#connectomics

[bpod-bpod]

Into the Dense

This study describes a new approach for homing in on details of the brain's densely packed neurons and their connections. Light-microscopy-based connectomics (LICONN) combined with tissue expansion and segmentation enables 3D reconstruction of networks at high-resolution

Read the published research article here

Image from work by Mojtaba R. Tavakoli and colleagues

Institute of Science and Technology Austria, Klosterneuburg, Austria

Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Nature, May 2025

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[simknowsstuff]

Apparently alters can be caused by a thing in the area of the brain that helps with personal identity and awareness, and memory designation areas may be heavily involved, with higher white matter volume tracts round there.

A part of it is definitely context however, and neural maturation in a state that is non-neurotypical may lead to structural differences in certain brain regions, which may make it easier to separately consolidate memory and use separate context for reaction and interaction within certain areas like the PTO junction

I'm by no means an expert however, this is just my rationalisation of some things i have

[thetendertongue]

connectome — a comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram." an organism's nervous system is made up of neurons which communicate through synapses. a connectome is constructed by tracing the neuron in a nervous system and mapping where neurons are connected through synapses

image from wikipedia, a rendering of a group connectome based on 20 different subjects.

[usa-journal]

Breakthrough in Fly Brain Research Paves Way for Understanding Human Cognition

Scientists have achieved a monumental breakthrough by mapping the fly brain, revealing the position, shape, and connections of all its 130,000 cells and 50 million intricate connections. This research represents the most detailed analysis of an adult animal's brain to date and is being hailed as a "huge leap" in understanding human cognition.

The fly's brain, though tiny, supports a range of complex behaviors, including walking, hovering, and even producing mating songs. Dr. Gregory Jefferis, a leader in the research from the Medical Research Council's Laboratory of Molecular Biology in Cambridge, emphasizes that this mapping could illuminate the mechanisms behind thought processes in humans. He noted the lack of understanding about how brain cell networks facilitate our interactions with the world.

Despite humans having a million times more neurons than the fruit fly, the new wiring diagram, or connectome, will aid scientists in deciphering cognitive functions. Published in the journal Nature, the imagery showcases a stunningly complex structure that reveals how a small organ can perform powerful computational tasks.

Dr. Mala Murthy, co-leader of the project from Princeton University, stated that this connectome will be transformative for neuroscientists, allowing for a better understanding of healthy brain function and the potential to compare it with malfunctioning brains.

Dr. Lucia Prieto Godino from the Francis Crick Institute supports this view, highlighting that while simpler organisms like worms and maggots have had their connectomes mapped, the fly’s intricate wiring is a significant achievement. This success paves the way for mapping larger brains, potentially leading to a human connectome in the future.

The research team has successfully identified separate circuits for various functions, illustrating how movement-related circuits are positioned at the base of the brain, while those responsible for vision are located on the sides. The study not only identifies these circuits but also explains their connections, enhancing our understanding of neural processing.

Interestingly, researchers are already applying these circuit diagrams to understand why flies are so hard to catch. The wiring related to vision quickly processes incoming threats, sending signals to the fly's legs to jump away faster than conscious thought.

To create the wiring diagram, researchers used a technique involving slicing the fly brain into 7,000 incredibly thin pieces, photographing each slice, and digitally reconstructing the whole. They employed artificial intelligence to analyze neuron shapes and connections, correcting over three million errors manually.

Dr. Philipp Schlegel from the Medical Research Council highlights that this data serves as a comprehensive map of brain connectivity, akin to a detailed Google Maps for the neural networks. This combined information will facilitate countless discoveries in neuroscience in the coming years.

While a human connectome remains elusive due to the complexity of the human brain, researchers believe that advancements in technology may allow for such mapping in about three decades. The fly brain research marks a significant step toward unlocking the mysteries of human cognition and understanding our own minds better.

The study was conducted by the FlyWire Consortium, an international collaboration of scientists dedicated to advancing neuroscience.

