Seeing the Brain With New CLARITY A new brain imaging technique called CLARITY allows neural structures to be reconstructed in three dimensions better than ever before. It does so by turning the brain “transparent”. Truly understanding the inner workings of the brain means studying not only how individual neurons function, but also how they are wired together. Even with techniques like the beautiful “brainbow”, untangling spaghetti-like long-range connections has proven difficult.  Stanford University neuroscientists have taken a step in that direction with their new CLARITY method. Neurons and other cells are normally labeled by sticking fluorescent tags on various proteins and other molecules that a researcher wants to study. That way we can literally see where and how they function. But looking into a three-dimensional brain is like peering into murky water: the fatty cell membranes and neuron sheaths just get in the way.  The Stanford researchers immobilized these mouse brains in a gel, then washed away all the murky muck. This left all the connections and proteins in their right place, free to be labeled in a clear block of brain Jell-O. For more: Head over to Nature News to read more, and be sure to watch their great, detailed video to find out more about how it was done. If you’re interested, here’s the research paper in this week’s Nature. 
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Seeing the Brain With New CLARITY A new brain imaging technique called CLARITY allows neural structures to be reconstructed in three dimensions better than ever before. It does so by turning the brain “transparent”. Truly understanding the inner workings of the brain means studying not only how individual neurons function, but also how they are wired together. Even with techniques like the beautiful “brainbow”, untangling spaghetti-like long-range connections has proven difficult.  Stanford University neuroscientists have taken a step in that direction with their new CLARITY method. Neurons and other cells are normally labeled by sticking fluorescent tags on various proteins and other molecules that a researcher wants to study. That way we can literally see where and how they function. But looking into a three-dimensional brain is like peering into murky water: the fatty cell membranes and neuron sheaths just get in the way.  The Stanford researchers immobilized these mouse brains in a gel, then washed away all the murky muck. This left all the connections and proteins in their right place, free to be labeled in a clear block of brain Jell-O. For more: Head over to Nature News to read more, and be sure to watch their great, detailed video to find out more about how it was done. If you’re interested, here’s the research paper in this week’s Nature. 
Zoom Info
Seeing the Brain With New CLARITY A new brain imaging technique called CLARITY allows neural structures to be reconstructed in three dimensions better than ever before. It does so by turning the brain “transparent”. Truly understanding the inner workings of the brain means studying not only how individual neurons function, but also how they are wired together. Even with techniques like the beautiful “brainbow”, untangling spaghetti-like long-range connections has proven difficult.  Stanford University neuroscientists have taken a step in that direction with their new CLARITY method. Neurons and other cells are normally labeled by sticking fluorescent tags on various proteins and other molecules that a researcher wants to study. That way we can literally see where and how they function. But looking into a three-dimensional brain is like peering into murky water: the fatty cell membranes and neuron sheaths just get in the way.  The Stanford researchers immobilized these mouse brains in a gel, then washed away all the murky muck. This left all the connections and proteins in their right place, free to be labeled in a clear block of brain Jell-O. For more: Head over to Nature News to read more, and be sure to watch their great, detailed video to find out more about how it was done. If you’re interested, here’s the research paper in this week’s Nature. 
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Seeing the Brain With New CLARITY

A new brain imaging technique called CLARITY allows neural structures to be reconstructed in three dimensions better than ever before. It does so by turning the brain “transparent”.

Truly understanding the inner workings of the brain means studying not only how individual neurons function, but also how they are wired together. Even with techniques like the beautiful “brainbow”, untangling spaghetti-like long-range connections has proven difficult. 

Stanford University neuroscientists have taken a step in that direction with their new CLARITY method. Neurons and other cells are normally labeled by sticking fluorescent tags on various proteins and other molecules that a researcher wants to study. That way we can literally see where and how they function. But looking into a three-dimensional brain is like peering into murky water: the fatty cell membranes and neuron sheaths just get in the way. 

The Stanford researchers immobilized these mouse brains in a gel, then washed away all the murky muck. This left all the connections and proteins in their right place, free to be labeled in a clear block of brain Jell-O.

