Todd Gillette

Ph.D. in Neuroscience
Research Assistant in the Center for Neural Informatics, Neural Structures, and Neural Plasticity (CN3)
Curator of the Neuroscience Knowledge Network (NKN)

Alignment and cluster analysis of neuronal tree sequences

Alignment of neurons represented as sequences of branching points can be used to detect clusters of similar neurons which can then be investigated for their stereotypical branching patterns. We use a modified sequence alignment procedure to produce pairwise similarity values between two neuronal sequences and then, after embedding the neurites (axons, dendrites, or apical dendrites) into a consistent abstract space, we found clusters in the space. By overlaying those clusters with known cell classes we found significant associations. There were strong associations by cell type, brain region, and species, indicating that neuronal branching patterns are indicative of neuronal type and function.

Big Neuron – Towards Big Data in Neuroscience

This year Hanchuan Peng (Allen Institute for Brain Science) began the next phase of the effort called Big Neuron. However, rather than a competition, this time the project would be a collaboration.

The key idea is to create a single platform on which all algorithms can be run, compared, and their results combined to form reconstructions better than any one could achieve alone.

Doctoral Dissertation

My dissertation, entitled “Comparative topological analysis of neuronal arbors via sequence representation and alignment”, is focused on applying bioinformatic approaches to neuronal morphology to enable new discoveries and increase understanding about how morphology and neuron function interrelate.

IBM’s TrueNorth – The first neuromorphic chip

IBM has recently released details of a neuromorphic chip named TrueNorth via their website, the press, and a research report in the journal Science. The research team, headed by Dharmendra Modha as part of the DARPA SyNAPSE Program, developed a chip containing a million “programmable spiking neurons” and 256 million synapses. The chips use 5.4 billion transistors on 4096 “neurosynaptic cores” which each has its memory (in the form of connection routing and timing delays) close to its “neuronal” processing units.

Stem cells used to treat a brain disease

While this latest research is a proof of concept, it’s a pretty impressive and important one. Scientists started out putting stem cells into mouse brains that were genetically modified to produce less myelin, essentially an electrical insulator of neuronal connections, and thus have various cognitive and motor deficits (abstract). Similar problems plague people through various demyelination diseases of the central nervous system (CNS), like multiple sclerosis, or of the peripheral nervous system (PNS), like Guillain-Barré syndrome. New cell growth was detected in the mouse brains, with a great proportion of the new cells being oligodendrocytes which are the cells responsible for covering neuronal connections with myelin (in the CNS). Substantial additional myelination was also observed with no clear negative effects.

Following these results the scientists ran a case study (abstract) on 4 boys with the genetic disorder Pelizaeus-Merzbacher disease which produces defective oligodendrocytes. The scientists injected stems cells, along with immunosuppression drugs, into the boys and saw substantial improvement in myelination near the implantation sites with no apparent adverse effects. Future studies will involve more patients and hopefully will lead to treatments of a number of highly debilitating diseases.

For another review of the …

Preview of “Automata”

When one ponders the possibilities of the future of robotics and “artificial” intelligence (perhaps more properly “synthetic intelligence” once we’ve actually got it figured out), one usually looks to hard science fiction books. Isaac Asimov in particular comes to mind.

A few movies have done an ok job, including the interesting but also very flawed “I, Robot” with Will Smith and Bridget Moynahan, and Terminator: Salvation…. Both were at least decent movies, but neither felt particularly realistic and both tried to pull on our emotions in fairly obvious ways that felt anything but organic… more

“On Intelligence” by Jeff Hawkins

This book is surprisingly good in its ability to reach both the lay reader (for at least the first half) and the reader familiar with neuroscience. Articles since its publications provide much greater detail and are very useful for those interested in going deeper, but On Intelligence serves very well as an introduction to the concepts. The ideas expressed in On Intelligence are important both for scientific advancement and for philosophical consideration. While one could argue that perhaps there are other forms of intelligence or ways to produce intelligence, Hawkins does a good job in arguing what intelligence is in terms of mammalian brains and what the basic neocortical unit does. While Hawkins brings these ideas together in an orderly framework, he does give credit to the many neuroscientists responsible for the various components and underlying ideas that make it possible. These ideas as a whole until recently have not been sufficiently discussed in the neuroscience community in my opinion, and I believe they will aid (and in fact already have aided) greatly in advancing our understanding of the brain and creating real “artificial” intelligence that isn’t actually artificial at all.

The balance between addressing the expert and lay audiences did at …

Analyzing Neuronal Morphology with Gene Sequencing Approaches

Analysis of neuronal morphology has until recently been limited to small data sets due to the amount of time necessary to generate a digitized representation of a neuron’s structure.

Recent efforts to curate data from many different labs working in parallel on vastly differing topics has led to the NeuroMorpho.Org database which currently provides access and metadata for over 10,000 neurons from a variety of species, cell types, brain regions, and experimental conditions.

‘Mental Floss’ Project Brings Artists and Scientists Together

Mason faculty and students create an interpretive 3-D sculpture called “Mental Floss.” The sculpture depicts 13 different neurons that are located in the hippocampus, the region of the brain responsible for processing autobiographical memories.

“Our goal for this project was to provoke viewers to ponder not only how intricate and complex the inner fabric of the brain appears, but also how beautiful and awe-inspiring it can be, providing a bridge between rational thought and emotions,” says Ascoli.

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