[epistemebabu]

what makes nails on a chalkboard so unpleasant to hear, anyway?

[in-sightjournal]

Ask A Genius 1251: Human Cognition, Paraconsistent Logic, and Knowledge Networks

Rick Rosner is an accomplished television writer with credits on shows like Jimmy Kimmel Live!, Crank Yankers, and The Man Show. Over his career, he has earned multiple Writers Guild Award nominations—winning one—and an Emmy nomination. Rosner holds a broad academic background, graduating with the equivalent of eight majors. Based in Los Angeles, he continues to write and develop ideas while…

[mdforhadhossain]

Connectomics: Mapping Your Brain's Connections Unlocks Secrets! @primalb...

[jcmarchi]

Neuroscientists create a comprehensive map of the cerebral cortex

New Post has been published on https://thedigitalinsider.com/neuroscientists-create-a-comprehensive-map-of-the-cerebral-cortex/

Neuroscientists create a comprehensive map of the cerebral cortex

By analyzing brain scans taken as people watched movie clips, MIT researchers have created the most comprehensive map yet of the functions of the brain’s cerebral cortex.

Using functional magnetic resonance imaging (fMRI) data, the research team identified 24 networks with different functions, which include processing language, social interactions, visual features, and other types of sensory input.

Many of these networks have been seen before but haven��t been precisely characterized using naturalistic conditions. While the new study mapped networks in subjects watching engaging movies, previous works have used a small number of specific tasks or examined correlations across the brain in subjects who were simply resting.

“There’s an emerging approach in neuroscience to look at brain networks under more naturalistic conditions. This is a new approach that reveals something different from conventional approaches in neuroimaging,” says Robert Desimone, director of MIT’s McGovern Institute for Brain Research. “It’s not going to give us all the answers, but it generates a lot of interesting ideas based on what we see going on in the movies that’s related to these network maps that emerge.”

The researchers hope that their new map will serve as a starting point for further study of what each of these networks is doing in the brain.

Desimone and John Duncan, a program leader in the MRC Cognition and Brain Sciences Unit at Cambridge University, are the senior authors of the study, which appears today in Neuron. Reza Rajimehr, a research scientist in the McGovern Institute and a former graduate student at Cambridge University, is the lead author of the paper.

Precise mapping

The cerebral cortex of the brain contains regions devoted to processing different types of sensory information, including visual and auditory input. Over the past few decades, scientists have identified many networks that are involved in this kind of processing, often using fMRI to measure brain activity as subjects perform a single task such as looking at faces.

In other studies, researchers have scanned people’s brains as they do nothing, or let their minds wander. From those studies, researchers have identified networks such as the default mode network, a network of areas that is active during internally focused activities such as daydreaming.

“Up to now, most studies of networks were based on doing functional MRI in the resting-state condition. Based on those studies, we know some main networks in the cortex. Each of them is responsible for a specific cognitive function, and they have been highly influential in the neuroimaging field,” Rajimehr says.

However, during the resting state, many parts of the cortex may not be active at all. To gain a more comprehensive picture of what all these regions are doing, the MIT team analyzed data recorded while subjects performed a more natural task: watching a movie.

“By using a rich stimulus like a movie, we can drive many regions of the cortex very efficiently. For example, sensory regions will be active to process different features of the movie, and high-level areas will be active to extract semantic information and contextual information,” Rajimehr says. “By activating the brain in this way, now we can distinguish different areas or different networks based on their activation patterns.”

The data for this study was generated as part of the Human Connectome Project. Using a 7-Tesla MRI scanner, which offers higher resolution than a typical MRI scanner, brain activity was imaged in 176 people as they watched one hour of movie clips showing a variety of scenes.

The MIT team used a machine-learning algorithm to analyze the activity patterns of each brain region, allowing them to identify 24 networks with different activity patterns and functions.

Some of these networks are located in sensory areas such as the visual cortex or auditory cortex, as expected for regions with specific sensory functions. Other areas respond to features such as actions, language, or social interactions. Many of these networks have been seen before, but this technique offers more precise definition of where the networks are located, the researchers say.