For more: Head over to Nature News to read more, and be sure to watch their great, detailed video to find out more about how it was done. If you’re interested, here’s the research paper in this week’s Nature. 

EyeWire: You Play a Game, Scientists Map Neurons Everyone wins! You guys should really check out EyeWire, an online game that helps you map neurons without any knowledge of biology. It’s revolutionary neuroscience, harnessing the power of thousands of video gamers to do a job that supercomputers can barely do. EyeWire is a citizen science game created by MIT’s Sebastian Seung and friends (shout out to Amy from the Seung group for showing me this game!). Seung, famous for his work on the connectome (and the book of the same name), studies how mapping the nervous system’s connections help us define its true function. Understanding how our nervous system works requires knowing more than how one neuron works, we have to understand how they connect to each other to create larger networks.  In EyeWire, you tour through pattern-filled cubes, clicking colored blobs to help the software map the arms of J cells (that’s one above), a type of neuron in the retina whose connections are very poorly understood. It’s seriously addictive, and you’ll be making a real difference in our understanding of the brain. So why make a game? This kind of pattern recognition is very hard for computers to do. The human brain is amazingly adept at picking out patterns, far better than even our most powerful machines.  My only minor complaint is that its popularity is making gameplay a little slow this first week. The great I F*cking Love Science Facebook page helped crash their servers yesterday, which are now back up, but new players are only being allowed in a handful at a time. So follow EyeWire on Facebook to find out when you can sign up. You’ll be glad you did. I’m sure that the hordes of It’s Okay To Be Smart and other Tumblr science readers can crash the servers better than any Facebook page can, right? Game on!
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EyeWire: You Play a Game, Scientists Map Neurons

Everyone wins! You guys should really check out EyeWire, an online game that helps you map neurons without any knowledge of biology. It’s revolutionary neuroscience, harnessing the power of thousands of video gamers to do a job that supercomputers can barely do.

EyeWire is a citizen science game created by MIT’s Sebastian Seung and friends (shout out to Amy from the Seung group for showing me this game!). Seung, famous for his work on the connectome (and the book of the same name), studies how mapping the nervous system’s connections help us define its true function. Understanding how our nervous system works requires knowing more than how one neuron works, we have to understand how they connect to each other to create larger networks. 

In EyeWire, you tour through pattern-filled cubes, clicking colored blobs to help the software map the arms of J cells (that’s one above), a type of neuron in the retina whose connections are very poorly understood. It’s seriously addictive, and you’ll be making a real difference in our understanding of the brain.

So why make a game? This kind of pattern recognition is very hard for computers to do. The human brain is amazingly adept at picking out patterns, far better than even our most powerful machines. 

My only minor complaint is that its popularity is making gameplay a little slow this first week. The great I F*cking Love Science Facebook page helped crash their servers yesterday, which are now back up, but new players are only being allowed in a handful at a time. So follow EyeWire on Facebook to find out when you can sign up. You’ll be glad you did.

I’m sure that the hordes of It’s Okay To Be Smart and other Tumblr science readers can crash the servers better than any Facebook page can, right?

Game on!

The Connectome Debate: Is Mapping the Mind of a Worm Worth It? The connectome-related skepticism has been ramping up lately. So you mapped the complete neural network of a tiny worm (C. elegans, above) … so what? So you draw some pretty brain structures that don’t provide neuron by neuron detail … so what? Ferris Jabr has a great write-up of the “so whats” and the “this is what” at SciAm. Want to get up to date on the connectome debate? Start here. Because a lone connectome is a snapshot of pathways through which information might flow in an incredibly dynamic organ, it cannot reveal how neurons behave in real time, nor does it account for the many mysterious ways that neurons regulate one another’s behavior. Without such maps, however, scientists cannot thoroughly understand how the brain processes information at the level of the circuit. In combination with other tools, the C. elegans connectome has in fact taught scientists a lot about the worm’s behavior; partial connectomes that researchers have established in the crustacean nervous system have been similarly helpful. Scientists are also learning how to make connectomes faster than before and to enhance the information they provide. Many researchers in the field summarize their philosophy like this: “A connectome is necessary, but not sufficient.” So it’s taught us a bit about the workings of the worm, but maybe not everything. Will it translate to elucidating the workings of the human brain? Time will tell. Good read. (via Scientific American)
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The Connectome Debate: Is Mapping the Mind of a Worm Worth It?

