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The Amazing Brain: Visualizing Data to Understand Brain Networks

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The NIH-led Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative continues to teach us about the world’s most sophisticated computer: the human brain. This striking image offers a spectacular case in point, thanks to a new tool called Visual Neuronal Dynamics (VND).

VND is not a camera. It is a powerful software program that can display, animate, and analyze models of neurons and their connections, or networks, using 3D graphics. What you’re seeing in this colorful image is a strip of mouse primary visual cortex, the area in the brain where incoming sensory information gets processed into vision.

This strip contains more than 230,000 neurons of 17 different cell types. Long and spindly excitatory neurons that point upward (purple, blue, red, orange) are intermingled with short and stubby inhibitory neurons (green, cyan, magenta). Slicing through the neuronal landscape is a neuropixels probe (silver): a tiny flexible silicon detector that can record brain activity in awake animals [1].

Developed by Emad Tajkhorshid and his team at University of Illinois at Urbana-Champaign, along with Anton Arkhipov of the Allen Institute, Seattle, VND represents a scientific milestone for neuroscience: using an adept software tool to see and analyze massive neuronal datasets on a computer. What’s also nice is the computer doesn’t have to be a fancy one, and VND’s instructions, or code, are publicly available for anyone to use.

VND is the neuroscience-adapted cousin of Visual Molecular Dynamics (VMD), a popular molecular biology visualization tool to see life up close in 3D, also developed by Tajkhorshid’s group [2]. By modeling and visualizing neurons and their connections, VND helps neuroscientists understand at their desktops how neural networks are organized and what happens when they are manipulated. Those visualizations then lay the groundwork for follow-up lab studies to validate the data and build upon them.

Through the Allen Institute, the NIH BRAIN Initiative is compiling a comprehensive whole-brain atlas of cell types in the mouse, and Arkhipov’s work integrates these data into computer models. In May 2020, his group published comprehensive models of the mouse primary visual cortex [3].

Arkhipov and team are now working to understand how the primary visual cortex’s physical structure (the cell shapes and connections within its complicated circuits) determines its outputs. For example, how do specific connections determine network activity? Or, how fast do cells fire under different conditions?

Ultimately, such computational research may help us understand how brain injuries or disease affect the structure and function of these neural networks. VND should also propel understanding of many other areas of the brain, for which the data are accumulating rapidly, to answer similar questions that still remain mysterious to scientists.

In the meantime, VND is also creating some award-winning art. The image above was the second-place photo in the 2021 “Show us Your BRAINs!” Photo and Video Contest sponsored by the NIH BRAIN Initiative.

References:

[1] Fully integrated silicon probes for high-density recording of neural activity. Jun JJ, Steinmetz NA, Siegle JH, Denman DJ, Bauza M, Barbarits B, Lee AK, Anastassiou CA, Andrei A, Aydın Ç, Barbic M, Blanche TJ, Bonin V, Couto J, Dutta B, Gratiy SL, Gutnisky DA, Häusser M, Karsh B, Ledochowitsch P, Lopez CM, Mitelut C, Musa S, Okun M, Pachitariu M, Putzeys J, Rich PD, Rossant C, Sun WL, Svoboda K, Carandini M, Harris KD, Koch C, O’Keefe J, Harris TD. Nature. 2017 Nov 8;551(7679):232-236.

[2] VMD: visual molecular dynamics. Humphrey W, Dalke A, Schulten K. J Mol Graph. 1996 Feb;14(1):33-8, 27-8.

[3] Systematic integration of structural and functional data into multi-scale models of mouse primary visual cortex. Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A. Neuron. 2020 May 6;106(3):388-403.e18

Links:

The Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

Models of the Mouse Primary Visual Cortex (Allen Institute, Seattle)

Visual Neuronal Dynamics (NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign)

Tajkhorshid Lab (University of Illinois at Urbana-Champaign)

Arkhipov Lab (Allen Institute)

Show Us Your BRAINs! Photo & Video Contest (BRAIN Initiative/NIH)

NIH Support: National Institute of Neurological Disorders and Stroke


The Amazing Brain: Toward a Wiring Diagram of Connectivity

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It’s summertime and, thanks to the gift of COVID-19 vaccines, many folks are getting the chance to take a break. So, I think it’s also time that my blog readers finally get a break from what’s been nearly 18 months of non-stop coverage of COVID-19 research. And I can’t think of a more enjoyable way to do that than by taking a look at just a few of the many spectacular images and insights that researchers have derived about the amazing brain.

The Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative, which is an NIH-led project aimed at revolutionizing our understanding of the human brain, happens to have generated some of the coolest—and most informative—imagery now available in neuroscience. So, throughout the month of August, I’ll share some of the entries from the initiative’s latest Show Us Your BRAINs! Photo and Video Contest.

With nearly 100 billion neurons and 100 trillion connections, the human brain remains one of the greatest mysteries in science. Among the many ways in which neuroscientists are using imaging to solve these mysteries is by developing more detailed maps of connectivity within the brain.