“Different regions are competing with each other for processing specific features, so when you map each function in isolation, you may get a slightly larger network because it is not getting constrained by other processes,” Rajimehr says. “But here, because all the areas are considered together, we are able to define more precise boundaries between different networks.”

The researchers also identified networks that hadn’t been seen before, including one in the prefrontal cortex, which appears to be highly responsive to visual scenes. This network was most active in response to pictures of scenes within the movie frames.

Executive control networks

Three of the networks found in this study are involved in “executive control,” and were most active during transitions between different clips. The researchers also observed that these control networks appear to have a “push-pull” relationship with networks that process specific features such as faces or actions. When networks specific to a particular feature were very active, the executive control networks were mostly quiet, and vice versa.

“Whenever the activations in domain-specific areas are high, it looks like there is no need for the engagement of these high-level networks,” Rajimehr says. “But in situations where perhaps there is some ambiguity and complexity in the stimulus, and there is a need for the involvement of the executive control networks, then we see that these networks become highly active.”

Using a movie-watching paradigm, the researchers are now studying some of the networks they identified in more detail, to identify subregions involved in particular tasks. For example, within the social processing network, they have found regions that are specific to processing social information about faces and bodies. In a new network that analyzes visual scenes, they have identified regions involved in processing memory of places.

“This kind of experiment is really about generating hypotheses for how the cerebral cortex is functionally organized. Networks that emerge during movie watching now need to be followed up with more specific experiments to test the hypotheses. It’s giving us a new view into the operation of the entire cortex during a more naturalistic task than just sitting at rest,” Desimone says.

The research was funded by the McGovern Institute, the Cognitive Science and Technology Council of Iran, the MRC Cognition and Brain Sciences Unit at the University of Cambridge, and a Cambridge Trust scholarship.

[goldislops]

Largest Brain Map Ever Reveals Fruit Fly’s Neurons in Exquisite Detail

Wiring diagram lays out connections between nearly 140,000 neurons and reveals new types of nerve cell

50 largest neurons of the fly brain connectome.

50 largest neurons of the fly brain connectome.

Tyler Sloan and Amy Sterling for FlyWire, Princeton University, (Dorkenwald et al., Nature, 2024)

Wiring diagram lays out connections between nearly 140,000 neurons and reveals new types of nerve cell

A fruit fly might not be the smartest organism, but scientists can still learn a lot from its brain. Researchers are hoping to do that now that they have a new map — the most complete for any organism so far — of the brain of a single fruit fly (Drosophila melanogaster). The wiring diagram, or ‘connectome’, includes nearly 140,000 neurons and captures more than 54.5 million synapses, which are the connections between nerve cells.

“This is a huge deal,” says Clay Reid, a neurobiologist at the Allen Institute for Brain Science in Seattle, Washington, who was not involved in the project but has worked with one of the team members who was. “It’s something that the world has been anxiously waiting for, for a long time.”

The map is described in a package of nine papers about the data published in Nature today. Its creators are part of a consortium known as FlyWire, co-led by neuroscientists Mala Murthy and Sebastian Seung at Princeton University in New Jersey.

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A long road

Seung and Murthy say that they’ve been developing the FlyWire map for more than four years, using electron microscopy images of slices of the fly’s brain. The researchers and their colleagues stitched the data together to form a full map of the brain with the help of artificial-intelligence (AI) tools.

But these tools aren’t perfect, and the wiring diagram needed to be checked for errors. The scientists spent a great deal of time manually proofreading the data — so much time that they invited volunteers to help. In all, the consortium members and the volunteers made more than 3 million manual edits, according to co-author Gregory Jefferis, a neuroscientist at the University of Cambridge, UK. (He notes that much of this work took place in 2020, when fly researchers were at loose ends and working from home during the COVID-19 pandemic.)

