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Freely access electrophysiological, morphological, and transcriptomic data measured from thousands of individual mouse & human brain cells via the Allen Cell Types Database: #openscience #SfN23

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allen institute

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30,847 görüntüleme • 2 yıl önce •via X (Twitter)

Sağlık & İyilikBilim & TeknolojiEğitim#openscience#SfN23
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Researchers can freely access the Allen Mouse Brain Common Coordinate Framework (v3), a complete and high-resolution 3D atlas of the mouse brain. Learn more about it at #SfN23
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Researchers can freely access the Allen Mouse Brain Common Coordinate Framework (v3), a complete and high-resolution 3D atlas of the mouse brain. Learn more about it at #SfN23

allen institute

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Beautiful new paper: methods for getting stem-cell derived retinal ganglion cells to integrate into the retina (mouse). Cells were capable of migrating & surviving. #NEIfunded Baranov Lab Levi Todd Mass Eye and Ear Harvard Ophthalmology PNASNews paper:
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Beautiful new paper: methods for getting stem-cell derived retinal ganglion cells to integrate into the retina (mouse). Cells were capable of migrating & surviving. #NEIfunded Baranov Lab Levi Todd Mass Eye and Ear Harvard Ophthalmology PNASNews paper:

Michael F. Chiang, MD

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🚨: A petri dish of human brain cells just learned to play DOOM
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🚨: A petri dish of human brain cells just learned to play DOOM

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Scientists have successfully trained a petri dish of human brain cells to play DOOM.
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Scientists have successfully trained a petri dish of human brain cells to play DOOM.

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Cells located in the midline of the embryo play crucial roles in development. These cells often influence cell fate decisions and guide axons to establish bilateral connections. Despite their importance, studying these transient cells and their complex interactions has been challenging. Today, we introduce human midline #assembloids—3D self-organizing cellular clusters derived from stem cells by the functional integration of floor plate #organoids and spinal cord #organoids. We demonstrate that midline assembloids enable cell specification and axon guidance in human neurons. Additionally, we use these assembloids to screen and identify human-enriched factors that control these processes. Work led by the incredible Massimo Onesto & Neal Amin!! More details in the preprint 👇
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Cells located in the midline of the embryo play crucial roles in development. These cells often influence cell fate decisions and guide axons to establish bilateral connections. Despite their importance, studying these transient cells and their complex interactions has been challenging. Today, we introduce human midline #assembloids—3D self-organizing cellular clusters derived from stem cells by the functional integration of floor plate #organoids and spinal cord #organoids. We demonstrate that midline assembloids enable cell specification and axon guidance in human neurons. Additionally, we use these assembloids to screen and identify human-enriched factors that control these processes. Work led by the incredible Massimo Onesto & Neal Amin!! More details in the preprint 👇

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When you realise you have more brain cells than your human
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When you realise you have more brain cells than your human

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Human skull and brain from the inside Credit: SciePro
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Human skull and brain from the inside Credit: SciePro

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This is only 1 Niagara emitter to handle thousands of decals as particles using Data Channels! Significantly lower overhead on the GameThread and only a single component per grid cell. This also adds instancing to the decals which is normally not supported for individual decal components. Working on this as part of data-oriented projectiles that run without Actors, asynchronous collision and supporting multiplayer (incl. client side prediction). Removes a huge amount of overhead from the CPU, more on that soon!
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This is only 1 Niagara emitter to handle thousands of decals as particles using Data Channels! Significantly lower overhead on the GameThread and only a single component per grid cell. This also adds instancing to the decals which is normally not supported for individual decal components. Working on this as part of data-oriented projectiles that run without Actors, asynchronous collision and supporting multiplayer (incl. client side prediction). Removes a huge amount of overhead from the CPU, more on that soon!

Tom Looman

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Scientists have mapped the vision centers of a mouse brain, the largest and most detailed such rendering of neural circuits in a mammalian brain:
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Scientists have mapped the vision centers of a mouse brain, the largest and most detailed such rendering of neural circuits in a mammalian brain:

Princeton University

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New Cell paper from Bergles lab at Johns Hopkins just built the most comprehensive map of brain myelin ever made — every oligodendrocyte, across the entire mouse brain, across the lifespan. The scale: >10 million cells per brain, terabyte-scale 3D lightsheet volumes, registered to the Allen Brain Atlas across 417 regions from 2 months to 2+ years of age. The technical stack: Custom tissue clearing (CUBIC-L + SHIELD + uRIMS with 40% urea) to preserve endogenous fluorescence. 3D Mask R-CNN for instance segmentation — not just semantic, instance — so it can distinguish individual cells within dense clusters at scale via overlapping sliding windows. Vision Transformer to classify newly-formed vs. mature oligodendrocytes using soma morphology. All cross-referenced against Allen ISH transcriptomics and MICrONS serial EM. What they found: Oligodendrocyte density varies 10,000-fold across brain regions. Left-right hemispheres: r=0.99. Sex: no significant difference. Strain: matters. The brain never stops myelinating. New oligodendrocytes are still being generated in 2-year-old mice. Prefrontal cortex L6 shows the fastest rates of new myelination into old age — the circuits for executive function keep rewiring throughout life. After demyelination, L4 sensory cortex is the most resilient — oligodendrocytes survive at higher rates. The hippocampus loses nearly everything and barely recovers. Degree of injury doesn't predict rate of recovery. These are independent axes. The Alzheimer's result is the most surprising: Dense-core plaques dominate in cortex and hippocampus. Diffuse/small-core plaques dominate in white matter fiber tracts. Old assumption: diffuse plaques are "less toxic." The data says the opposite — small plaques in fiber tracts cause more myelin loss per plaque than dense-core plaques in gray matter. Plaque load and oligodendrocyte loss are essentially uncorrelated (ρ=0.22). The damage is plaque-type and location specific, not load-dependent. For MS and AD research: you can't read off white matter injury from gray matter plaque burden. The pathology in fiber tracts is running on different rules. Data: Paper:
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New Cell paper from Bergles lab at Johns Hopkins just built the most comprehensive map of brain myelin ever made — every oligodendrocyte, across the entire mouse brain, across the lifespan. The scale: >10 million cells per brain, terabyte-scale 3D lightsheet volumes, registered to the Allen Brain Atlas across 417 regions from 2 months to 2+ years of age. The technical stack: Custom tissue clearing (CUBIC-L + SHIELD + uRIMS with 40% urea) to preserve endogenous fluorescence. 3D Mask R-CNN for instance segmentation — not just semantic, instance — so it can distinguish individual cells within dense clusters at scale via overlapping sliding windows. Vision Transformer to classify newly-formed vs. mature oligodendrocytes using soma morphology. All cross-referenced against Allen ISH transcriptomics and MICrONS serial EM. What they found: Oligodendrocyte density varies 10,000-fold across brain regions. Left-right hemispheres: r=0.99. Sex: no significant difference. Strain: matters. The brain never stops myelinating. New oligodendrocytes are still being generated in 2-year-old mice. Prefrontal cortex L6 shows the fastest rates of new myelination into old age — the circuits for executive function keep rewiring throughout life. After demyelination, L4 sensory cortex is the most resilient — oligodendrocytes survive at higher rates. The hippocampus loses nearly everything and barely recovers. Degree of injury doesn't predict rate of recovery. These are independent axes. The Alzheimer's result is the most surprising: Dense-core plaques dominate in cortex and hippocampus. Diffuse/small-core plaques dominate in white matter fiber tracts. Old assumption: diffuse plaques are "less toxic." The data says the opposite — small plaques in fiber tracts cause more myelin loss per plaque than dense-core plaques in gray matter. Plaque load and oligodendrocyte loss are essentially uncorrelated (ρ=0.22). The damage is plaque-type and location specific, not load-dependent. For MS and AD research: you can't read off white matter injury from gray matter plaque burden. The pathology in fiber tracts is running on different rules. Data: Paper:

