A virtual journey through the Allen Institute for Brain Science’s Electron Microscopy (EM) imaging program

Published on April 9, 2014 by Allen Institute for Brain Science

The 12 full-length, undergraduate-level video lectures below are entitled “Coding & Vision 101” and are produced by the Allen Institute for Brain Science as an educational resource for the community.

Published to YouTube in late 2015 and early 2015 by Allen Institute for Brain Science

Allen Institute webpage for all videos

Lecture 1: A Walk-through of the Mammalian Visual System

“From the retina to the superior colliculus, the lateral geniculate nucleus into primary visual cortex and beyond, R. Clay Reid gives a tour of the mammalian visual system highlighting the Nobel-prize winning discoveries of Hubel & Wiesel.”

Lecture 2: What is Meant by Computation?

“From Universal Turing Machines to McCulloch-Pitts and Hopfield associative memory networks, Christof Koch explains what is meant by computation.”

https://www.youtube.com/watch?v=dwOGh6qkzG4

Lecture 3: The Structure of the Neocortex

“In an overview of the structure of the mammalian neocortex, Dr. Clay Reid explains how the mammalian cortex is organized ...

“This movie displays 21 mapping experiments from the Allen Mouse Brain Connectivity Atlas: a tool to investigate how different regions of the brain are connected. The density of axons at each voxel (dot) are displayed as overlapping circles color-coded by the area of the brain from which the axons are projecting. This animation shows how projections from different regions of the cortex divide the thalamus and striatum into distinct domains. The Allen Mouse Brain Connectivity Atlas is available to everyone online at www.brain-map.org.“

Published on April 9, 2014 by Allen Institute for Brain Science

A brief tour of the Allen Institute’s new building, under construction in Seattle’s South Lake Union neighborhood

Published on October 14, 2014 by Allen Institute

The art and science of measuring the electrical activity of many individual neurons at the same time

Published on March 24, 2015  by Allen Institute for Brain Science

“This video shows a composite of 80 injection sites of a viral tracer in the cortex (round spheres) and their major projections into the thalamus. We can clearly see that the spatial pattern of the injections is conserved in the thalamus. This kind of information was only previously available in piecemeal form, but with the comprehensive, standardized data in the Allen Mouse Brain Connectivity Atlas, we can reproducibly measure and visualize this topography.”

Published on February 27, 2014 by Allen Institute for Brain Science

“Brain mapping and integrating multimodal data across subjects and projects.”

Dr. Arthur Toga is Provost Professor of Ophthalmology, Neurology, Psychiatry and the Behavioral Sciences, Radiology and Engineering at the University of Southern California, and serves as the inaugural Director of the USC Institute for Neuroimaging and Informatics. He also holds an appointment in the USC Viterbi School of Engineering. A leading authority on neuroimaging, informatics, mapping brain structure and function, and brain atlasing, Dr. Toga is the former Distinguished Professor of Neurology, University Professor, Vice Chair of the Department of Neurology, Associate Dean at the Geffen School of Medicine, and Co-Director of the UCLA Brain Mapping Center.

Published on October 3, 2013  by Allen Institute for Brain Science

Commercializing auditory neuroscience

Dr. Donald “Lloyd” Watts has worked as an engineer at Microtel Pacific Research, Synaptics and Arithmos. In 1997, he joined Paul Allen’s Interval Research Corporation and continued his research in reverse-engineering the human auditory pathway. In 2000, he founded Audience, Inc., to commercialize his research, with investment from Paul Allen, Carver Mead and Allan Crawford. He served as Chairman and Chief Executive Officer from 2000-2005, leading the development of the company’s core technologies. In 2005, he transitioned to the role of Audience’s Chief Technology Officer. In 2011, he became Chief Scientist. In 2013, he retired from Audience.

