Rapid Visual Inventory & Comparison of Complex 3D Structures

NSF Scientific Visualization Challenge 2011 1st place video:
Prototype of Brad Marsh's geometric abstraction concept to visually simplify complex data by Graham Johnson, Brad Marsh, and Andrew Noske.
http://www.wired.com/wiredscience/201...

This entry demonstrates a new visualization standard we've developed so that complex three-dimensional (3D) datasets can be computationally 'morphed' into much simpler 3D geometric abstractions that are more "visually intuitive" than the original images. Our approach can be used to streamline the scientific analysis of multiple parameters simultaneously for complex 3D images and/or to more effectively communicate key insights afforded from such data to a wide variety of audiences (both scientists and the general public), including schoolchildren.

This animation explains how we've applied this unique process for rendering extraordinarily complex biological data (3D image maps generated by 'cellular tomography') into simplified geometric models that are much easier to interpret. The original 3D maps of pancreatic 'beta' cells precisely capture (at the 'nanoscale') both the extraordinary beauty and complexity of the molecular machinery within cells. Even for experts, however, such complex data remain difficult to visually interpret without painstaking image analysis. In contrast, the abstracted versions computed from the original 3D models employ simple geometric shapes to accurately depict the size, number and length of the various different 'compartments' or 'organelles' within each cell. In addition, these objects can be easily reorganized in 3D space, such that the simplified geometric models reveal "at-a-glance" how the complex internal landscape of insulin-secreting cell undergoes dramatic changes in response to different metabolic demands, physiological states and chronic disease conditions, such as diabetes [1,2].

1. Mapping the β-cell in 3D at the nanoscale using novel cellular electron tomography and computational approaches. Noske AB, Marsh BJ. In: BetaSys - Systems Biology of Regulated Exocytosis in Pancreatic β-Cells (Booß-Bavnbek B, Klösgen B, Larsen J, Pociot B, Renström E, Eds.). 2011. Springer. Series: Systems Biology, 2(8):147-183.
http://www.springer.com/new+%26+forth...

2. Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. Noske AB, Costin AJ, Morgan GP, Marsh BJ. Journal of Structural Biology. 2008. 161(3):298-313.
www.ncbi.nlm.nih.gov/pubmed/18069000

A figure [CELLuloid] that artistically summarizes this animation as a series of movie frames can be viewed at:
http://www.grahamj.com/bradmarsh/Mars...


CONTRIBUTOR TEAM
Graham Johnson PhD: implementation of 3D geometric abstraction concept, computer graphic animation, narration
Molecular Graphics Laboratory
Department of Molecular Biology
The Scripps Research Institute
La Jolla, CA, USA

Andrew B Noske PhD: data acquisition, segmentation, image analysis
Structural Cell Biology Group
Division of Molecular Cell Biology
Institute for Molecular Bioscience
The University of Queensland
St Lucia, QLD, AUSTRALIA

Brad J Marsh PhD: development of geometric abstraction concept, data acquisition, image analysis, project supervision
Structural Cell Biology Group
Division of Molecular Cell Biology
Institute for Molecular Bioscience
The University of Queensland
St Lucia, QLD, AUSTRALIA

SPECIAL ACKNOWLEDGEMENTS
Mr Garry Morgan, The University of Queensland
Mr Adam Costin, The University of Queensland
Prof. Ronald A Milligan, The Scripps Research Institute
Prof. David N Mastronarde, University of Colorado

• Category

  Science & Technology

[headthroughawindow]

I am curious about whether you have been able to visualize smaller structures, such as filamentous actin or microtubules, before and after glucose stimulation in your 3D EM reconstructions?

[Graham Johnson]

The topographers working on the project in Brad Marsh's lab can see microtubules in these reconstructions. Cell 3 has them traced out for a portion of the cell. This lab and other labs also do more high resolution reconstructions that allow such structures to be resolved in more detail.

[headthroughawindow]

Thanks for the quick reply. I will look more into the publications from Dr. Marsh's lab. Are other people outside the lab (like myself) who can use a program or website to look at these reconstructions, if they've been published? I'm thinking it would be really cool to be able to look at it in a PyMol kind of scenario where I could zoom in and rotate on my own. Thanks!

[Graham Johnson]

Science software is rarely user friendly, but you sound like you have some experience, so I'm sure you're already aware of that.

You can install the software they use called IMOD, including some extra plugins that Andrew Noske developed at bio3d.colorado.edu / imod / Be sure to follow the tutorials to get up and running... IMOD is quite nice once you know your way around.

Some labs use another software called Amira, but its very expensive. amira.com I see they have a free trial.

[DJDepRemixes]

Sounds like Toby off of the office

[Graham Johnson]

Good Call...never noticed that.

[DJDepRemixes]

kinda of freaked me out with the similarity but great video.

[art4med]

Thanks for responding; of course I truly admire your work!

[art4med]

Surely you are not calling for cell shape to vary as membranes like soap bubbles, the usual medium for visualization of complex math that is otherwise unsustainable? :' )

Whatever the case, you must admit that the spherical representation often seen in animation is more-often 'inaccurate' within "solid" media of tissues.

[art4med]

Congrats again on your award: I applaud your composition, color choices, and lighting as well. And thanks for the introduction (after some digging) to IMOD out of UCBoulder.