Bo Wang

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The most detailed 3D reconstruction of a cell ever created. Blows my mind every time. But what exactly are we looking at here? The average human cell contains: ~ 15-20 total distinct organelle types, totalling between ~1-10 million working together per cell. All these nano-machines in the cell are made up of proteins. ~ 8,000-10,000 distinct types of unique proteins, adding up to between 40 million - 10 trillion total proteins making up all those cellular systems. ~ 10,000 - 15,000 distinct types of RNA shuttling information around the cell, totalling up to ~10 million RNA molecules moving around the cell simultaneously. ~ Billions of Lipid molecules packed together into the cell membrane, which is also packed tightly with millions more protein-based nano-machines. And let's not forget billions of lines of DNA information to build and run it all. That's TRILLIONS of of individual molecular pieces working together to make a single cell function. That means there is more complexity in a single cell than humanity's largest cities. And people still believe this wasn't Divinely Designed. This is God's Glory on Display. But to make the point. A cell couldn't have evolved from some nebulous simpler "protocell" because even the simplest cells still require massive complexity. The "simplest" cell ever created was engineered by scientists knocking out pieces of a functional cell until it stopped functioning. Here is what they found is the absolute necessary minimal requirements of a cell to function: - Over ~531,000 lines of coded DNA information - 473 total genes to create hundreds of unique protein products (they later added 19 genes back in because the cell was so weak) - Hundreds of thousands of total proteins all working together - Extensive regulatory networks guiding all these interactions If the cell doesn't have all these systems in place, from the start... it doesn't live. Cell rely on an intricate network of complex systems, which are themselves built from complex interconnected pieces woven together into an incomprehensibly complex web of functionilty. Only intelligence has ever been observed creation vast interconnected systems like this. Life was clearly Created. It couldn't happen any other way.
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The most detailed 3D reconstruction of a cell ever created. Blows my mind every time. But what exactly are we looking at here? The average human cell contains: ~ 15-20 total distinct organelle types, totalling between ~1-10 million working together per cell. All these nano-machines in the cell are made up of proteins. ~ 8,000-10,000 distinct types of unique proteins, adding up to between 40 million - 10 trillion total proteins making up all those cellular systems. ~ 10,000 - 15,000 distinct types of RNA shuttling information around the cell, totalling up to ~10 million RNA molecules moving around the cell simultaneously. ~ Billions of Lipid molecules packed together into the cell membrane, which is also packed tightly with millions more protein-based nano-machines. And let's not forget billions of lines of DNA information to build and run it all. That's TRILLIONS of of individual molecular pieces working together to make a single cell function. That means there is more complexity in a single cell than humanity's largest cities. And people still believe this wasn't Divinely Designed. This is God's Glory on Display. But to make the point. A cell couldn't have evolved from some nebulous simpler "protocell" because even the simplest cells still require massive complexity. The "simplest" cell ever created was engineered by scientists knocking out pieces of a functional cell until it stopped functioning. Here is what they found is the absolute necessary minimal requirements of a cell to function: - Over ~531,000 lines of coded DNA information - 473 total genes to create hundreds of unique protein products (they later added 19 genes back in because the cell was so weak) - Hundreds of thousands of total proteins all working together - Extensive regulatory networks guiding all these interactions If the cell doesn't have all these systems in place, from the start... it doesn't live. Cell rely on an intricate network of complex systems, which are themselves built from complex interconnected pieces woven together into an incomprehensibly complex web of functionilty. Only intelligence has ever been observed creation vast interconnected systems like this. Life was clearly Created. It couldn't happen any other way.

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Real footage of cell division at kidney cells
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Real footage of cell division at kidney cells

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How to freeze the first row and column of your data table without the mouse. 🤓
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How to freeze the first row and column of your data table without the mouse. 🤓

Excel Dictionary

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the definition of “sharing one brain cell” #HalZey
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the definition of “sharing one brain cell” #HalZey

fran𝜗𝜚˚⋆

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A stroke can destroy brain cells within minutes, often leaving people with long‑term problems in movement, memory, or speech. But scientists may have found a way to help the brain heal itself. In studies of mice, researchers injected stem cells into areas of the brain damaged by stroke. These stem cells began turning into early‑stage brain cells, and many later developed into active neurons that connected with surrounding tissue. The treatment did more than just grow cells.
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A stroke can destroy brain cells within minutes, often leaving people with long‑term problems in movement, memory, or speech. But scientists may have found a way to help the brain heal itself. In studies of mice, researchers injected stem cells into areas of the brain damaged by stroke. These stem cells began turning into early‑stage brain cells, and many later developed into active neurons that connected with surrounding tissue. The treatment did more than just grow cells.

Science Postcard

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Very excited to share our new preprint on visual processing in the octopus! Led by Judit Pungor judit, together with Mea (josc) 🐙 and Angelique Allen, we measured the functional organization of visual responses in the octopus brain. 🐙👁️ 1/n
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Very excited to share our new preprint on visual processing in the octopus! Led by Judit Pungor judit, together with Mea (josc) 🐙 and Angelique Allen, we measured the functional organization of visual responses in the octopus brain. 🐙👁️ 1/n

Cris Niell

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"Creatine causes cancer to spread" -- that headline comes from a real 2021 mouse study. But what does the human data actually say? In the new Health Longevity Secrets episode, I break down both halves of the science: (1/6)
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"Creatine causes cancer to spread" -- that headline comes from a real 2021 mouse study. But what does the human data actually say? In the new Health Longevity Secrets episode, I break down both halves of the science: (1/6)

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Cells attacking cancer cell. What cells can do this?
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Cells attacking cancer cell. What cells can do this?

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Biggest medical discoveries of the week (🧵) 1/10 Spinal cord injury triggers activation of T cells, inflammation, and death of neurons Editing the T cell receptor, using mRNA, suppressed this, and helped recovery from the injury (in mice!) (Paper:
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Biggest medical discoveries of the week (🧵) 1/10 Spinal cord injury triggers activation of T cells, inflammation, and death of neurons Editing the T cell receptor, using mRNA, suppressed this, and helped recovery from the injury (in mice!) (Paper:

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