But the work wasn’t finished: the map still had to be annotated, a process in which the researchers and volunteers labelled each neuron as a particular cell type. Jefferis compares the task to assessing satellite images: AI software might be trained to recognize lakes or roads in such images, but humans would have to check the results and name the specific lakes or roads themselves. All told, the researchers identified 8,453 types of neuron — much more than anyone had expected. Of these, 4,581 were newly discovered, which will create new research directions, Seung says. “Every one of those cell types is a question,” he adds.

The team was surprised by some of the ways in which the various cells connect to one another, too. For instance, neurons that were thought to be involved in just one sensory wiring circuit, such as a visual pathway, tended to receive cues from multiple senses, including hearing and touch1. “It’s astounding how interconnected the brain is,” Murthy says.

Exploring the map

The FlyWire map data have been available for the past few years for researchers to explore. This has enabled scientists to learn more about the brain and about fruit flies — findings that are captured in some of the papers published in Nature today.

In one paper, for example, researchers used the connectome to create a computer model of the entire fruit-fly brain, including all the connections between neurons. They tested it by activating neurons that they knew either sense sweet or bitter tastes. These neurons then launched a cascade of signals through the virtual fly’s brain, ultimately triggering motor neurons tied to the fly’s proboscis — the equivalent of the mammalian tongue. When the sweet circuit was activated, a signal for extending the proboscis was transmitted, as if the insect was preparing to feed; when the bitter circuit was activated, this signal was inhibited. To validate these findings, the team activated the same neurons in a real fruit fly. The researchers learnt that the simulation was more than 90% accurate at predicting which neurons would respond and therefore how the fly would behave.

In another study, researchers describe two wiring circuits that signal a fly to stop walking. One of these contains two neurons that are responsible for halting ‘walk’ signals sent from the brain when the fly wants to stop and feed. The other circuit includes neurons in the nerve cord, which receives and processes signals from the brain. These cells create resistance in the fly’s leg joints, allowing the insect to stop while it grooms itself.

One limitation of the new connectome is that it was created from a single female fruit fly. Although fruit-fly brains are similar to each other, they are not identical. Until now, the most complete connectome for a fruit-fly brain was a map of a ‘hemibrain’ — a portion of a fly’s brain containing around 25,000 neurons. In one of the Nature papers out today, Jefferis, Davi Bock, a neurobiologist at the University of Vermont in Burlington, and their colleagues compared the FlyWire brain with the hemibrain.

Some of the differences were striking. The FlyWire fly had almost twice as many neurons in a brain structure called the mushroom body, which is involved in smell, compared with the fly used in the hemibrain-mapping project. Bock thinks the discrepancy could be because the hemibrain fly might have starved while it was still growing, which harmed its brain development.

The FlyWire researchers say that much work remains to be done to fully understand the fruit-fly brain. For instance, the latest connectome shows only how neurons connect through chemical synapses, across which molecules called neurotransmitters send information. It doesn’t offer any information about electrical connectivity between neurons or about how neurons chemically communicate outside synapses. And Murthy hopes to eventually have a male fly connectome, too, which would allow researchers to study male-specific behaviours such as singing. “We’re not done, but it’s a big step,” Bock says.

This article is reproduced with permission and was first published on October 2, 2024.

[bpod-bpod]

Monkey Matter

The brain uses a complex network of bundles of nerve cells – neurons – to transfer information as we interpret and respond to the world around us. Many of its details are still a mystery, leaving scientists searching for new angles on this vital living supercomputer. Here, researchers examine a monkey’s brain using x-rays at the European synchrotron. Particles forced to loop in circles at high speeds are fired at the tissue sample, uncovering new details based on how the particles scatter. The experiments reveal nerve cell projections known as axons (highlighted as thin multi-coloured lines) and blood vessels (orange) inside a complex region of the cerebral cortex of a monkey. Interestingly, researchers find some groups of axons form layers or laminar structures, adding to our picture of the human brain’s similar connectome.

