First Movie Of An Entire Brain’s Neuronal Activity — The Physics arXiv Blog — Medium

First Movie Of An Entire Brain’s Neuronal Activity — The Physics arXiv Blog — Medium: ...Schrödel, Prevedel and co developed a way to ensure that the genes only fluoresce in the nucleus of each neuron. That makes active neurons much easier to tell apart...

...light sculpting. This works by bouncing the spot of laser light off a grating that stretches it out. This creates a disc of light that images an area of the brain in one go rather than a single point. In affect, it produces a cross-sectional image of brain activtiy.

The advantage is that the light disc need only be scanned in one direction to capture the whole volume of the brain. And this can be done at a rate that allows the team to film the neuronal activity of the entire brain at a rate of 80 frames per second.

Neuroscientists find cortical columns in brain not uniform, challenging large-scale simulation models | KurzweilAI

Neuroscientists find cortical columns in brain not uniform, challenging large-scale simulation models | KurzweilAI: The study was based on recent advances in high-resolution imaging and reconstruction techniques (confocal microscopy and automated image-processing routines)... enabling researchers to automatically and reliably detect the 3D location and type of every nerve cell throughout the entire brain...
“By determining the exact numbers and distributions of nerve cells within almost 100 cortical columns, the substantial differences observed across columns within the same animal argue against the principle of cortical uniformity.”

Nanoscale neuronal activity measured for the first time | KurzweilAI

Nanoscale neuronal activity measured for the first time | KurzweilAI: “The nanopipette hovers above the surface of the sample and scans the structure to reveal its three-dimensional topography. The same nanopipette then attaches to the surface at selected locations on the structure to record electrical activity.

Imaging most of a worm’s brain activity at high resolution and in a single operation | KurzweilAI

Imaging most of a worm’s brain activity at high resolution and in a single operation | KurzweilAI: Visualizing the neurons also requires tagging them with a fluorescent protein that lights up when it binds to calcium, signaling the nerve cells’ activity.

“The neurons in a worm’s head are so densely packed that we could not distinguish them on our first images...”

“Our solution was to insert the calcium sensor into the nuclei rather than the entire cells, thereby sharpening the image so we could identify single neurons.”

Video: Near-Whole Brain Activity Map in Fish | MIT Technology Review

Video: Near-Whole Brain Activity Map in Fish | MIT Technology Review: ...researchers reported that they were able to watch the individual activity of nearly all the neurons in a fish’s brain at the same time...

Now, HHMI has put together a video about the work, and it’s worth a look. Neuroscientist Philipp Keller explains how some of the technology behind the experiment works. Best of all, we get to see more of the complex flickering constellations of brain cells—fish thoughts in action. This work is the first time researchers have been able to look at the activity of nearly all neurons in a vertebrate brain.

How to reconstruct from brain images which letter a person was reading | KurzweilAI

How to reconstruct from brain images which letter a person was reading | KurzweilAI: The researchers “taught” the model how 1200 voxels (volumetric pixels) of 2x2x2 mm from the brain scans correspond to individual pixels in different versions of handwritten letters...
“In our further research we will be working with a more powerful MRI scanner,” said Sanne Schoenmakers, who is working on a thesis about decoding thoughts. “Due to the higher resolution of the scanner, we hope to be able to link the model to more detailed images. We are currently linking images of letters to 1200 voxels in the brain; with the more powerful scanner we will link images of faces to 15,000 voxels.”

Transparent brains make neuroscience clearer

Transparent brains make neuroscience clearer: First, they remove the brain from a mouse and infuse it with a see-through gel that collects in the neurons' lipid membranes. As the gel solidifies, it takes the shape of the membranes and creates a matrix that holds the cells' proteins, DNA and RNA in place. Then the team adds a second chemical that dissolves the lipids, leaving a transparent brain made out of gel that retains the brain's proteins, DNA and RNA in their original positions.

The technique – which the researchers have named Clarity – makes it easy to see the structure of individual neurons, and preserves the fragile interconnections in near-perfect detail...

The team has successfully turned a 0.5-millimetre-thick section of human brain transparent, but working with larger chunks of human brain may be a challenge, as human neurons have a large amount of fatty protein surrounding their axons that must all be dissolved.

