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J Struct Biol. 2018 Mar;201(3):252-257. doi: 10.1016/j.jsb.2017.11.012. Epub 2017 Nov 23.

MRCZ - A file format for cryo-TEM data with fast compression.

Author information

1
Center for Cellular Imaging and NanoAnalytics (C-CINA), University of Basel, Basel, Switzerland. Electronic address: robbmcleod@gmail.com.
2
Center for Cellular Imaging and NanoAnalytics (C-CINA), University of Basel, Basel, Switzerland.
3
Department of Physics, University of Limerick, Limerick, Ireland.

Abstract

The introduction of fast CMOS detectors is moving the field of transmission electron microscopy into the computer science field of big data. Automated data pipelines control the instrument and initial processing steps which imposes more onerous data transfer and archiving requirements. Here we conduct a technical demonstration whereby storage and read/write times are improved 10× at a dose rate of 1 e-/pix/frame for data from a Gatan K2 direct-detection device by combination of integer decimation and lossless compression. The example project is hosted at github.com/em-MRCZ and released under the BSD license.

KEYWORDS:

Data management; File archiving; Lossless compression

PMID:
29175288
DOI:
10.1016/j.jsb.2017.11.012
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