Posted: February 3, 2009

New Versatile Tomography Solution for Life Sciences on JEOL Transmission Electron Microscopes

(Nanowerk News) JEOL 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
Tomography results from resin-embedded basal bodies. Left to right:  raw, aligned data; reconstruction viewed top to bottom; volume rendering in Chimera
Tomography results from resin-embedded basal bodies. Left to right: raw, aligned data; reconstruction viewed top to bottom; volume rendering in Chimera. (Data courtesy of Dr. Geimer, Univ. Bayreuth)
SerialEM Acquisition
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).
About JEOL
JEOL is a world leader in electron optical equipment and instrumentation for high-end scientific and industrial research and development. Core product groups include electron microscopes (SEMs and TEMs), instruments for the semiconductor industry (electron beam lithography and a series of defect review and inspection tools), and analytical instruments including mass spectrometers, NMRs and ESRs.
JEOL USA, Inc., is a wholly owned subsidiary of JEOL, Ltd., Japan, was incorporated in the United States in 1962. The company has 13 regional service centers that offer unlimited emergency service and support in the U.S.
For more information about JEOL USA, Inc. or any JEOL products, visit, or call 978-535-5900.
Source: JEOL (press release)
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