USA is pleased to offer the latest tomography solutions for transmission
electron microscopy (TEM). Tomography, or three-dimensional (3D) reconstruction
of multiple TEM images, has developed in the past decade as one of the more
important applications in the field of life sciences and, more recently, in
the field of materials science.
Through its applications group, JEOL USA offers support for tomography comprised
of three software packages: SerialEM and IMOD, both developed at the University
of Colorado (Boulder), and Chimera, which was developed at the University of
California San Francisco. Each of these packages is freely available and has
become the de facto academic standard for routine tomography acquisitions, processing
and visualization of resin-embedded as well as beam-sensitive vitrified specimens.
“The use of these very sophisticated software packages for tomography
with full support from JEOL is not only unique, it resonates extremely well
with our customers and thus provides us with a very strong competitive advantage,”
said Dr. Jaap Brink, Biological Applications Manager at JEOL. This comprehensive
tomography solution has been successfully applied to the TEMs in the JEOL line-up,
starting with the recently introduced 120 kV JEM-1400 up to and including the
300 kV liquid helium-cooled energy-filtered JEM-3200FSC. “The success
of this process reflects to a significant degree the commitment of the developers
in releasing high-quality software and their responsiveness to user requests,”
said Brink. Example of 3D tomography .avi files can be seen on the JEOL USA
website at www.jeolusa.com/Tomography.
SerialEM has a powerful combination of features that enables automated image
acquisition, registration, and alignment of single- or dual axis tilt series
using a unique and robust prediction algorithm. SerialEM employs a versatile
montaging system that can be used, for example, to acquire a montage of the
entire grid across the TEM sample. A very stable and highly flexible low dose
system can be used in conjunction with either an in-column, Omega energy filter
or a post-column energy filter. A script-driven environment allows for repetitive
and time-consuming tasks to be performed in an unattended mode of operation.
IMOD 3D Reconstruction
IMOD, a suite of processing and modeling programs, is being used for the processing
of the tilt series into 3D reconstructions as well as 3D reconstruction starting
from serial section data. Through an easy-to-use Java-powered interface, IMOD
provides for transparent support for single- and dual-axis tilt series as well
as extensive filtering operations of the aligned and reconstructed data. IMOD
can be adapted to either single or multi-processor computing platforms.
Chimera 3D Visualization
Chimera is used for the visualization of 3D reconstructions. This highly extensible,
interactive molecular graphics program can be used to visualize many data forms,
including atomic and molecular structures and 3D tomographic reconstructions.
Powerful and Versatile Combination
The combination of SerialEM, IMOD and Chimera is considered as an extremely
powerful and versatile troika of software products for every aspect of tomography,
not only because of the strong commitment of the developers and JEOL’s
applications group, but also because of the strong support from users worldwide
as evident from the very active user forums for all three packages.
The choice of software from these US-based laboratories funded at the level
of National Resources ensures continued support and development, for example,
as in workshops and tutorials. SerialEM and IMOD are copyrighted by the Boulder
Laboratory for 3-Dimensional Electron Microscopy of Cells ("BL3DEMC")
and the Regents of the University of Colorado (supported by NIH/NCRR RR00592
and NIH/NIBIB R01EB005027). The UCSF Chimera package is copyrighted by the Resource
for Biocomputing, Visualization, and Informatics at the University of California,
San Francisco (supported by NIH P41 RR-01081).