MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography

Abstract

The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages. Following extensive discussions, the authors, who represent leading software packages in the field, propose a set of extensions to the MRC format standard designed to accommodate these variants, while restoring interoperability. The MRC format is equivalent to the map format used in the CCP4 suite for macromolecular crystallography, and the proposal also maintains interoperability with crystallography software. This Technical Note describes the proposed extensions, and serves as a reference for the standard.

Automated batch fiducial-less tilt-series alignment in Appion using Protomo

“…Additionally, while Protomo is fully capable of processing dual-axis tilt-series (Winkler and Taylor, 2013), the potential of implementing fully automated dual-axis tilt-series alignment in Appion has yet to be realized, yet is possible. Other potential improvements include uploading tilt-series alignment runs to the database, the full support of raw image formats in addition to the mrc file format (Cheng et al, 2015), and the implementation of automated 3D particle picking from tomograms into the Appion infrastructure.…”

Recent developments in theCCP-EMsoftware suite

“…Closely related to the CCP4 map format, it can be used to store individual micrographs, stacks of twodimensional images, three-dimensional volumes and stacks of three-dimensional volumes. Several variants of the MRC format had emerged, but recently the developers of several major EM software packages agreed a standardized definition, known as the MRC2014 format (Cheng et al, 2015), together with a process for agreeing future revisions. In order to allow developers to use MRC files as easily and flexibly as possible, we have written mrcfile.py, which is an open-source, standalone Python library for the reading, writing and validation of MRC2014 files.…”

Databases and Archiving for CryoEM

“…The participants also felt that it would be desirable to have community wide efforts on the subject of format standardization and harmonization. Subsequent to this meeting there has been an initiative to try and clarify and standardize the definition of the MRC map format (Cheng et al, 2015) and to develop an EM exchange format that could be used to represent EM related metadata such as particle coordinates and coordinate transformations (Marabini et al, 2016). Meeting participants also recognized a problem with the deposition rates for electron tomography lagging behind that of single-particle EM.…”