National Center for Macromolecular Imaging

Software Development at the NCMI

Imaging, Reconstruction, Annotation and Visualization

The National Center for Macromolecular Imaging (NCMI) is a research facility primarily focused on electron cryomicroscopy (cryo-EM) of molecules and macromolecular assemblies. Using various techniques it is now possible to obtain 3-D structures of such specimens at subnanometer resolution. Our mission is to develop this technology and make it accessible to the scientific community. We are equipped with state of the art electron cryomicroscopes, sample preparation equipment, including vitrification robots and computational resources for 3-D reconstructions. A significant portion of our resources is devoted to developing software for data acquisition, 3-D reconstructions, structural analysis and visualization of the results. In electron cryomicroscopy, numerous challenges must be overcome to achieve subnanometer resolution structures. An electron beam can very easily damage a biological specimen, thus as few electrons as possible must be used to observe high-resolution features of macromolecules. This requirement means that the signal to noise ratio of each image is also very low. To compensate for this, tens to hundreds of thousands of images of the same kind of molecule are collected to boost the signal to noise ratio in the final 3-D reconstruction. Current reconstructions require datasets on the order of tens of gigabytes, but the amount of data required to achieve higher resolutions will double for every angstrom gained in resolution. Macromolecules by their very nature are complex assemblies of proteins and/or nucleic acids. Dissecting and analyzing these 3-D reconstructions and their various components is a significant challenge in itself. Our work has resulted in a collection of software packages that work in a number of computational environments to meet the diverse challenges in pushing the limits of cryo-EM.

The National Center for Macromolecular Imaging (NCMI) is a research facility primarily focused on electron cryomicroscopy (cryo-EM) of molecules and macromolecular assemblies. Using various techniques it is now possible to obtain 3-D structures of such specimens at subnanometer resolution. Our mission is to develop this technology and make it accessible to the scientific community. We are equipped with state of the art electron cryomicroscopes, sample preparation equipment, including vitrification robots and computational resources for 3-D reconstructions. A significant portion of our resources is devoted to developing software for data acquisition, 3-D reconstructions, structural analysis and visualization of the results.

In electron cryomicroscopy, numerous challenges must be overcome to achieve subnanometer resolution structures. An electron beam can very easily damage a biological specimen, thus as few electrons as possible must be used to observe high-resolution features of macromolecules. This requirement means that the signal to noise ratio of each image is also very low. To compensate for this, tens to hundreds of thousands of images of the same kind of molecule are collected to boost the signal to noise ratio in the final 3-D reconstruction. Current reconstructions require datasets on the order of tens of gigabytes, but the amount of data required to achieve higher resolutions will double for every angstrom gained in resolution. Macromolecules by their very nature are complex assemblies of proteins and/or nucleic acids. Dissecting and analyzing these 3-D reconstructions and their various components is a significant challenge in itself. Our work has resulted in a collection of software packages that work in a number of computational environments to meet the diverse challenges in pushing the limits of cryo-EM.

Active projects:
  • EMAN2.1
  • EMAN2.1-SPT
  • EMEN2
  • GORGON
  • MPSA

  • Inactive projects(still available):
  • EMTool
  • FitCTF
  • GlobalRefine
  • Mr. T
  • JAMES
  • PC2MRC
  • SAVR
  • SAIL
  • Active Projects:

    EMAN2.1 (Electron Microscopy ANalysis) is a general purpose scientific image processing suite. Its primary focus is improving the resolution and quality of single particle reconstructions, but it also offers many general purpose tools for quantitative image analysis, and has been used with (greyscale) light microscopy, AFM and even FMRI data. At its foundation is a flexible C++ library with complete Python bindings. Through the high level commands/GUI, single particle reconstructions can be performed with minimal human effort to near atomic resolution. EMAN2 is our most mature and comprehensive software package and as a result is at the core of much of our software development at NCMI.

