Allen Institute releases new data and visualizations for Allen Brain Observatory

June 21, 2017, Allen Institute for Brain Science
Optical physiology manager, Jerome Lecoq, Ph.D. and optical physiology research associate, Kate Roll, inspect one of the standardized microscope platforms from the Allen Brain Observatory used to record the real-time cellular activity in the visual cortex of mice as they were shown a variety of stimuli, pictures and movies. Credit: Allen Institute

The Allen Institute for Brain Science today announced the release of new data and analysis tools for the Allen Brain Observatory: a highly standardized survey of cellular-level neuronal activity in the mouse visual system. In addition to bringing the total number of cells surveyed to nearly 40,000, the release includes key improvements to algorithms that decrease noise and match cells across experiments, leading to a more robust and usable resource for researchers around the world to study how visual information is processed in the brain.

"The data contained in the Allen Brain Observatory is vast and rich, and as we produce and share the data we are always thinking of ways to make it as usable as possible while retaining its complexity and multidimensionality," says Lydia Ng, Ph.D., Senior Director of Technology at the Allen Institute for Brain Science. "These updates to the Allen Brain Observatory—the and refreshed analysis—will be of great utility to our users, since they provide critical improvements to how the data are presented."

As part of the release, activity from more than 13,000 new cells have been added to the dataset, and data from all previous cells has been reprocessed to incorporate additional features, including tracking the position of the mouse's gaze during experiments. Allen Institute scientists also improved how individual cells are aligned across different experiments, and how signals from overlapping cells can be separated.

The Allen Brain Observatory also added new visualizations, including tools for receptive fields that show how neurons respond to in space. All the new are also available as part of the Allen Software Development Kit (SDK), which can be used to analyze the data in depth.

This release marks the final update to the Allen Brain Observatory dataset for 2017, with updates to other Allen Brain Atlas resources planned for the fall.

This video explains how Allen Institute for Brain Science researchers developed the Allen Brain Observatory and what it can tell us about processing of visual information in the brain. Credit: Allen Institute
A small sample of the novel data visualizations for each of the nearly 40,000 neurons contained in the Allen Brain Observatory. Mice were presented with a large variety of visual stimuli to determine the "tuning," or preference, of each individual cell to visual features. Credit: Allen Institute

Explore further: Allen Cell Types Database updated with new data and models

Related Stories

Allen Cell Types Database updated with new data and models

March 17, 2017
The Allen Institute for Brain Science has released additional data and computer models of cell activity for inclusion in the Allen Cell Types Database: a publicly available tool for researchers to explore and understand the ...

Team announces mapping of the mouse cortex in 3-D

October 27, 2016
The Allen Institute for Brain Science has completed the three-dimensional mapping of the mouse cortex as part of the Allen Mouse Common Coordinate Framework (CCF): a standardized spatial coordinate system for comparing many ...

Allen Brain Observatory launched

July 13, 2016
The Allen Institute for Brain Science today announced the release of the Allen Brain Observatory: a highly standardized survey of cellular-level activity in the mouse visual system. This dynamic tool empowers scientists to ...

Allen Institute for Brain Science announces new data release on Allen Brain Atlas resources

December 20, 2013
The Allen Institute for Brain Science recently announced major updates to the online public resources available through the Allen Brain Atlas data portal. The updates include feature enhancements and data additions to four ...

Data release from the Allen Institute for Brain Science expands online atlas offerings

June 7, 2012
The Allen Institute for Brain Science announced today its latest public data release, enhancing online resources available via the Allen Brain Atlas data portal and expanding its application programming interface (API).

Allen Cell types database launched

May 14, 2015
The Allen Institute for Brain Science announced today that it is taking the first major scientific step to create a searchable standards database for the brain with the launch of the Allen Cell Types Database. This first ...

Recommended for you

Wiring diagram of the brain provides a clearer picture of brain scan data

December 14, 2018
Already affecting more than five million Americans older than 65, Alzheimer's disease is on the rise and expected to impact more than 13 million people by 2050. Over the last three decades, researchers have relied on neuroimaging—brain ...

Scientists identify method to study resilience to pain

December 14, 2018
Scientists at the Yale School of Medicine and Veterans Affairs Connecticut Healthcare System have successfully demonstrated that it is possible to pinpoint genes that contribute to inter-individual differences in pain.

Parents' brain activity 'echoes' their infant's brain activity when they play together

December 13, 2018
When infants are playing with objects, their early attempts to pay attention to things are accompanied by bursts of high-frequency activity in their brain. But what happens when parents play together with them? New research, ...

In the developing brain, scientists find roots of neuropsychiatric diseases

December 13, 2018
The most comprehensive genomic analysis of the human brain ever undertaken has revealed new insights into the changes it undergoes through development, how it varies among individuals, and the roots of neuropsychiatric illnesses ...

Researchers find the cause of and cure for brain injury associated with gut condition

December 13, 2018
Using a mouse model of necrotizing enterocolitis (NEC)—a potentially fatal condition that causes a premature infant's gut to suddenly die—researchers at Johns Hopkins say they have uncovered the molecular causes of the ...

Researchers discover abundant source for neuronal cells

December 13, 2018
USC researchers seeking a way to study genetic activity associated with psychiatric disorders have discovered an abundant source of human cells—the nose.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.