Telescience: Resources for Electron Tomography

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Telescience Resources for Electron Tomography

• Maryann Martone
• Eric Bushong, Naoko Yamada, Thomas Deerinck, and
  Mark. H. Ellisman
• National Center for Microscopy and Imaging
  Research
• University of California, San Diego

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Subcellular to Molecular
Tissue to cells to subcellular
Filling the Resolution Gaps
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1. What is high voltage electron microscopy and
electron tomography? 2. What are they good
for? 3. Why do we need a 3 MeV microscope? 4.
Telescience portal for remote microscopy
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HVEM
Photooxidation of Neuron Filled with Lucifer
Yellow
Tomographic Volume
After Photooxidation
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Why are dendritic spines important?

• Receive the majority of excitatory synapses in
  the central nervous system
• Are able to change their size, shape and number
  rapidly in response to environmental influences

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Why are dendritic spines difficult to study?

• Too small to be resolved completely by light
  microscopy
• Too large to be studied by conventional EM
• In both light and electron microscope, require 3D
  evaluation to determine their size and shape

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High Voltage Electron Microscopy

• Conventional TEM 100-200 keV
• High Voltage TEMs 400 keV - 3 MeV
• Higher accelerating voltages thicker sections
  (1-10 µm)

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Spiny Dendrite 4 µm thick section
selectively stained
Spiny Dendrite 100 nm Thin Section
High Voltage Electron Microscopy
1 µm
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Electron Tomography
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Need for HVEM

• As specimen is tilted through high angles, the
  effective section thickness doubles and triples

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60
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Why 3 MeV?

• For some specimens, thicker sections (gt 2 µm) are
  necessary

Striatal spiny dendrites stained by intracellular
injection/photooxidation
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Research Center for Ultra High Voltage Electron
Microscopy at Osaka University National Center
for Microscopy and Imaging Research
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Fragile-X Syndrome
-most common form of inherited mental
retardation -light microscopic examination found
alterations in dendritic spines -3MeV tomography
is being used to provide quantitative analysis
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Knock-out
Control
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Multicomponent Structures
Hippocampal Synapse 0.5 µm thick section
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Simulations with MCell

• High resolution 3D views of subcellular domains

• Tomographic reconstructions provide structural
  template for modeling studies

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Tomography Workflow
Modeling studies
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Bottlenecks in Tomography Processing Stream

• Data collection and digitization (if using film)
• Alignment and normalization
• Volume reconstruction
• Segmentation
• Modeling

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Stephen Peltier, Abel Lin, Tomas Molinas, David
Lee
Manage your Data
Control Batch Jobs
Remotely Control Instruments
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• Telescience Portal
• Provides a centralized interface to applications
  that use grid resources for tomography, including
  remote microscopy, instruments, image viewers,
  analysis tools, computational resources and
  federated databases
• Abstracts the complexity of high performance
  computing and new computational methodology from
  the end user.
• Automatically stores, manages, and archives data
  without end user intervention but still allows
  for manual manipulation.

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The Telescience Workflow The Telescience workflow
was designed to provide a contiguous series of
steps to guide the user through the individual
steps leading up to a successful reconstruction.

• Preparatory work
• Schedule equipment
• Remote control of instrument
• Pre-tomo utilities
• Computation
• Segment and visualize

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Next Generation Remote Instrumentation Control
Applet
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Running a Globus-Tomography job (Gtomo) Gtomo
is an application that distributes computation
using Globus to render a three-dimensional
reconstruction.
This page gives you the option of running your
job over a variety of computational resources.
Just select the computational resources you would
like to use, the parameters, and click submit.
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Storing Data The user can move the data from
the microscope to the appropriate SRB collection
and remote database.
There are several ways to move your data into the
portal and SRB. These methods accommodate moving
files from the microscope (first option), moving
data from the NCMIR file system (second option),
or uploading data from your local computer (third
option).
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Database Federation
Are changes in axon diameter and/or number
present in the optic nerve of EAE animals before
the development of gross structural changes?
Integrated View
Integrated View Definition
Mediator
Wrapper
Wrapper
Wrapper
Wrapper
Web
CaBP, Expasy
MRI
histology
Electron microscopy
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Advantages and Uses of Telescience Approach
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FasTomo Quick feedback for tomographic
reconstruction
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Telescience and Wireless Technology

• Access to advanced computational tools via
  wireless handheld devices.
• The ability to review the status and progress of
  large computational tasks.
• The ability to move data to and from the portal
  using SRB.

SC2001
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Telescience
Education and Outreach

• Brings advanced technology into the classroom
• Point and click interfaces students can acquire
  images immediately
• Used by high school students and college students
• Reliability and flexibility needed

April 27th Williams College-San Diego
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High Resolution Montaging
1 mm
100 µm
19000 X 11000 montage
Custom X, Y, Z precision stage Images knit
together with IMOD (Mastronarde)
10 µm
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Biomedical imaging utilizing Grid computing

• Grid computing for the non-computer scientist
• Point and click interface to grid computing.
• Reconstruction of large datasets
• Currently too cumbersome
• Rapid feedback
• Would greatly improve efficiency
• Visualization of large data
• Distributed data management