Written by John Ankers

Video from work by Hans Martin Kjer and colleagues

Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark

Video originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in eLife, February 2025

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[in-sightpublishing]

Ask A Genius 984: What is the purpose of an interview?

Author(s): Rick Rosner and Scott Douglas Jacobsen Publication (Outlet/Website): Ask A Genius Publication Date (yyyy/mm/dd): 2024/06/28 Rick Rosner: You’ve probably done more than 1,000 interviews and have certainly asked me more than me 1,000 questions over the past 10 years. You’ve talked to hundreds of people in your interviewing career. So, you’ve developed an idea of what interviews are…

[transgenderer]

Researchers are hoping to do that now that they have a new map — the most complete for any organism so far — of the brain of a single fruit fly (Drosophila melanogaster). The wiring diagram, or ‘connectome’, includes nearly 140,000 neurons and captures more than 54.5 million synapses, which are the connections between nerve cells.

n one paper2, for example, researchers used the connectome to create a computer model of the entire fruit-fly brain, including all the connections between neurons. They tested it by activating neurons that they knew either sense sweet or bitter tastes. These neurons then launched a cascade of signals through the virtual fly’s brain, ultimately triggering motor neurons tied to the fly’s proboscis — the equivalent of the mammalian tongue. When the sweet circuit was activated, a signal for extending the proboscis was transmitted, as if the insect was preparing to feed; when the bitter circuit was activated, this signal was inhibited. To validate these findings, the team activated the same neurons in a real fruit fly. The researchers learnt that the simulation was more than 90% accurate at predicting which neurons would respond and therefore how the fly would behave.

In another study3, researchers describe two wiring circuits that signal a fly to stop walking. One of these contains two neurons that are responsible for halting ‘walk’ signals sent from the brain when the fly wants to stop and feed. The other circuit includes neurons in the nerve cord, which receives and processes signals from the brain. These cells create resistance in the fly’s leg joints, allowing the insect to stop while it grooms itself.

is there some like deceptive hype language here or is this just like. absolutely bonkers. full fly brain in the computer

[mostlysignssomeportents]

Ray Nayler’s “Where the Axe Is Buried”

I'm on a 20+ city book tour for my new novel PICKS AND SHOVELS. Catch me in SAN DIEGO at MYSTERIOUS GALAXY next MONDAY (Mar 24), and in CHICAGO with PETER SAGAL on Apr 2. More tour dates here.

Ray Nayler's Where the Axe Is Buried is an intense, claustrophobic novel of a world run by "rational" AIs that purport to solve all of our squishy political problems with empirical, neutral mathematics:

https://us.macmillan.com/books/9780374615369/wheretheaxeisburied/

In Naylor's world, we there are two blocs. "The west," where the heads of state have been replaced with chatbots called "PMs." These PMs propose policy to tame, rubberstamp legislatures, creating jobs programs, setting monetary and environmental policies, and ruling on other tricky areas where it's nearly impossible to make everyone happy. These countries are said to be "rationalized," and they are peaceful and moderately prosperous, and have finally tackled the seemingly intractable problems of decarbonization, extreme poverty, and political instability.

In "the Republic" – a thinly veiled version of Russia – the state is ruled by an immortal tyrant who periodically has his consciousness decanted into a blank body after his own body falls apart. The state maintains the fiction that each president is a new person, manufacturing families, friends, teachers and political comrades who can attest to the new president's long history in the country. People in the Republic pretend to believe this story, but in practice, everyone knows that it's the same mind running the country, albeit sometimes with ill-advised modifications, such as an overclocking module that runs the president's mind at triple human speeds.

The Republic is a totalitarian nightmare of ubiquitous surveillance and social control, in which every movement and word is monitored, and where social credit scores are adjusted continuously to reflect the political compliance of each citizen. Low social credit scores mean fewer rations, a proscribed circle of places you can go, reduced access to medical care, and social exclusion. The Republic has crushed every popular uprising, acting on the key realization that the only way to cling to power is to refuse to yield it, even (especially) if that means murdering every single person who takes part in a street demonstration against the government.