The connectome-related skepticism has been ramping up lately. So you mapped the complete neural network of a tiny worm (C. elegans, above) … so what? So you draw some pretty brain structures that don’t provide neuron by neuron detail … so what?

Ferris Jabr has a great write-up of the “so whats” and the “this is what” at SciAm. Want to get up to date on the connectome debate? Start here.

Because a lone connectome is a snapshot of pathways through which information might flow in an incredibly dynamic organ, it cannot reveal how neurons behave in real time, nor does it account for the many mysterious ways that neurons regulate one another’s behavior. Without such maps, however, scientists cannot thoroughly understand how the brain processes information at the level of the circuit. In combination with other tools, the C. elegans connectome has in fact taught scientists a lot about the worm’s behavior; partial connectomes that researchers have established in the crustacean nervous system have been similarly helpful. Scientists are also learning how to make connectomes faster than before and to enhance the information they provide. Many researchers in the field summarize their philosophy like this: “A connectome is necessary, but not sufficient.”

So it’s taught us a bit about the workings of the worm, but maybe not everything. Will it translate to elucidating the workings of the human brain? Time will tell. Good read.

(via Scientific American)

Source: scientificamerican.com

Anti-connectome-ism

That sure is pretty. 

Do we really stand to learn as much as claimed from deciphering a map of all the brain’s neural connections? Researchers like Sebastian Seung are banking on it. However, not everyone agrees that the “connectome” holds the potential Seung and company claim. 

Aside from the technical difficulty of creating such a map, Mo Costandi notes that even with all the connections traced, the mystery wouldn’t be unraveled:

“… a connectivity map is unlikely to tell use everything we’d like to know about the brain. In the late 1980s, researchers published an almost complete connectome of the nematode worm Caenorhabditis elegans, after years of laborious work involving slicing the organism into thousands of ultra-thin sections then examining the sections under the microscope and reconstructing them. This tiny, millimetre-long organism doesn’t even have a brain as such – its entire nervous system contains a grand total of 302 neurons. And yet, the nematode connectome has taught us far less than we thought it would about how this apparently simple nerve net generates the worm’s behaviours.”

In a dynamic organ such as the brain, whose synapses and connections are always changing, adapting and morphing, there’s certainly the question of whether spending so much time and money on connectome science will pay off in the end. We have to get more than just pretty pictures out of this, you know.

I highly recommend reading Mo’s full piece, if just for the bit at the end where he shares a rather scathing anti-connectome email. The term “pukeworthy” is invoked. 

Finally, connectome evangelist Sebastian Seung sat down to debate the idea with neuroscientist Tony Movshon a few months back, moderated by Carl Zimmer and Robert Krulwich. Revisit BrainBrawl 2012.

Phineas Gage’s Connectome In 1848, railroad worker Phineas Gage had a 3.5-foot, 13 pound tamping iron blown through the front of his skull in a construction accident. Hell of a way to start your Wednesday (yes, I checked). He survived. The story of Phineas Gage is now the stuff of legend, taught to first-year neuroscience students around the world. How did this man survive a rod through the frontal lobe? Doctors that wrote of him later spoke of extreme behavioral changes, a man who was “. . . fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows”. Unfortunately, the legend of Phineas Gage’s post-injury brain is largely exaggerated, or at least based on rather thin evidence. But still, he was still a changed man, even if not in the extreme ways his legend suggests. UCLA’s Jack Van Horn has reconstructed a model of Phineas Gage’s connectome. In the image above, the lower left image shows the “connectogram” of 110 healthy right-handed males, the major highways and byways between brain regions (the brain stem is at 6 o’clock, left and right hemispheres at 9 and 3 o’clock). The lower right image shows the connections that were likely disrupted by the iron spike through Gage’s frontal lobe. Mo Costandi has a great write-up that you should check out. We now have a map of the damage to Gage’s brain. But do we really know any more about his supposed behavioral changes? Thanks to the exaggerations and sideshow mentality of those who studied hm while alive, likely not. BONUS: Be sure to check out Robert Krulwich and Carl Zimmer moderating this debate on how much stock we should put in the connectome. (via Neurophilosophy blog)
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Phineas Gage’s Connectome

