arivis in Science publication from Eric Betzig's group: "Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution"

How to Visualize and Analyze Images of Entire Brains at Nanoscale Resolution with Vision4D

Science paper "Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution" published on 18 Jan 2019: Vol. 363, Issue 6424
DOI: 10.1126/science.aau8302 
Co-Corresponding authors: Eric Betzig, Ed Boyden
Authors contributed equally to this work: Ruixuan Gao, Shoh M. Asano, Srigokul Upadhyayula

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A new paper from Eric Betzig and Ed Boyden and their collaborators at Janelia Research Campus, MIT, the University of California at BerkeleyHarvard Medical School/Boston Children’s Hospital, explains how to rapidly image entire brains (fly and mouse) at nanoscale resolution to reveal neuronal circuits and brain structure. In the collaboration between Eric Betzig's group and Ed Boyden's group, the researchers used lattice light sheet microscopy to image expansion microscopy specimens, resulting in a ~1000x speedup in nanoresolution imaging. With this powerful new technique they see complete neural circuits spanning millimeters or more.

arivis Vision4D was effectively used for the visualization, exploration, and analysis of these multiple terabyte images (up to tens of terabytes per sample). Several tools of arivis Vision4D and the high-performance Analysis Pipeline helped the authors gain new insights from their information-rich images and demonstrate the importance of this new technology.

 

Movies from the Science Publication

Credit: Gao et al./ Science 2019

In this multi-terabyte image of mouse visual cortex, a neuron was efficiently isolated, in its entirety, revealing its morphology and neighboring structures. Using the 2D Viewer and the Drawing Tools, an initial 3D mask around the neuron was generated, which was subsequently refined (contracted precisely onto the neuron and then dilated by a fixed amount) with the Analysis Pipeline. The easy to use storyboard functionality with thumbnails allowed easy and intuitive creation of movies.

arivis Vision4D features:

» 2D Viewer

» Drawing Tools

» Analysis Pipeline

» Storyboard

Credit: Gao et al./ Science 2019

In this multi-terabyte image of mouse primary somatosensory cortex, two adjacent layer V pyramidal neurons were found to exhibit substantially different patterns of Homer1 expression (arivis Vision4D, 4D Viewer). They were then efficiently isolated by first creating 3D masks with the Drawing Tools in arivis Vision4D, and then refining each mask with the Analysis Pipeline of arivis Vision4D. Raw voxel data from within each mask was then used for quantitation of Homer1 structures.

arivis Vision4D features:

» 2D Viewer

» Drawing Tools

» Analysis Pipeline

Credit: Gao et al./ Science 2019

A multi-TB volume showing a subset of neurons in the fly brain, their associated nc82-positive structures, and all nc82-positive puncta across the entire brain. Masked neuron images were imported into Vision4D and converted into dilated region masks for each brain compartment. The masks enabled the authors to use Region-of-Interest Clipping in the 4D Viewer, so that voxels within the specific masks could be shown sequentially and at high-resolution. Custom color gradients were also made and applied for rendering each brain region.

arivis Vision4D features:

» 4D Viewer

» Custom color gradients

» ROI clipping

Credit: Gao et al./ Science 2019

The easy to use storyboard functionality with thumbnails allowed easy and intuitive creation of movies in arivis Vision4D.

arivis Vision4D features:

» Storyboard

Press:

» EurekAlert: How to rapidly image entire brains at nanoscale resolution

» The Harvard Gazette: Science at the speed of ‘light-sheet’ - New technique enables subcellular imaging of brain tissue 1,000 times faster than other methods

» Howard Hughes Medical Institute News: How-to-rapidly-image-entire-brains-at-nanoscale-resolution

» MIT News: Mapping the brain at high resolution - New 3-D imaging technique can reveal, much more quickly than other methods, how neurons connect throughout the brain

» MIT Synthetic Neurobiology Group - Publication detail

» UC Berkeley: Berkeley News - Thanks to rapid, 3D imaging, anyone can tour the fly brain

Publication:

» Science

 

 

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