For example, the image featured above from the contest shows a dense weave of neurons in the anterior cingulate cortex, which is the part of the brain involved in learning, memory, and some motor control. In this fluorescence micrograph of tissue from a mouse, each neuron has been labeled with green fluorescent protein, enabling you to see how it connects to other neurons through arm-like projections called axons and dendrites.

The various connections, or circuits, within the brain process and relay distinct types of sensory information. In fact, a single neuron can form a thousand or more of these connections. Among the biggest challenges in biomedicine today is deciphering how these circuits work, and how they can misfire to cause potentially debilitating neurological conditions, including Alzheimer’s disease, Parkinson’s disease, autism, epilepsy, schizophrenia, depression, and traumatic brain injury.

This image was produced by Nicholas Foster and Lei Gao in the NIH-supported lab of Hong Wei Dong, University of California, Los Angeles. The Dong Lab is busy cataloging cell types and helping to assemble a wiring diagram of the connectivity in the mammalian brain—just one of the BRAIN Initiative’s many audacious goals. Stay tuned for more throughout the month of August!

Links:

Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

Dong Lab (University of California, Los Angeles)

Show Us Your BRAINs! Photo and Video Contest (BRAIN Initiative/NIH)

NIH Support: National Institute of Mental Health


Celebrating the Fourth with Neuroscience Fireworks

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There’s so much to celebrate about our country this Fourth of July. That includes giving thanks to all those healthcare providers who have put themselves in harm’s way to staff the ERs, hospital wards, and ICUs to care for those afflicted with COVID-19, and also for everyone who worked so diligently to develop, test, and distribute COVID-19 vaccines.

These “shots of hope,” created with rigorous science and in record time, are making it possible for a great many Americans to gather safely once again with family and friends. So, if you’re vaccinated (and I really hope you are—because these vaccines have been proven safe and highly effective), fire up the grill, crank up the music, and get ready to show your true red, white, and blue colors. My wife and I—both fully vaccinated—intend to do just that!

To help get the celebration rolling, I’d like to share a couple minutes of some pretty amazing biological fireworks. While the track of a John Philip Sousa march is added just for fun, what you see in the video above is the result of some very serious neuroscience research that is scientifically, as well as visually, breath taking. Credit for this work goes to an NIH-supported team that includes Ricardo Azevedo and Sunil Gandhi, at the Center for the Neurobiology of Learning and Memory, University of California, Irvine, and their collaborator Damian Wheeler, Translucence Biosystems, Irvine, CA. Azevedo is also an NIH National Research Service Award fellow and a Medical Scientist Training Program trainee with Gandhi.

The team’s video starts off with 3D, colorized renderings of a mouse brain at cellular resolution. About 25 seconds in, the video flashes to a bundle of nerve fibers called the fornix. Thanks to the wonders of fluorescent labeling combined with “tissue-clearing” and other innovative technologies, you can clearly see the round cell bodies of individual neurons, along with the long, arm-like axons that they use to send out signals and connect with other neurons to form signaling circuits. The human brain has nearly 100 trillion of these circuits and, when activated, they process incoming sensory information and provide outputs that lead to our thoughts, words, feelings, and actions.

As shown in the video, the nerve fibers of the fornix provide a major output pathway from the hippocampus, a region of the brain involved in memory. Next, we travel to the brain’s neocortex, the outermost part of the brain that’s responsible for complex behaviors, and then move on to explore an intricate structure called the corticospinal tract, which carries motor commands to the spinal cord. The final stop is the olfactory tubercle —towards the base of the frontal lobe—a key player in odor processing and motivated behaviors.

Azevedo and his colleagues imaged the brain in this video in about 40 minutes using their imaging platform called the Translucence Biosystems’ Mesoscale Imaging System™. This process starts with a tissue-clearing method that eliminates light-scattering lipids, leaving the mouse brain transparent. From there, advanced light-sheet microscopy makes thin optical sections of the tissue, and 3D data processing algorithms reconstruct the image to high resolution.

Using this platform, researchers can take brain-wide snapshots of neuronal activity linked to a specific behavior. They can also use it to trace neural circuits that span various regions of the brain, allowing them to form new hypotheses about the brain’s connectivity and how such connectivity contributes to memory and behavior.

The video that you see here is a special, extended version of the team’s first-place video from the NIH-supported BRAIN Initiative’s 2020 “Show Us Your BRAINS!” imaging contest. Because of the great potential of this next-generation technology, Translucence Biosystems has received Small Business Innovation Research grants from NIH’s National Institute of Mental Health to disseminate its “brain-clearing” imaging technology to the neuroscience community.

As more researchers try out this innovative approach, one can only imagine how much more data will be generated to enhance our understanding of how the brain functions in health and disease. That is what will be truly spectacular for everyone working on new and better ways to help people suffering from Alzheimer’s disease, Parkinson’s disease, schizophrenia, autism, epilepsy, traumatic brain injury, depression, and so many other neurological and psychiatric disorders.