In 1848, railroad worker Phineas Gage had a 3.5-foot, 13 pound tamping iron blown through the front of his skull in a construction accident. Hell of a way to start your Wednesday (yes, I checked). He survived.

The story of Phineas Gage is now the stuff of legend, taught to first-year neuroscience students around the world. How did this man survive a rod through the frontal lobe? Doctors that wrote of him later spoke of extreme behavioral changes, a man who was “. . . fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows”.

Unfortunately, the legend of Phineas Gage’s post-injury brain is largely exaggerated, or at least based on rather thin evidence. But still, he was still a changed man, even if not in the extreme ways his legend suggests.

UCLA’s Jack Van Horn has reconstructed a model of Phineas Gage’s connectome. In the image above, the lower left image shows the “connectogram” of 110 healthy right-handed males, the major highways and byways between brain regions (the brain stem is at 6 o’clock, left and right hemispheres at 9 and 3 o’clock). The lower right image shows the connections that were likely disrupted by the iron spike through Gage’s frontal lobe.

Mo Costandi has a great write-up that you should check out. We now have a map of the damage to Gage’s brain. But do we really know any more about his supposed behavioral changes? Thanks to the exaggerations and sideshow mentality of those who studied hm while alive, likely not.

BONUS: Be sure to check out Robert Krulwich and Carl Zimmer moderating this debate on how much stock we should put in the connectome.

(via Neurophilosophy blog)

Source: Guardian

BRAINBRAWL 2012!!!

The Main Event? Connectomics: Sebastian Seung vs. Tony Movshon.

We’ve all seen the pictures in the past couple months. The connectome, the brain’s wiring diagram, has been drawn in unprecedented detail, and is organized in a surprisingly simple fashion. If we can describe every neuron in the brain, can we know precisely how the brain works?

Carl Zimmer and Radiolab’s Robert Krulwich moderate a discussion on whether we are more or less than our connectome. It’s a room full of amazingly smart people, talking about the Big Questions in neuroscience. Here’s the complete video, thanks to Neuwrite.

As Stuart Firestein asks, “Does a parts list and a wiring diagram provide a satisfactory description of a brain, and maybe even a way to repair it?”

(by armenenikolopov)

Source: youtube.com

infoneer-pulse: Spectacular Brain Images Reveal Surprisingly Simple Structure Stunning new visuals of the brain reveal a deceptively simple pattern of organization in the wiring of this complex organ. Instead of nerve fibers travelling willy-nilly through the brain like spaghetti, as some imaging has suggested, the new portraits reveal two-dimensional sheets of parallel fibers crisscrossing other sheets at right angles in a gridlike structure that folds and contorts with the convolutions of the brain. This same pattern appeared in the brains of humans, rhesus monkeys, owl monkeys, marmosets and galagos, researchers report today (March 29) in the journal Science. » via Live Science Haha, that’s hilarious. Simple! Yes, the diffusion mapping of water in billions of neurons that interconnect in ways that we have yet to even fathom. We totally have this figured out. Right?The connectome is more anatomy lesson than brain map at this point. It draws a guiding track for future discovery, but let’s not let LiveScience or anyone make us think that patterns and pretty pictures mean that we have simplified the workings of the most complex computer on Earth (and maybe elsewhere), m’kay?
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infoneer-pulse:

Spectacular Brain Images Reveal Surprisingly Simple Structure

Stunning new visuals of the brain reveal a deceptively simple pattern of organization in the wiring of this complex organ.

