EMAN

EMAN processes transmission electron microscopy (TEM) single-particle images to produce 3D reconstructions and perform contrast transfer function (CTF) correction for structural analysis.

Key Features:

• Single-Particle Reconstruction: Semiautomated single-particle reconstruction supporting initial model generation with no symmetry, single-axis rotational symmetry, or icosahedral symmetry and capable of achieving resolutions beyond ~10 Å.
• Iterative Model Refinement: Classification by model-based projection matching with iterative refinement, including simultaneous fitting of CTF parameters from multiple micrographs and automatic amplitude and phase CTF correction within the refinement loop.
• Extensive Image Processing Library: Core C++ library of over 500 image-processing functions organized modularly with introspection capabilities for algorithm extension.
• 3D Transformation Class: Rewritten 3D transformation class that facilitates translation between Euler angle standards and symmetry conventions.
• Parallelism System: Flexible parallelism framework introduced in EMAN2 to support scalable processing of large datasets.
• Python Scripting Support: Python scripting interfaces that allow modification and extension of program behavior without recompilation.

Scientific Applications:

• Single-Particle Reconstruction: Generation of high-resolution 3D structures from TEM single-particle datasets under varied symmetry conditions.
• Cryo-Electron Tomography (cryo-ET): Application to subvolume averaging and reconstruction workflows in cryo-ET studies.
• Helical Reconstruction: Processing and reconstruction of helical specimens from electron micrographs.
• 2-D Crystallography: Analysis and reconstruction workflows applicable to two-dimensional crystal data.
• Whole-Cell Tomography: Use in whole-cell tomography datasets for structural analysis at cellular scale.

Methodology:

Iterative refinement using classification by model-based projection matching; simultaneous fitting of CTF parameters from multiple micrographs; and automatic amplitude and phase CTF correction within the refinement loop.