Wishing all of you a happy and healthy July Fourth!

Links:

Brain Research Through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

NIH National Research Service Award

Medical Scientist Training Program (National Institute of General Medical Sciences/NIH)

Small Business Innovation Research and Small Business Technology Transfer (NIH)

Translucence Biosystems (Irvine, CA)

Sunil Gandhi (University of California, Irvine)

Ricardo Azevedo (University of California, Irvine)

Video: iDISCO-cleared whole brain from a Thy1-GFP mouse (Translucence Biosystems)

Show Us Your BRAINs! Photo & Video Contest (Brain Initiative/NIH)

NIH Support: National Institute of Mental Health; National Eye Institute


3D Neuroscience at the Speed of Life

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This fluorescent worm makes for much more than a mesmerizing video. It showcases a significant technological leap forward in our ability to capture in real time the firing of individual neurons in a living, freely moving animal.

As this Caenorhabditis elegans worm undulates, 113 neurons throughout its brain and body (green/yellow spots) get brighter and darker as each neuron activates and deactivates. In fact, about halfway through the video, you can see streaks tracking the positions of individual neurons (blue/purple-colored lines) from one frame to the next. Until now, it would have been technologically impossible to capture this “speed of life” with such clarity.

With funding from the NIH-led Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative, Elizabeth Hillman at Columbia University’s Zuckerman Institute, New York, has pioneered the pairing of a 3D live-imaging microscope with an ultra-fast camera. This pairing, showcased above, is a technique called Swept Confocally Aligned Planar Excitation (SCAPE) microscopy.

Since first demonstrating SCAPE in February 2015 [1], Hillman and her team have worked hard to improve, refine, and expand the approach. Recently, they used SCAPE 1.0 to image how proprioceptive neurons in fruit-fly larvae sense body position while crawling. Now, as described in Nature Methods, they introduce SCAPE “2.0,” with boosted resolution and a much faster camera—enabling 3D imaging at speeds hundreds of times faster than conventional microscopes [2]. To track a very wiggly worm, the researchers image their target 25 times a second!

As with the first-generation SCAPE, version 2.0 uses a scanning mirror to sweep a slanted sheet of light across a sample. This same mirror redirects light coming from the illuminated plane to focus onto a stationary high-speed camera. The approach lets SCAPE grab 3D imaging at very high speeds, while also causing very little photobleaching compared to conventional point-scanning microscopes, reducing sample damage that often occurs during time-lapse microscopy.

Like SCAPE 1.0, since only a single, stationary objective lens is used, the upgraded 2.0 system doesn’t need to hold, move, or disturb a sample during imaging. This flexibility enables scientists to use SCAPE in a wide range of experiments where they can present stimuli or probe an animal’s behavior—all while imaging how the underlying cells drive and depict those behaviors.

The SCAPE 2.0 paper shows the system’s biological versatility by also recording the beating heart of a zebrafish embryo at record-breaking speeds. In addition, SCAPE 2.0 can rapidly image large fixed, cleared, and expanded tissues such as the retina, brain, and spinal cord—enabling tracing of the shape and connectivity of cellular circuits. Hillman and her team are dedicated to exporting their technology; they provide guidance and a parts list for SCAPE 2.0 so that researchers can build their own version using inexpensive off-the-shelf parts.

Watching worms wriggling around may remind us of middle-school science class. But to neuroscientists, these images represent progress toward understanding the nervous system in action, literally at the speed of life!

References:

[1] . Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms. Bouchard MB, Voleti V, Mendes CS, Lacefield C, et al Nature Photonics. 2015;9(2):113-119.

[2] Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0. Voleti V, Patel KB, Li W, Campos CP, et al. Nat Methods. 2019 Sept 27;16:1054–1062.

Links:

Using Research Organisms to Study Health and Disease (National Institute of General Medical Sciences/NIH)

The Brain Research through Advancing Innovative Neurotechnologies® (BRAIN) Initiative (NIH)

Hillman Lab (Columbia University, New York)

NIH Support: National Institute of Neurological Disorders and Stroke; National Heart, Lung, and Blood Institute


Distinctive Brain ‘Subnetwork’ Tied to Feeling Blue

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Woman looking distressed

Credit: :iStock/kieferpix

Experiencing a range of emotions is a normal part of human life, but much remains to be discovered about the neuroscience of mood. In a step toward unraveling some of those biological mysteries, researchers recently identified a distinctive pattern of brain activity associated with worsening mood, particularly among people who tend to be anxious.

In the new study, researchers studied 21 people who were hospitalized as part of preparation for epilepsy surgery,  and took continuous recordings of the brain’s electrical activity for seven to 10 days. During that same period, the volunteers also kept track of their moods. In 13 of the participants, low mood turned out to be associated with stronger activity in a “subnetwork” that involved crosstalk between the brain’s amygdala, which mediates fear and other emotions, and the hippocampus, which aids in memory.


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