Instead of nerve fibers travelling willy-nilly through the brain like spaghetti, as some imaging has suggested, the new portraits reveal two-dimensional sheets of parallel fibers crisscrossing other sheets at right angles in a gridlike structure that folds and contorts with the convolutions of the brain.

This same pattern appeared in the brains of humans, rhesus monkeys, owl monkeys, marmosets and galagos, researchers report today (March 29) in the journal Science.

» via Live Science

Haha, that’s hilarious. Simple! Yes, the diffusion mapping of water in billions of neurons that interconnect in ways that we have yet to even fathom. We totally have this figured out. Right?

The connectome is more anatomy lesson than brain map at this point. It draws a guiding track for future discovery, but let’s not let LiveScience or anyone make us think that patterns and pretty pictures mean that we have simplified the workings of the most complex computer on Earth (and maybe elsewhere), m’kay?

(via scinerds)

Source: livescience.com

scipsy: Images produced with Diffusion spectrum magnetic resonance imaging (DSI) a new tool developed by Van J Wedeen. Here’s an interview, and here’s a slide show. Random fact: These methods capture six dimensions of information (three spatial and three about water diffusion) to create the images. So we’re getting really good at drawing images of the brain’s elaborate connectome. Now if only we can start drawing more realistic conclusions about how it all relates to our biology and eventually our personalities. This is an incredibly cool technique that is simplifying our view of brain structure, while at the same time complicating our view of brain biology.
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scipsy: Images produced with Diffusion spectrum magnetic resonance imaging (DSI) a new tool developed by Van J Wedeen. Here’s an interview, and here’s a slide show. Random fact: These methods capture six dimensions of information (three spatial and three about water diffusion) to create the images. So we’re getting really good at drawing images of the brain’s elaborate connectome. Now if only we can start drawing more realistic conclusions about how it all relates to our biology and eventually our personalities. This is an incredibly cool technique that is simplifying our view of brain structure, while at the same time complicating our view of brain biology.
Zoom Info
scipsy: Images produced with Diffusion spectrum magnetic resonance imaging (DSI) a new tool developed by Van J Wedeen. Here’s an interview, and here’s a slide show. Random fact: These methods capture six dimensions of information (three spatial and three about water diffusion) to create the images. So we’re getting really good at drawing images of the brain’s elaborate connectome. Now if only we can start drawing more realistic conclusions about how it all relates to our biology and eventually our personalities. This is an incredibly cool technique that is simplifying our view of brain structure, while at the same time complicating our view of brain biology.
Zoom Info
scipsy: Images produced with Diffusion spectrum magnetic resonance imaging (DSI) a new tool developed by Van J Wedeen. Here’s an interview, and here’s a slide show. Random fact: These methods capture six dimensions of information (three spatial and three about water diffusion) to create the images. So we’re getting really good at drawing images of the brain’s elaborate connectome. Now if only we can start drawing more realistic conclusions about how it all relates to our biology and eventually our personalities. This is an incredibly cool technique that is simplifying our view of brain structure, while at the same time complicating our view of brain biology.
Zoom Info

scipsy:

Images produced with Diffusion spectrum magnetic resonance imaging (DSI) a new tool developed by Van J Wedeen. Here’s an interview, and here’s a slide show.

Random fact: These methods capture six dimensions of information (three spatial and three about water diffusion) to create the images.

So we’re getting really good at drawing images of the brain’s elaborate connectome. Now if only we can start drawing more realistic conclusions about how it all relates to our biology and eventually our personalities. This is an incredibly cool technique that is simplifying our view of brain structure, while at the same time complicating our view of brain biology.

(via scinerds)

Source: scipsy

poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
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poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
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poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
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poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
Zoom Info
poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
Zoom Info
poptech: The Human Connectome Project Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it. The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.
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poptech:

The Human Connectome Project

Navigate the brain in a way that was never before possible; fly through major brain pathways, compare essential circuits, zoom into a region to explore the cells that comprise it, and the functions that depend on it.

The Human Connectome Project aims to provide an unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve never before realized conclusions about the living human brain.

(via theatlantic)

Source: poptech.org