High-resolution Brain Atlas finished

High-resolution Brain Atlas finished: Working with just two whole male brains and a single hemisphere from a third, the team used around 900 precise subdivisions and 60,000 gene expression probes to create the atlas.

This image is a 3D rendering of just one of the genes in internal brain structures overlaid onto an MRI scan. The level of gene expression at the different points on the map is indicated on a colour scale, with blue dots reflecting relatively low expression and red dots reflecting high expression.

Mapping the brain’s superhighways

Mapping the brain’s superhighways: Scientists led by Van Wedeen of Massachusetts General Hospital and Harvard Medical School in Boston used a scanning technique called diffusion magnetic resonance imaging that detects the direction of traffic flow along white matter tracts, the brain’s information superhighways. The scans revealed that these brain signals form a grid, made up of parallel and perpendicular tracts woven together into curved sheets.

This grid is a general feature of primate brains, Wedeen and colleagues report in the March 30 Science. Brains of rhesus monkeys, owl monkeys, marmosets and prosimian galagos contained similar geometric patterns to those found in human volunteers, suggesting the grid’s deep evolutionary roots.

Fusion plasma research helps neurologists to hear above the noise

Fusion plasma research helps neurologists to hear above the noise:  MEG has great potential as a useful diagnostic tool - it is non-invasive and much more comfortable for the subject than other techniques - but the neuromagnetic signal varies fast, the signal to noise ratio is low meaning that such data are challenging to understand.

These challenges - extracting signal from noise in observations that can only be made from external sensors - are also often faced in magnetically confined plasmas for fusion. Fusion plasma researchers at the University of Warwick have developed methods to deal with data analysis problems similar to those faced by the neuroscientists. The Warwick researchers have now shared these methods and analytical techniques with their neuroscientific colleagues in Cambridge and Birkbeck. Together they have been able to carry out new studies that are already beginning to provide new insights into the brain's network - they have made the first map of the dynamically changing network of the brain as it deals with the 'surprise' of the different sounds.

Download Knowledge Directly to Your Brain, Matrix-Style

Download Knowledge Directly to Your Brain, Matrix-Style: Led by BU neuroscientist Takeo Watanabe, researchers used a method called decoded fMRI neurofeedback to stimulate the visual cortex. First they showed participants circles at different orientations. Then they used fMRI to watch the participants’ brain activity. The researchers were then able to train the participants to recreate this visual cortex activity.

The volunteers were again placed in MRI machines and asked to visualize shapes of certain colors. The participants were asked to “somehow regulate activity in the posterior part of the brain” to make a solid green disc as large as they could. They were told they would get a paid bonus proportional to the size of this disc, but they weren’t told anything about what the disc meant. The researchers watched the participants’ brain activity and monitored the activation patterns in their visual cortices.

Neurons illuminate as they fire, may open new ways to trace brain signals

Neurons illuminate as they fire, may open new ways to trace brain signals: Cohen and his team infected brain cells that had been cultured in the lab with a genetically altered virus that contained the protein-producing gene. Once infected, the cells began manufacturing the protein, allowing them to light up.

When a neuron fires, its voltage reverses for a very short time, about a thousandth of a second, he explained. “This brief spike in voltage travels down the neuron and then activates other neurons downstream. Our protein is sitting in the [outside] membrane of the neurons, so as that pulse washes over the proteins, they light up, giving us an image of the neurons as they fire.”

We can now see how these signals spread through the neuronal network, said Cohen.

Digital holographic microscopy allows for 50 times better resolution in viewing neurons | KurzweilAI

Digital holographic microscopy allows for 50 times better resolution in viewing neurons | KurzweilAI: The technique accurately visualizes the electrical activities of hundreds of neurons simultaneously, at up to 500 images per second — without damaging them with electrodes...

To understand how DHM works, imagine a large rock in an ocean of perfectly regular waves. As the waves deform around the rock and come out the other side, they carry information about the rock’s shape. This information can be extracted by comparing it to waves that did not smash up against the rock, and an image of the rock can be reconstructed.
DHM does this with a laser beam by pointing a single wavelength at an object (in this case, neurons), collecting the distorted wave on the other side, and comparing it to a reference beam.

