Software tools for molecular microscopy

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

Computation in electron microscopy

Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.

Utilizing the Dyn2 dimerization-zipper as a tool to probe NPC structure and function

The discovery of dynein light chain 2 (Dyn2) as a member of the nucleoporins in yeast led to a series of applications to study NPC structure and function. Its intriguing ability to act as a hub for the parallel dimerization of two short amino acid sequence motifs (DID) prompted us to utilize it as a tool for probing nucleocytoplasmic transport in vivo. Further, the distinct structure of the Dyn2-DID rod, which is easily visible in the electron microscope, allowed us to develop a precise structural label on proteins or protein complexes. This label was used to identify the position of subunits in NPC subcomplexes or to derive at pseudo-atomic models of single large Nups. The versatility for various applications of the DID-Dyn2 system makes it an attractive molecular tool beyond the nuclear pore and transport field.

Electron microscopic imaging of integrin

Rotary-shadowed samples often used for electron microscopy do not preserve native integrin conformations. Negatively stained integrins - or, more desirably, unstained integrins in a cryo-condition - are now being used with sophisticated imaging techniques. Additionally, a single-particle analysis (SPA) of integrins is advanced by the recent determination of several crystal structures of integrins. Nevertheless the conformational flexibility of integrins limits the ability of SPA to image physiologic conformations. To solve this problem, we apply electron tomography to purified integrin, thereby obtaining high-quality three-dimensional (3-D) images that fit well to the atomic structures. We have also taken typical SPA approaches to obtain a 3-D reconstruction of integrin, using conditions that favor the bent conformation.

Software tools for molecular microscopy: an open-text Wikibook

We provide a brief description of a Wikibook open-content textbook that was set up with a goal of providing a comprehensive and continually updated list of all of the software packages of interest to the cryo-EM community. While the content of the Wikibook will change over time, here we provide a snapshot of the current state of software tools available, and encourage the members of this community to view the pages, add content, correct errors, and make any other contributions that might be useful.

A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map.

Appion: an integrated, database-driven pipeline to facilitate EM image processing

The use of cryoEM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to a reliable 3D reconstruction through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that extends existing software applications and procedures. The user manages and controls the software modules via web-based forms, and all results are similarly available using web-based viewers directly linked to the underlying database, enabling even naive users to quickly deduce the quality of their results. The Appion API was designed with the principle that applications should be compatible with a broad range of specimens and that libraries and routines are modular and extensible. Presented here is a description of the design and architecture of the working Appion pipeline prototype and some results of its use.