Tag: Allen Institute

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Neuroscientists draw up ‘parts list’ for brain cells

Neurons
Neuroscientists used a new, gene-based classification of mouse brain cell types and additional information about neuron shape to uncover two new types of neurons involved in movement. (Credit: Michael Economo, Janelia Research Campus / Lucas Graybuck, Allen Institute)

How many different kinds of cells are there in the brain? At least 133 kinds, including two types of neurons not recognized before, according to a pair of studies featured on the cover of this week’s issue of the journal Nature.

The “parts list” builds on 15 years of work at Seattle’s Allen Institute, focused on analyzing genetic activity in nearly 24,000 of the 100 million brain cells in the mouse cortex. Each cell type exhibited a different combination of genes that were turned on or off.

“This is by far the most comprehensive, most in-depth analysis of any regions of the cortex in any species,” senior study author Hongkui Zeng, executive director of structured science at the Allen Institute for Brain Science, said in a news release. “We can now say that we understand the distribution rules for its parts list.”

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Seattle skyline turns blue for Allen Institute

CenturyLink Field in blue
CenturyLink Field’s arches were lit up in blue to boost autism awareness in April. On Tuesday night, they’ll go blue again in honor of the Allen Institute’s 15-year celebration. (Seahawks Photo / Corky Trewin)

If you see a lot of blue lights around Seattle landmarks this week, it’s not in honor of the Seahawks — this time, the color scheme is paying tribute to another one of Microsoft co-founder Paul Allen’s pet projects, the Allen Institute.

Hot spots such as CenturyLink Field, home of the Seahawks; and Columbia Tower, Seattle’s tallest building, will be turning on their cool-blue mood lighting to celebrate the 15th anniversary of the institute’s founding in 2003.

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Scientists discover mysterious human brain cell

Rosehip neuron
This is a digital reconstruction of a rosehip neuron from a human brain. (Tamás Lab, University of Szeged)

A gene-by-gene, neuron-by-neuron search has turned up a new breed of brain cell that may serve as a fine-scale “volume control” for neural activity in humans.

The novel type of brain cell, known as a rosehip neuron, is described in a study published today by Nature Neuroscience.

“It’s very rare, and you only see it, so far, in a human,” study co-author Ed Lein, an investigator at the Seattle-based Allen Institute for Brain Science, told GeekWire.

Lein’s group at the Allen Institute and a Hungarian research team at the University of Szeged, headed by Gábor Tamás, narrowed in on the neurons using two different lines of inquiry.

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Scientists get time on a telescope for the brain

Jerome Lecoq in lab
Jerome Lecoq, senior manager of optical physiology at the Allen Institute for Brain Science, sets up a microscope in the Allen Brain Observatory. The observatory is run by a team of nearly 100 engineers, scientists and technicians. (Allen Institute Photo)

OpenScope is open for business.

The Seattle-based Allen Institute for Brain Science has taken a page from the playbook for the Hubble Space Telescope to create its latest channel for open-access neuroscience.

Like Hubble’s handlers, the institute is taking requests from researchers for access to its experimental platform for observing neural activity in mice.

Leaders of the project went so far as to consult with leaders in the astronomy community, particularly at the W.M. Keck Observatory in Hawaii, to learn how they divvy up telescope time.

“We seek to do the same in neuroscience, where we now have a brain-based observatory,” Christof Koch, the Allen Institute’s chief scientist and president, said today in a news release.

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Brain scientists meet to share big data

Louis-David Lord
Oxford University neuroscientist Louis-David Lord discusses the effect of psychedelic drugs on the brain during the CNS 2018 meeting at the University of Washington;. (GeekWire Photo / Alan Boyle)

What’s the best way to fine-tune brain stimulation to stop tremors? How do brain-wave patterns shift as we grow up? Can psychedelic drugs reverse the descent into depression? Such questions are being addressed in Seattle this week during a conference that blends big data and brain science.

“We bring numbers to the game, with quantitative methods and computer modeling to understand brain data,” Emory University’s Astrid Prinz, president of the Organization for Computational Neurosciences, told GeekWire.

About 500 brain experts from 29 countries are attending the group’s annual meeting, CNS 2018, which has been jointly organized by the Allen Institute for Brain Science and the University of Washington.

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Allen Institute boosts its brain cell database

Mouse brain
The Allen Brain Explorer can display a virtual mouse brain in 3-D. (Allen Institute for Brain Science)

The Allen Institute for Brain Science has added about 900 virtual mouse brain cells to its Allen Cell Types Database, bringing the total to slightly more than 1,900 cells available for study.

But wait: There’s more.

Today’s release also includes a new, browser-based beta version of a 3-D viewer called the Allen Brain Explorer, which lets users explore the anatomy and connectivity maps for the mouse brain. The Allen Mouse Brain Connectivity Atlas has been freshened up with more information. More details about RNA transcription in mouse, human and macaque brain cells have been added as well.

The upgrades are all part of the open-science mission for the Allen Institute, which Microsoft co-founder Paul Allen created in 2003 and has supported to the tune of half a billion dollars.

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Biologists use AI to flesh out cell’s inner workings

3-D cell model
A 3-D view of human cells is color-coded to highlight substructures. (Allen Institute for Cell Science)

What happens when you cross cell biology with artificial intelligence? At the Allen Institute for Cell Science, the answer isn’t super-brainy microbes, but new computer models that can turn simple black-and-white pictures of live human cells into color-coded, 3-D visualizations filled with detail.

The online database, known as the Allen Integrated Cell, is now being made publicly available — and its creators say it could open up new windows into the workings of our cells.

“From a single, simple microscopy image, you could get this very high-contrast, integrated 3-D image where it’s very easy to see where all the separate structures are,” Molly Maleckar, director of modeling at the Seattle-based Allen Institute, told GeekWire.

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Huge database shows virtual neurons at work

Neuron
A computerized model provides a detailed biophysical representation of a neuron’s firing pattern. (Allen Institute for Brain Science via YouTube)

Seattle’s Allen Institute for Brain Science has created a publicly available database of computerized neuron models that could be used as building blocks to study how brains work in the real world.

The two sets of computer models are described in studies published by Nature Communications, and are available on the Web via celltypes.brain-map.org. The supporting code for the computer models can be accessed via the Allen Institute’s GitHub space.

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Will common-sense AI keep us safer?

Elephant and basketball
Which object would fit through the doorway? The elephant vs. basketball choice is an example of the common-sense questions that pose a challenge for artificial intelligence programs. (AI2 Illustration)

Microsoft co-founder Paul Allen’s new $125 million initiative to give artificial intelligence programs more common sense has another goal that’s closer to home: making AI safer for humans.

That’s the way Oren Etzioni, the CEO of the Seattle-based Allen Institute for Artificial Intelligence, explained it in an exclusive interview with GeekWire about Project Alexandria.

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AI2 program will help engineers build startups

Allen Institute meeting
Team members at the Allen Institute for Artificial Intelligence celebrate the launch of Semantic Scholar during an impromptu meeting at the institute’s Seattle headquarters. (AI2 Photo via Glassdoor)

Is technical expertise the key to success in the fast-moving world of artificial intelligence market? Or is it entrepreneurship?

Top-notch engineers with a yen to build a startup can get the best of both worlds through a newly created CTO residency program at Seattle’s Allen Institute for Artificial Intelligence, or AI2.

“Google has DeepMind, Facebook has FAIR, Microsoft has Microsoft Research AI,” Jacob Colker, managing director of the AI2 Incubator, told GeekWire. “But AI2 is one of the few places where entrepreneurs and early-stage startups can access the same kind of talent that’s available to the big guys.”

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