Remote, realtime visualization of multidimensional biological images

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Remote, real-time visualization of
multidimensional biological images

• Christopher J. Gilpin1, Katherine Luby-Phelps1
  and Kelly P. Gaither2
• 1UT Southwestern Medical Center at Dallas
• 2TACC UT Austin

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Data Sources

• Laser scanning confocal microscopy
• 3 colour channels plus time
• Electron microscopy
• Single channel grey scale volumes

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Why Teragrid?

• Workstation solution not possible due to
• Data size
• Data complexity
• Speed

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Size of Cells
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Diagram of a whole cell
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Confocal laser scanning microscopy
Red channel
Green channel
Merged channels
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Electron Tomography

• 3D structure visualisation in the 2-5nm range

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Electron TomographyBack Projection
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Electron Tomography
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Synaptic nerve terminalRaw data tilt series
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Synaptic nerve terminal3D reconstruction
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Electron TomographyGolgi membranesTraditional
Visualisation
Tomogram Modeling Reconstruction
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Synaptic membranes
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Visualisation

• Remote connection to Maverick at TACC
• Parallel ParaView running in a VNC session
• Bypass Local hardware and software

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Remote session
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Scale of the problem

• A typical cell is 50µm in diameter
• Volume of a typical cell is 65500 µm3
• Image resolution is 0.7nm/pixel
• Total pixels per cell is 180 x1012

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Future work

• Data segmentation and feature detection
• Scaling ParaView to uncouple data processing from
  graphic output
• Genetic manipulation of synaptic structure
• Search volumes using protein templates