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JEOL USA Tomography Solution

JEOL USA offers tomography support that consists of three software packages. 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.

-- view our technical note regarding (S)TEM tomography

Software Packages

SerialEM Tomography Software

SerialEM has a powerful combination of features that enable 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 to acquire a montage of the entire grid across the TEM sample.

A very stable and highly flexible minimum 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 Tomography Software

IMOD, a suite of processing and modeling programs, processes the tilt series as well as serial section data into 3D reconstructions. 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.

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).

Chimera Visualization Software

Chimera is used for the visualization of 3D reconstructions. This highly extensible, interactive molecular graphics program that can be used to visualize many data forms, including atomic and molecular structures as well as density maps such as the 3D reconstructions.

Chimera was developed at the University of California San Francisco.

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).

3D Reconstruction of frozen hydrated keyhole limpet hemocyanin recorded at 300 kV and energy filtered using a 20 eV slit centered at the zero-loss peak. Total dose for the entire +/- 60° tilt series was 34 electrons/Angstrom2. Different molecular projections can be seen with high contrast that correspond to individual KLH molecules (~30 x 35 nm) in different orientations in the vitreous ice.

0.25mm diameter mosaic of mouse retinal microneuroma at 5000X. Provided by: Marc Lab retinal reconstruction project.

Video Clips

Tomography results from resin-embedded basal bodies. Data courtesy of Dr. Geimer, Univ. Bayreuth.