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| EMAN2 | |
|---|---|
| Name | EMAN2 |
| Developer | University of California, San Francisco; Laboratory of Molecular Biology contributors |
| Released | 2003 |
| Programming language | Python (programming language), C++ |
| Operating system | Linux, macOS, Microsoft Windows |
| License | GNU General Public License |
EMAN2 is a software suite for single-particle electron microscopy image processing, three-dimensional reconstruction, and structural analysis. It provides tools for particle picking, image alignment, classification, and model validation used in cryo-electron microscopy workflows by structural biologists at institutions such as University of California, San Francisco, Max Planck Society, and European Molecular Biology Laboratory. The project integrates contributions from research groups that include participants from National Institutes of Health, Howard Hughes Medical Institute, and collaborations with centers like Diamond Light Source and European Synchrotron Radiation Facility.
EMAN2 traces origins to early computational efforts in electron microscopy at laboratories including MRC Laboratory of Molecular Biology and teams influenced by work at Stanford University and Harvard University. Development accelerated with funding sources including National Science Foundation grants and cooperative agreements with National Center for Biotechnology Information collaborators. Major milestones parallel advances at facilities such as Brookhaven National Laboratory and initiatives like the Protein Data Bank expansion and the Human Genome Project era computational boost. EMAN2 evolved through contributions from researchers connected to Columbia University, Massachusetts Institute of Technology, and international groups at University of Cambridge and ETH Zurich.
The architecture is modular, combining high-level scripting in Python (programming language) with optimized routines in C++ to interface with libraries from Intel-optimized math packages and community tools developed at Los Alamos National Laboratory. The design reflects interoperability with standards developed at Electron Microscopy Data Bank and aligns with pipelines in centers like National Center for Electron Microscopy. EMAN2’s components interoperate with external packages produced by teams at University of Oxford and Max Planck Institute for Biophysical Chemistry, enabling integration with processing suites from RELION-oriented groups and visualization tools from The Scripps Research Institute and University of California, San Diego developers.
EMAN2 offers particle picking modules influenced by algorithms used in projects at California Institute of Technology and Johns Hopkins University, automated classification routines paralleling approaches from Yale University and statistical methods developed at Princeton University. It supports iterative refinement workflows comparable to implementations at Swiss Federal Institute of Technology in Zurich labs. Tools include symmetry handling used in studies at European Molecular Biology Organization labs, sub-tomogram averaging techniques similar to protocols at University of Toronto, and validation metrics aligned with practices at University College London and Imperial College London.
Common workflows encompass motion correction, CTF estimation, particle extraction, two-dimensional classification, three-dimensional refinement, and map validation—steps employed by teams at University of California, Berkeley, University of Pennsylvania, and Weizmann Institute of Science. Applications span structural determination of viruses studied at Centers for Disease Control and Prevention, molecular machines investigated by groups at Rudolf Magnus Institute affiliates, and membrane protein reconstructions typical of research at National Institute of General Medical Sciences. Users in pharmaceutical settings at companies like Pfizer and Novartis have adapted pipelines for drug-target studies paralleling academic protocols from Rockefeller University.
EMAN2 reads and writes widely used formats adopted by archives like EMDataBank and integrates with model repositories such as the Protein Data Bank. It interfaces with file types generated by microscopes produced by Thermo Fisher Scientific, JEOL, and Hitachi instrumentation. Compatibility extends to visualization and modeling tools originating from ChimeraX developers at University of California, San Francisco and simulation packages from Argonne National Laboratory, facilitating exchange with community standards promoted by International Union of Crystallography meetings and workshops at Cold Spring Harbor Laboratory.
Development is driven by an open-source community comprising contributors from University of California, San Francisco, National Institutes of Health, European Molecular Biology Laboratory, and academic labs at University of Cambridge and University of Tokyo. The community engages through training courses at Cold Spring Harbor Laboratory, conferences such as the Microscopy and Microanalysis meeting, and collaborations with consortia including Cryo-EM Map Challenge organizers and societies like Biophysical Society. Documentation and user support reflect pedagogical efforts similar to summer schools at EMBL-EBI and workshops at Brookhaven National Laboratory.
Performance benchmarks reference datasets commonly used by groups at University of Wisconsin–Madison and validation protocols aligning with criteria set by repositories like Electron Microscopy Public Image Archive and standards discussed at International Society for Advancement of Cytometry meetings. Accuracy assessments often compare results to reconstructions published by teams at Cold Spring Harbor Laboratory, Salk Institute, and California Institute of Technology, and incorporate cross-validation approaches similar to methods from National Institute of Standards and Technology. The software’s scalability has been evaluated on computing resources including clusters at Lawrence Berkeley National Laboratory and high-performance computing centers associated with XSEDE.
Category:Electron microscopy software