Science Publication (Eric Betzig) 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 

Expansion microscopy and light sheet microscopy imaged using arivis Vision4D

A new paper from Eric Betzig and Ed Boyden and their collaborators at Janelia Research Campus, the MIT, the University of California at Berkeley, the Harvard 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.

Direct volume rendering of a group of densely-packed neuron terminals in the fly brain, Vision4D,

Image Courtesy: Eric Betzig, Janelia Research Campus, Shoh Asano, MIT and Pfizer, arivis AG, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Multi-terabyte image of mouse visual cortex, a neuron was efficiently isolated, in its entirety, revealing its morphology and neighboring structures

Image Courtesy: Eric Betzig, Janelia Research Campus, Shoh Asano, MIT and Pfizer, arivis AG, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Neuronal processes and myelination patterns across the mouse primary visual cortex 

View Movie

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 in arivis Vision4D, 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 of arivis Vision4D. 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

 


Relationship of post-synaptic Homer1 to neuronal processes across the mouse primary somatosensory cortex

View Movie

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


DANs and DAN-associated presynaptic sites in different neuropil domains of an adult Drosophila brain.

View Movie

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


Dorsal paired medial (DPM) neurons and DPM-associated presynaptic sites in an adult Drosophila brain

View Movie

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

 

 

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

Additional movies

Segmented neuron Object spanning a multi-TB image of the fly brain. Initially the neuron was masked with Magic Wand and Draw Objects Tools in arivis Vision4D, and was then segmented algorithmically in the arivis Vision4D Analysis Pipeline

Image Courtesy: Eric Betzig, Janelia Research Campus, Yoshinori Aso, Janelia Research Campus, Rui Gao (MIT), arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Segmentation of tangled neurons in the fly brain, masked manually with arivis InViewR and then shown by Clipping-on-Objects in arivis Vision4D 

Image Courtesy: Eric Betzig, Janelia Research Campus, Yoshinori Aso, Janelia Research Campus, Rui Gao (MIT), arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Raw sculpted 3D segmentation seeds for several neurons are shown (various colors) with raw data (green) in the fly brain, done with arivis InViewR 

Image Courtesy: Eric Betzig, Janelia Research Campus, Gokul Upadhyayula, Harvard, arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet

Touching neurons segmented in the fly brain. These were seeded manually with arivis InViewR and then segmented with the arivis Vision4D Analysis Pipeline 

Image Courtesy: Eric Betzig, Janelia Research Campus, Yoshinori Aso, Janelia Research Campus, Rui Gao, MIT, arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Segmentation of the cytoplasmic (non-membrane) portion of very closely-associated neurons and their bifurcations in the fly brain, done manually with the Draw Objects tools in arivis Vision4D 

Image Courtesy: Eric Betzig, Janelia Research Campus, arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

Segmentations of parts of neurons in the fly brain, arivis Vision4D 

Image Courtesy: Eric Betzig, Janelia Research Campus, Shoh Asano, MIT and Pfizer, arivis AG, Chris Zugates, Source: expansion microscopy (ExM) and Lattice Light Sheet (LLS)

 

arivis Vision4D on the latest cover of the Science Journal!

Great images from combined expansion and lattice light sheet microscopy visualized with arivis Vision4D on the latest cover of the Science! Explore neural circuits across the whole drosophila brain and mouse mouse primary somatosensory cortex. » link to article


 

Press:

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

» The Harvard Gazette: Science at the speed of ‘light-sheet’

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

» MIT News: Mapping the brain at high resolution

» MIT Synthetic Neurobiology Group

» UC Berkeley: Berkeley News

Publication:

» Science

 

If you would like to speak to us in advance please feel free to contact us:

Office Germany
Headquarters Imaging



Office USA
Dependence North America