    EMAN2.1-SPT (Electron Microscopy ANalysis-SPT) Distributed with EMAN2.1 is a complete suite of tools for subtomogram averaging, also known as single particle tomography. In this approach, tomograms of cells, cell sections or purified molecules are reconstructed in 3-D, then individual particles are selected, classified, aligned and averaged in 3-D. This is the 3-D extension of the normal single particle analysis methods EMAN2.1 focuses on. While resolutions are lower, this method can study molecules in-vivo and offers much more accuracy when studying heterogeneity/flexibility.

    EMEN2 A web-based object-oriented database and electronic lab notebook system. This system was developed in-house in python build upon BerkeleyDB and other open-source software packages. It is currently used by over 1000 users worldwide and can be used to flexibly archive imaging data as well as to quickly and flexibly document arbitrary wet-lab experiments

    GORGON is an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes. The long term goal of the gorgon project is to be able to address to every part of the molecular modeling pipeline starting from the initial volumetric reconstruction of the complex all the way to the final placement of each individual atom.

    MPSA is a software package for cryoEM reconstructions based on the common-line method in Fourier space. Originally developed for symmetry-breaking reconstructions of tailed phages, the package is currently capable of asymmetric, symmetry-breaking, and symmetric (such as icosahedral) reconstruction. The software utilizes a Monte Carlo-based optimization algorithm, multi-path simulated annealing, to speed up image processing. The package is capable of simultaneously refining the center, orientation and defocus of a particle image.

    Inactive projects - Still available:

    EMTool Generic graphical tool for EM image processing. Reads/writes a variety of formats, performs filters, etc. This program is quite functional, but no longer under active development. Most of its features have been subsumed by programs in the EMAN suite.

    FitCTF Automated Fitting of Contrast Transfer Function Parameters.
    Features:
    1. Fit structural factors by simutaneous fitting of multiple micrographs
    2. Fit astigmatism and drift
    3. Automated batch mode fitting, no need of initial seeding
    4. Fast (seconds)
    5. Robust. Defocus and background are VERY reliable
    6. Compatible with GUI program ctfit program in EMAN
    7. Cross platform: Linux, Windows and any platform that EMAN and Matlab run

    GlobalRefine Shared memory model parallel implementations of orientation and center refinement of icosahedral virus particle images based on common-lines.

    05.09.97

    Download 1.0 - released on 05/09/97

    JAMES (JEOL Automated Microscopy Expert System) is a software package designed to facilitate high-resolution electron cryomicroscopy. JAMES runs on Windows to integrate several commercial software packages necessary to operate a modern electron cryomicroscope. It intelligently handles several of the repetitive procedures performed by a skilled electron microscopist in collecting high-resolution data. JAMES is fully integrated with our database so data, and the corresponding metadata, can be automatically deposited.

    Mr. T is a tomography software written in Python. Mr T uses the JAMES libraries to control the electron microscope and detector. Image processing is accomplished with EMAN.

    Software dependencies:

  • 5-axis control on FasTEM (JEOL)
  • Digital Micrograph (Gatan)
  • JAMES
  • EMAN
  • Python
  • Python Numeric
  • Python Imaging Library

  • PC2MRC Conversion tool from Perkin-Elmer's SCANSALOT to MRC format.

    Download 1.0 - released on 12/19/96


    SAVR (Semi-Automated Virus Reconstruction) is a suite of programs intended to make image processing simple and rapid for icosahedral 3-D reconstructions to subnanometer resolution. SAVR, an expert system that integrates the most CPU intensive and iterative steps using Python, is portable across platforms and has been parallelized to run on both shared and distributed memory platforms. SAVR also allows the incorporation of new algorithms and facilitates the management of the increasingly large data sets needed to achieve higher resolution reconstructions.

    SAIL (Scientific Animation Integration Library) is a collection of modules developed under IRIS Explorer for the 3-D visualization and data management of large macromolecule structures. Contained within the SAIL modules is the ability to read, write, segment, analyze and annotate the various types of 3-D datasets. Also included with SAIL is an animation toolkit for the construction of MPEG/MPEG2 animations.