Published on October 3, 2013 by Allen Institute for Brain Science

Published on November 12, 2012  by Allen Institute for Brain Science

Dr. Cori Bargmann, recent winner of the Kavli Prize in Neuroscience and a pioneer in methods of looking at C. elegans to uncover how neural circuits operate, presented the idea that particular classes of genes — neuropeptides to be specific — are good places to look for the genetic origin of behavior. Because much of the genome is conserved across species and throughout time, new behaviors may be created by redeploying old genes in different ways.

Uncovering the basic building blocks of behavior, she believes, is an unsolved question in neuroscience that is now becoming solvable.

“The question is not whether calbindin is expressed in the hippocampus, but whether it has something to do with the unique functions of human memory capabilities,” Bargmann said. “That is a hard question.” Certain kinds of molecules relate to innate behaviors that are shared across ...

Published on October 12, 2012  by Allen Institute for Brain Science

“Brain rhythms and cognition”

From physics to electrophysiology and imaging, Dr. Miller and his lab focus on broad and far-reaching approaches to neuroscience questions. This symposium talk focused on questions similarly posed by Sabine Kastner, namely the relationship between action potential timing and brain function. By recording neural activity in monkeys as they switch among two tasks, Miller found that over half of the recording sites in the network for one task also appear to participate in the network for the other task. This suggests that circuitry in the prefrontal cortex may overlap and that oscillations are the key to selecting appropriate networks for the task that needs to be performed. Miller showed that neural ensembles, or networks, in close proximity oscillate out of phase with one another to avoid being simultaneously activated. That is, the oscillations bind neural ensembles ...

“Deciphering the mammalian brain transcriptome”

Published on November 12, 2012  by Allen Institute for Brain Science

The development, structure and function of our brains are guided by selective usage of the 20,000-odd genes in our genomes. Taking advantage of the Allen Institute’s anatomically and genomically comprehensive atlases of gene expression in the developing brain in species from mouse to human, Dr. Lein explores the molecular logic of gene expression in the brain. How do gene expression profiles relate to the functional and cellular architecture of the brain, and what makes the human brain unique? Focusing on the human neocortex, the outermost layer of the brain, Lein showed that molecular similarities reflect spatial proximity across the neocortex; such that neighboring cortical regions are more similar to one another than to more distant regions. Surprisingly, these molecular similarities vary across the cortex in a graded fashion, in contrast to models of cortical architecture ...

“The role of thalamo-cortical interactions in spatial attention”

Similar to the questions posed by Ila Fiete and Earl Miller, Dr. Kastner asks: How do large-scale networks achieve cognition? How do the connections between molecules and neurons give rise to complex visual processing that we as primates enjoy? The basic premise of her work relies on the assumption that spike timing may play a critical role in brain function, particularly for higher cognitive functions, and that how neurons are connected may have important implications on the function of their networks. By simultaneously recording neural activity from three areas in the brain’s attentional network, Kastner has developed a hypothesis that identifies one area as performing a synchronizing function between the other two in order to optimize the transmission of information between them. She maintains that the pulvinar, a collection of nuclei in the back of the thalamus, is strongly connected to the ...

“A new class of neural population codes”

Dr. Fiete is a theoretician, the only member of such discipline at this year’s symposium, whose work relates closely to various approaches of other speakers. An Alfred P. Sloan Foundation Fellow, a Searle Scholar, and a McKnight Scholar, Fiete studies coding of sensory or memory information in neural populations, ultimately seeking to unravel the meanings in such patterns. She aims to reduce noise-induced errors in measurements and recording of brain activity by searching for a type of neural population code that, for over six decades now, has been known to exist theoretically but has not been unambiguously described. Most neural codes in the sensory and motor cortices tend to follow a classical population code, where accuracy increases with population size. These, however, are considered weak codes. The brain makes up for this, posits Fiete, by organizing in an interleaving system she compared to ...

