Allen brain atlas completed

A few days ago the Allen Institute for Brain Science issued a press release announcing the completion of the Allen Brain Atlas.

“The Allen Brain Atlas (ABA) is an interactive, genome-wide image database of gene expression in the mouse brain. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. ”

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OpenStim: The Open Noninvasive Brain Stimulator

Transcranial magnetic stimulation (TMS) is a popular technology for stimulating human cortical neurons, due to its safety, noninvasiveness, and efficacy. A TMS device is just a little coil of wire, through which 10,000 Amps of current is cranked during a period of only a few hundred microseconds; the resultant rapidly-changing magnetic field induces eddy currents in the brain. Depending on the protocol used, TMS can drive/inhibit a region of cortex corresponding to roughly a cubic centimeter or two, and is being explored for the treatment of depression, the reduction of auditory hallucinations during schizophrenia, and the alleviation of tinnitus and migraines. Thousands of papers on medicine and psychology have been written using this tool.

Yet the device itself is expensive and rare — they can run from $20,000 to $50,000 or even more, despite the fact that they are, in essence, a coil, a switch, a bank of capacitors, and a power supply. Much of the art lies in making the devices safe and fail-proof. Is it possible to hack/engineer a system that is safe, fault-tolerant, efficacious, and inexpensive? And furthermore, can we facilitate a community that will devise such devices, and share information about protocols and approaches to brain hacking?

This past August at Foo Camp, a hackers’ conference in Northern California, a group of people got together and set out to do just that. We are designing a safe, noninvasive, modular, and “open source” brain stimulator that will open up the field of circuit modulation to a wider audience. Members of the group include therapists and mental health professionals, engineers, programmers, and others interested in either the development of such devices, or the sharing of information on this front. Key to the design is safety — we want to make sure that the devices we create are as safe as devices on the market. Also, all the information is released under the Creative Commons “Attribution and Sharealike” license. This is a new model for “open source” medical device development — which may move it beyond the domain of simply creating “cool toys,” and to creating real devices.

You can find out more information, or contribute to the project, or learn from the project, at


New brain/mind theory

My website “Quad Nets: Device Models of Brains” is online at

“Quad Nets” proposes a new kind of “artificial intelligence” that uses devices other than computers. Chiefly presented through Images, the Quad Net approach integrates physics, neuroscience and psychology in primal forms, initially rudimentary, but suitable for unlimited development in size and complexity.

I am an amateur and have privately worked in these areas for many years. Unfortunately, I have not found a means of communication through established channels. I hope that the readers of this blog will provide needed critical review. Thanks to the “neurodudes” for making this medium available.

Bob Kovsky (rlk “at”

Slice culture: Preserving circuitry in culture

As many of you know, my experimental background is in hippocampal culture. Recently, I attended a hippocampal slice culture workshop given by members of the Hayashi lab here at MIT. I never really knew too much about the pros and cons of slice culture. After seeing the technique, I wrote up a little summary of the major differences from the point of view of someone who uses culture:

  1. slice culture can be done quickly. if you’ve got the mediums made, it takes 10-15 mins start to finish!
  2. hayashi lab uses P7 rats. Anywhere from P0 to P10 is viable for slice culture. Younger is better for certain genetics work (eg. transfection with gene gun). at P7, you get about 20 slices/hippocampus.
  3. P7 rat hippocampus can be dissected with only the aid of a magnifying glass! It’s macroscopic.
  4. coronal slicing results in a mostly intact hippocampal circuit: DG->CA3->CA1. In vivo, synapses form at P10.
  5. slicing is done with a tissue chopper. a vibratome is too slow (faster = more viable slice culture). 300-350um slices are used for patching and/or imaging. you can go thicker for imaging-only.

The biggest advantage over culture seems to be that you get an intact-ish hippocampal circuit. The biggest advantage over acute slice is that you don’t need to slice every day (and wait for recovery 1 hour post-slicing).
Neat technique.

Neuroengineering and the MIT TR35 innovators

Today MIT’s Technology Review magazine released its annual list of innovators under the age of 35 who were nominated for recognition. Interestingly, almost a full quarter are doing work relating to or impacting the field of neuroengineering — including ways to tag synapses with quantum dots, activate neurons remotely, improve machine vision, classify whole-brain states for prosthetic purposes, and make nanowire arrays.

High-Res fMRI PCA Analysis of Face Recognizing Cortex

A recent study by Grill-Spector, Sayres, and Ress uses high-resolution fMRI imaging to explore the fusiform face area, a part of the temporal lobe known to activate when looking at faces.

They do a PCA analysis on their study and find 3 principal components that account for 95% of the variance, and the components related to 1) faces, 2) sculptures/cars and 3) animals. From the study:

Our results suggest two hypotheses for the functional organization in this part of cortex. First, the face- and nonface-selective subregions may be part of a common cortical region, which processes both face and nonface stimuli. Alternatively, the face-selective subregions may constitute the ‘‘true FFA’’ (and may contain only highly selective face neurons), whereas the other subregions may comprise a segregated subsystem. However, the fact that face-selective patches are not spatially contiguous on the cortex (Fig. 5) raises the question of which of them might be considered the FFA, or whether these spatially segregated subregions might behave functionally as a computational unit. Future studies may elucidate whether these face patches are interconnected, which would allow them to operate as one computational unit (for example, by studying connectivity between subregions in the FFA).

The study also contrasts the use of high-resolution fMRI, capable of resolving at 1mm voxels with the standard fMRI, capable of resolving at 3mm.

Two neural prosthetics papers

The July 13 issue of Nature included some neural prosthetics papers, one of which was the paper reporting 9 months of stimulation of Matthew Nagle, a tetraplegic who received the first trial of the 96-electrode BrainGate implant in his right precentral gyrus (motor cortex (MI) for arm). The authors were Leigh R. Hochberg, Mijail D. Serruya, Gerhard M. Friehs, Jon A. Mukand, Maryam Saleh, Abraham H. Caplan, Almut Branner, David Chen, Richard D. Penn and John P. Donoghue.

picture of Matthew Nagle using the BrainGate implant picture of the BrainGate multi-electrode array
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