Mapping connectomes in the visual cortex | KurzweilAI

Mapping connectomes in the visual cortex | KurzweilAI: The researchers used high-resolution imaging of neurons in the visual cortex of mouse brains, which contains thousands of neurons and millions of different connections. Using high-resolution imaging, they were able to detect which of these neurons responded to a particular stimulus, for example, a horizontal edge.

Taking a slice of the same tissue, the researchers then applied small currents to a subset of neurons in turn to see which other neurons responded and which of them were synaptically connected. By repeating this technique many times, the researchers were able to trace the function and connectivity of hundreds of nerve cells in the visual cortex.

Brain imaging provides window into consciousness | KurzweilAI

Brain imaging provides window into consciousness | KurzweilAI: While progress has been made in elucidating the range of brain function in those who are severely injured, Dr. Schiff urges caution. “Although everyone wants to use a tool like this, fMRI is not yet capable of making clear measurements of cognitive performance. There will be a range of possible responses reflecting different capabilities in these patients that we have to further explore and understand,” he says.

Harvard Researchers Illuminate Connections Among Brain Cells in Technicolor | Popular Science

Harvard Researchers Illuminate Connections Among Brain Cells in Technicolor | Popular Science: In 2007, Harvard scientists figured out how to combine fluorescent proteins to create an entire color palette, and then used it to make mouse neurons glow so they could be traced through the brain. The “Brainbow” technique has helped scientists follow neurons’ connections, which had been almost impossible to untangle.
Fruit fly researchers have now done the same thing, producing a dual Brainbow of methods for making Drosophila neurons glow. It is much simpler and faster than staining individual neurons, another method for mapping brain connections.

Functional boost for magnetic resonance imaging

Functional boost for magnetic resonance imaging: "Their approach side-steps to some extent the problems inherent in current approaches to fMRI, namely low signal-to-noise ratio, high data volumes, differences between patients or subjects and artifacts caused by the movement of the person being scanned. Their approach allows them to turn large amounts of often noisy data into discrete sequences of neural activity events. The team has demonstrated how well their approach works by analyzing data from fMRI scans on volunteers involved in the simple activities of drinking a glass of water or a glass of glucose solution."

Advance makes MRI scans more than seven times faster

Advance makes MRI scans more than seven times faster: The faster scans are made possible by combining two technical improvements invented in the past decade that separately boosted scanning speeds two to four times over what was already the fastest MRI technique, echo planar imaging (EPI). Physical limitations of each method prevented further speed improvements, "but together their image accelerations are multiplied," Feinberg said...
"Other techniques which capture signals derived from neuronal activity, EEG or MEG, have much higher temporal resolution; hundred microsecond neuronal changes. But MRI has always been very slow, with 2 second temporal resolution," Feinberg said. "Now MRI is getting down to a few hundred milliseconds to scan the entire brain, and we are beginning to see neuronal network dynamics with the high spatial resolution of MRI."

How to Train Your Own Brain - Technology Review

How to Train Your Own Brain - Technology Review: "In addition, focusing on a limited region adds extra noise to the system—much like looking too closely at just one swatch of a Pointillist painting—the mix of odd colors doesn't make sense until you step back and see how the dots fit together. Psychologist Anna Rose Childress, Jeremy Magland, and their colleagues at the University of Pennsylvania have overcome this issue by designing a new system of whole-brain imaging and pairing it with an algorithm that let them determine which regions of the brain are most centrally involved in a certain thought process."

Video: 3-D Image Shows Brain's Circuitry In Highest Resolution Ever | Popular Science

Video: 3-D Image Shows Brain's Circuitry In Highest Resolution Ever | Popular Science: But his new method, which involves taking nano-thin slices of a mouse’s cortex, lets scientists actually count the synapses and catalog them according to their type. Called array tomography, it uses high-resolution photography, fluorescent proteins and a supercomputer to put everything together.

Smith and colleagues took a slab of mouse cortex and sliced it into 700-nanometer-thick sections. The sections were then stained with antibodies that would match 17 synapse-related proteins, and the scientists also added fluorescent molecules that glow in different colors in response to light. The antibodies were added in groups of three, and the brain tissue started changing colors. A computer took massive amounts of high-resolution pictures during each staining session, which were ultimately stitched together into a 3-D image...