Resources

Rutgers-New Jersey Cryo-Electron Microscopy and Tomography Core Facility
The Rutgers-New Jersey Cryo-Electron Microscopy and Tomography Core Facility located in The Rutgers Center for Integrative Proteomics Research has transitioned from the planning stages to the final steps, with its formal opening expected in October, 2016. An FEI Talos Arctica 200kV electron microscope is now housed in a custom-built cryoEM suite, adjacent to three sample preparation rooms, a support/mechanical room, and a remote control room, totaling 1500 sq. ft., with space allocated and being outfitted for a 300kV microscope. The Talos Arctica is equipped with a state-of-the-art Gatan K2 direct electron detector mounted on a BioQuantum energy filter.  The latest phase plate technology, designed to significantly enhance contrast in electron images is also available. In this configuration, the microscope is capable of generating images of biological molecules, complexes, and machines at better than 3 angstroms resolution. Automated cryogenic specimen handling of up to 10 specimens in a cassette system, a computer controlled specimen stage, and automated data acquisition software allow high throughput processing of specimens and acquisition of > 1000 images per day for single particle analysis. Our facility will allow scientists to obtain high-resolution images of biological macromolecular complexes preserved in the native state in thin layers of vitreous ice/buffer that can be aligned, averaged, and computer reconstructed to yield moderate to high-resolution 3D mass density maps, addressing the pressing need for structural information for complex biological systems.

Institute for Quantitative Bioinformatics at Rutgers
The IQB@R brings basic and applied researchers together with clinicians pursuing grand challenges in biomedical research using quantitative tools of measurement and analysis from chemistry, computer science, engineering, mathematics, physics, and statistics.

Rutgers Cell Biology and Neuroscience Department
Cell Biology and Neuroscience (CBN) provides an exciting and challenging academic environment by combining excellence in research with a strong commitment to undergraduate and graduate education.  CBN research encompasses the complementary areas of cell biology, developmental biology and neurobiology with an emphasis on fundamental problems in cell signaling and communication. Current areas of focus are biomolecular recognition and cell communication as well as molecular mechanisms of neuronal signaling and synaptic plasticity.  CBN takes a comprehensive approach that begins with introductory lecture courses, continues with advanced topics seminar courses, and culminates in advanced laboratory coursework.

National Center for Macromolecular Imaging at Baylor College of Medicine
The missions of the National Center for Macromolecular Imaging (NCMI) include technology development driven by a diverse spectrum of biological samples to (1) achieve reliable atomic resolution structures of molecular machines; (2) derive structures from conformationally variable machines, and (3) characterize subcellular complexes within intact cells in normal and pathological states.

EMAN

New York Structural Biology Group- Simons Electron Microscopy Center 
The Simons Electron Microscopy Center provides expertise and resources for understanding both molecular and cellular structures. Molecular structure determination is enabled by high-end transmission electron microscopes (TEMs), direct detection cameras, and computational support for single particle analysis. Cellular structure determination is enabled by tomographic reconstructions using the TEMs and a focused ion beam (FIB) scanning electron microscope (SEM). SEMC is supported by dues from member institutions as well as the Simons Foundation.

G. Jensen - The California Institute of Technology
These are the video lectures to get started in Cryo Electron Microscope (EM). There are 7 parts of lectures: basic anatomy of EM, fourier transforms and reciprocal space for the beginner, image formation, fundamental challenges in biological EM, tomography, single-particle analysis, and 2-D crystallography.

IMOD
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.

RELION
RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). It is developed in the group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Briefly, the ill-posed problem of 3D-reconstruction is regularised by incorporating prior knowledge: the fact that macromolecular structures are smooth, i.e. they have limited power in the Fourier domain. In the corresponding Bayesian framework, many parameters of a statistical model are learned from the data, which leads to objective and high-quality results without the need for user expertise. The underlying theory is given in Scheres (2012) JMB. A more detailed description of its implementation is given in Scheres (2012) JSB. In general, this is a useful tool for subtomogram averaging.