syGlass View Data Showcase:

Computational 3D histological phenotyping of whole zebrafish, Cheng Lab

In a new manuscript published in eLife, “Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography," Dr. Keith Cheng’s team report on an imaging method, histotomography, which has the power to produce high-contrast, 3D reconstructions of whole, mm to cm-scale organisms at subcellular resolution at a throughput that is sufficient for large-scale studies. This 3D form of histology required customizing sample preparation, sample fixation, and imaging parameters of micro-CT. The resulting 3D reconstructions allow virtual histology-like “sections” in any plane and 3D rendering at any scale to reveal anatomic and microanatomic phenotypes affecting organ systems, tissues, and cells in context.



The isotropic nature of the reconstructed data is seamlessly suited for Virtual Reality. The high performance visualization experience that syGlass offers not only allows researchers to explore their data in real time, a feat previously thought impossible using today’s available computational power, but also share the experience with anyone, using syGlass’s free viewer, syGlass View. Published syGlass project files as well as other datasets included with the paper are available on DataDyrad. Up to date science by The Chenglab is available at their website, Chenglab.io




















DATASETS FROM CHENG LAB AVAILABLE FOR SYGLASS VIEW



Thumbnail Image Volume Image Modality
Zebrafish Brain Segmentation and Nuclear Detection (741.8 Mb)
Project representing five stages of the cell detection pipeline (reconstruction, nuclear probabilities, segmented nuclei, brain region segmentation, nuclei in anatomical context).
X-ray Histotomography
Zebrafish Embryonic to Juvenile Development (3.976 Gb)
Developmental project featuring five samples (2, 3, 4, 5 and 33 days post fertilization) zebrafish reconstructed with microCT.
X-ray Histotomography
Zebrafish Juvenile 1.43um voxel size.syg (3.213 Gb)
High resolution 33 days post fertilization juvenile zebrafish reconstructed with microCT.
X-ray Histotomography





SYSTEM REQUIREMENTS






Required Hardware

Operating System: Windows 10

GPU: NVIDIA GeForce GTX 1060 or better (No AMD Support)

RAM: 4GB or more

Bluetooth (Windows Mixed Reality only)


Supported VR Systems

• HTC Vive and Vive Pro

• Oculus Rift with Touch controllers

• Windows Mixed Reality

○ HP, Dell, Samsung, Acer, Lenovo

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FAQs



What is syGlass View?

syGlass View is a free version of syGlass that allows for the exploration of a curated set of image volumes provided by researchers and educators.

Where does the data come from?

syGlass customers publish the data sets that are available in syGlass View. If you are interested in communicating your own data too, contact us to learn more.

What’s the benefit scientific communication in VR?

Virtual reality allows users to process information in a fraction of the time. Spend less time trying to comprehend 3D structures in two dimensions, and more time gaining valuable insights into the data.

Do I need a VR headset?

Exploring image volumes is faster and more natural in virtual reality. However, syGlass View also has a desktop viewer that does not require a VR headset.