactions are falling on a deaf brain.

We all can make personal judgments that we are conscious right here and right now. But, making this sort of judgment for another individual when their interactions with the world are limited or apparently absent is not only challenging, but also ethically dangerous as your decision can mean life or death. But now, a new, low-cost study on the interactions of patients who are considered to be in a “minimally conscious state” (MCS) is showing a very exciting result that basic learning seems to take place in some individuals.

The type of learning is simple–the sort of classic conditioning demonstrated by Pavlov’s dog who salivated at the sound of a bell. Here, a tone is sounded followed by a light air puff to the eye. This is certainly an annoyance, so a conscious observer would tend to squeeze their eyelid shut to protect the pupil. After a short time of the repeated events, patients who physically responded to the air puff and who were seemingly unconscious demonstrated the same eyelid reaction after only the sounding of the tone.

The open question is to wonder if this sort of basic learning is so fundamental that true human consciousness is not required. So, Pavlov’s dog might be somewhat smart, but still not conscious. Or, if only a minimum level of consciousness is needed for basic learning (as the result of new, functional connections developing in the brain’s neural network), then a simple test of a successful Pavlovian response could be an important benchmark for determining the state of a patient who cannot communicate with the world. The hope would be that if simple learning is still possible, then further recovery and improvement in the brain’s responses could also be anticipated with additional therapies.

It’s certainly not a clear test of consciousness, but the approach is so simple and does not carry the enormous costs of brain imaging technologies. Therefore, essentially any hospital with low-conscious patients can perform this sort of experiment, which can further develop our weak understanding of human consciousness, and to improve the successful predictions required by doctors when dealing with patients on the verge of life or unconscious death.

“Conditional Consciousness: Patients in Vegetative States Can Learn, Predicting Recovery” :: Scientific American :: September 20, 2009 :: [ READ ]

Read more about MCS by Dr. Douglas I. Katz from [ READ ]

Guiding the Regrowth of Neuron Connections with Microtubes

Polycaprolactone Microtubes, from

When peripheral nerves are damaged or even severed due to injury or disease, then dramatic disabilities can result in the affected individual. This may range from local paralysis of senses to the painful disorder ofneuropathy.

Neurons that loose their primary connections to one another through the axon–the main nerve fiber that transports electrical signals from the cell body to other neurons–are very slow to re-grow, and will likely die due to inactivity. If they do re-develop and connect, then the nervous system can re-learn how to have a reasonably-functioning network, but full recovery to its original condition is difficult.

To encourage and guide this re-growth process, a European collaboration of researchers are developing a new neurotechnology based on fabricated polymer microtubes that can be implanted and monitored during axon regeneration. Centered at the University of Glasgow’s Centre for Cell Engineering and Department of Electronics and Electrical Engineering under Dr. Mathis Riehle, the team plans to surgically insert these specialized tubes between two neurons whose axon fibers are severed. With a little electrical stimulation along the tube, they anticipate that the fibers will begin to grow along the length of the tube and establish a new neural connection on the other side… the neuronal equivalent of the “light at the end of the tunnel.”

The successful development of this technique will certainly mean significant improvements in recovery for patients with peripheral nerve damage. It may also pave the way for a more focused neuroengineering method for creating new connections in the human nervous system, and even helping living nerves functionally connect to implanted devices. Controlling the development and re-development of neuron networks will become a major leap for future neurotechnological advances.

“Scientists hope tiny tubes can help repair damaged nerves” :: :: August 16, 2009 :: [ READ ]

BrainGate Enters Round 2 of Clinical Trials

The BrainGate collaboration, lead by Dr. John Donoghue from the Department of Neuroscienceat Brown University, recently announced they have began recruiting patients to join in the clinical trials of the second iteration of their neural interface system.

The first round of trials was run by Cyberkinetics, an independent neurotech company founded by Dr. Donoghue, but they have pulled out of this next phase due to funding difficulties. Now, a purely academic team based at the Massachusetts General Hospital, these exciting trials will help guide the next generation of neurotechnological interfaces between human brain activity and direct actions on a computer and, eventually, control of prosthetic devices.

The near-term goal of this research is to develop a technology that can assist patients with degenerative neurological paralysis where their brain is trying to talk to its body, but the body just isn’t listening. The BrainGate system trains itself to decode electrical activity in the brain and translate recorded signals into a computer for control of an external device. In effect, BrainGate is a bridge that re-routes neural communication to a device that would be designed to replace lost function.

With previous work, the critical success was converting brain activity into the control of a cursor on a computer screen. Although this seems to be a trivial activity, the understanding of the neuroscience behind the actual relationship between specific brain activity and the mechanical control of our environment remains a vital bit of understanding required for the future of neurotechnology. Now, with the BrainGate2 trials starting soon, opportunities to discover new science will hopefully bring us closer to successful devices for assisting patients with ALS, spinal cord injuries, stroke patients, and many others with empowering technologies to live their lives to the fullest.

“Brain-computer interface begins new clinical trial for paralysis” :: EurekAlert :: June 10, 2009 :: [ READ PRESS RELEASE ]

Interfacing with Electrocorticography

Recently, we discussed the developments from the Wadsworth Center of a minimally-invasive, thin-film technology to enhance electrocorticography (ECoG) recordings (read). Similar to the more common electroencephalogram (EEG) method, which uses an array of electrodes stuck on your outer skull to receive electrical signals from your neurons, the ECoG uses an array of electrodes embedded just on the surface of your brain allowing for a more direct electrical view of neural activity. This view still covers an averaged signal from a large number of talking neurons and still does not see individual electrical signals. However, by having the bony skull out of the way, the electrodes sure have a more clear shot for picking up the electric fields.

The importance of this work from Wadsworth is that the brain and it’s violent bodyguard, the immune system, doesn’t really like to have things hanging around that the body didn’t make on its own. So, typical implanted devices will quickly be destroyed by attacking antibodies. Here, the specialized implanted ECoG devices are lasting six to twelve months in human patients, but their goal is to improve the device life-cycle to five to ten years.

Through their collaboration with clinical neurologists and biomedical engineers at Washington University in St. Louis, Missouri, the Wadsworth group, lead by Gerwin Schalk, is taking the technology to the next step by integrating the recording activity with specialized software that maps the brain activity with computer control. The implanted ECoG providing its more detailed map of brain activity allows for a specific correlation to be observed between physically clicking a computer mouse button, for example, and the resulting pattern of neural firings in the brain. The patient can then train their thoughts to reproduce similar neuron activity and, with a direct connection to the computer, the mouse click appears without the click.

The interfacing process is being licensed to a start-up company in St. Louis called Neurolutions, who will be working to improve the software and training process to bring it to market for applications in neuroprosthetics. The challenge for further advancement begins with the unfortunately situation that just clicking a mouse button doesn’t get us very far in life. Just moving fingers and arms requires multi-dimensional spatial control, and with that comes an an unknown number of different neural patterns being required to simply raise your arm to reach the mouse on top of the desk. All of the corresponding neural activity–move shoulder up, rotate elbow, lift index finger, shift arm to the right, etc.– will need to be mapped, trained, and accessed to control a prosthetic device… and each human might have different neural patterns for the same physical motion.

“Reading the Surface of the Brain” :: Technology Review :: June 3, 2009 [ READ ]

“Brain-Computer Interface Technology Licensed to Missouri Firm” :: NY State Dept. of Health Press Release :: March 25, 2009 :: [ READ ]

Last updated October 19, 2020