By contrast, the western states with their chatbot PMs are more open – at least superficially. However, the "rationalized" systems use less obvious – but no less inescapable – soft forms of control that limit the social mobility, career chances, and moment-to-moment and day-to-day lives of the people who live there. As one character who ventures from the Republic to London notes, it is a strange relief to be continuously monitored by cameras there to keep you safe and figure out how to manipulate you into buying things, rather than being continuously monitored by cameras seeking a way to punish you.

The tale opens on the eve of the collapse of these two systems, as the current president of the Republic's body starts to reject the neural connectome that was implanted into its vat-grown brain, even as the world's PMs start to sabotage their states, triggering massive civil unrest that brings the west to its knees, one country after another.

This is the backdrop for a birchpunk† tale of AI skulduggery, lethal robot insects, radical literature, swamp-traversing mechas, and political intrigue that flits around a giant cast of characters, creating a dizzying, in-the-round tour of Nayler's paranoid world

† Russian-inflected cyberpunk with Baba Yaga motifs and nihilistic Russian novel vibes

And what a paranoid world it is! Nayler's world shows two different versions of Oracle boss (and would-be Tiktok owner) Larry Ellison, who keeps pumping his vision of an AI-driven surveillance state where everyone is continuously observed, recorded and judged by AIs so we are all on our "best behavior":

https://fortune.com/2024/09/17/oracle-larry-ellison-surveillance-state-police-ai/

This batshit idea from one of tech's worst billionaires is a perfect foil for a work of first-rate science fiction like Where the Axe Is Buried, which provides an emotional flythrough of how such a world would obliterate the authentic self, authentic relationships, and human happiness.

Where the Axe Is Buried conjures up that world beautifully, really capturing the deadly hopelessness of a life where the order is fixed for all eternity, thanks to the flawless execution of perfect, machine-generated power plays. But Axe shows how the embers of hope smolder long after they should have been extinguished, and how they are always ready to be kindled into a roaring, system-consuming wildfire.

If you'd like an essay-formatted version of this post to read or share, here's a link to it on pluralistic.net, my surveillance-free, ad-free, tracker-free blog:

https://pluralistic.net/2025/03/birchpunk/#cyberspace-is-everting

[covid-safer-hotties]

Reference archived on our website

Abstract COVID-19 is associated with increased risk for cognitive decline but very little is known regarding the neural mechanisms of this risk. We enrolled 49 adults (55% female, mean age = 30.7 ± 8.7), 25 with and 24 without a history of COVID-19 infection. We administered standardized tests of cognitive function and acquired brain connectivity data using MRI. The COVID-19 group demonstrated significantly lower cognitive function (W = 475, p < 0.001, effect size r = 0.58) and lower functional connectivity in multiple brain regions (mean t = 3.47 ±0.36, p = 0.03, corrected, effect size d = 0.92 to 1.5). Hypo-connectivity of these regions was inversely correlated with subjective cognitive function and directly correlated with fatigue (p < 0.05, corrected). These regions demonstrated significantly reduced local efficiency (p < 0.026, corrected) and altered effective connectivity (p < 0.001, corrected). COVID-19 may have a widespread effect on the functional connectome characterized by lower functional connectivity and altered patterns of information processing efficiency and effective information flow. This may serve as an adaptation to the pathology of SARS-CoV-2 wherein the brain can continue functioning at near expected objective levels, but patients experience lowered efficiency as brain fog.

[charseraph]

Your "bad ending" setting reminds me of the short dystopian satire story "I Sexually Identify as an Attack Helicopter" by Isabel Fall. The story does contain explicit sexual content so if you choose to read it, there's your warning. Mainly, I'm reminded because of the hypermilitaristic setting, merging of humans and weaponry, and mind-alteration through technology.

God yes I read that story by @cydork’s recommendation a few weeks ago. Easily became one of my favorite stories for its allusions to greater world state and its whole tactical connectome manipulation science.