“Neurotechnology: Fixing broken brains by decoding cortex”

Dr. Donoghue’s lab works in both basic and applied neuroscience, studying network computation on one end, and restoring lost motor cortical function on the other end. His work has culminated in BrainGate, a human brain-computer interface that senses neural activity in the motor cortex and decodes it to instruct a robotic arm or a cursor, reconnecting the cortex to lost action in the case of spinal cord injury or paralyzing disease such as amyotrophic lateral sclerosis. Donoghue showed video clips from his lab featuring long-paralyzed patients successfully navigating a robotic arm to drink their favorite beverage or guiding a computer cursor to communicate with loved ones. Among other noteworthy aspects of this work are the two notions that 1) the program actually decodes activity in the motor cortex rather than using a binary measure of activity (e.g., on or off) and 2) individual neurons in the motor cortex retain activity and function, even in quadriplegics who have not used this area of the brain in over a dozen years. While the functional utility of this work is self-evident, the value and applications to basic neuroscience are no less important. In going from a plan ...

“Using human genetics and stem cells to study brain development”

Ricardo Dolmetsch, recently joining the Allen Institute team from Stanford University, discussed his plans for a research program in molecular networks. The goals of the program, he described, are to 1) identify the molecular networks that control neuronal development and function, 2) understand the cellular and molecular basis of neurdevelopmental diseases, and 3) generate public resources that facilitate the study of brain development and developmental diseases. In a landscape of increasing data collection and “big science”, Dolmetsch suggested a refined and potentially more efficient tactic towards reaching these goals: use human genetic diversity to prioritize data collection. The idea is to genotype human cells to identify critical signaling pathways and molecular hubs that regulate brain development and are affected in disease. The neuroscience community has been uncovering mountains of copy number variants (CNVs) and rare mutations (RMs) that tip the ...

Functional magnetic resonance imaging (fMRI) detects the location of functions in the brain better than any other method we have today. While localization is necessary, it is not sufficient for understanding how the brain works. Dr. Gallant suggests the reverse approach – to search for functional maps. That is, he uses brain activity to determine or reconstruct what a subject was looking at. To this end the Gallant lab has constructed the WordNet model, which is able to predict what an observer is seeing from 2,000 nouns and verbs. The process uses brain activity in fMRI to predict from semantic models while an observer watches a video, and the results are remarkably accurate. Dr. Gallant explains how encoding models, decoding models, and functional maps of the brain are all closely related. “Once you have encoding, you get decoding for free,” he proclaims.

Published on November 13, ...

Molecular architecture of the circadian clock in mammals

Dr. Joseph Takahashi is Chair of the Department of Neuroscience and an Investigator of the Howard Hughes Medical Institute at the University of Texas Southwestern Medical Center. He currently holds the Loyd B. Sands Distinguished Chair in Neuroscience. Before moving to UT Southwestern, Dr. Takahashi was the Walter and Mary Elizabeth Glass Professor in the Life Sciences at Northwestern University. Dr. Takahashi has pioneered the use of forward genetics and positional cloning in the mouse as a tool for discovery of genes underlying neurobiology and behavior, and his discovery of the mouse and human clock genes led to a description of a conserved circadian clock mechanism in animals.

Published on October 3, 2013  by Allen Institute for Brain Science

Title: Fluid dynamics in the brain

Dr. Gregor Eichele is Director and Scientific Member at the Max-Planck-Institute of Biophysical Chemistry, Goettingen, Germany. At the Max-Planck Genes and Behavior Department, Dr. Eichele investigates the dynamic interplay between gene expression, development and behavior. His research focuses on mammalian brain development and takes advantage of a gene expression database in which a very large number of gene expression patterns are stored. Dr. Eichele’s second focus of research is on circadian clocks which determine sleep/wake and daily feeding patterns, regulate the 24-hour patterns of production of certain hormones and steer other biological activities that are tied to the recurring day/night cycle. His third focus of research concerns functional genomics. Work using robotic in situ hybridization reveals in detail the spatial and temporal dynamics of the transcriptome in the developing and adult mammalian brain.

Published on October 3, 2013  by Allen Institute for Brain Science

OnAir Post: Gregor Eichele: 2013 Annual Symposium