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The impact of data reduction and lossy image formats on electron microscope images

By Edward Eng, Mykhailo Kopylov, Carl J Negro, Sarkis Dallaykan, William J. Rice, Kelsey D. Jordan, Kotaro Kelley, Bridget Carragher, Clinton S. Potter

Posted 24 Oct 2018
bioRxiv DOI: 10.1101/451427

Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. Coupled with the adoption of automated pipelines, significant infrastructure support is required to sustain high throughput workflows. In particular, data generation rates may outpace the ability to deploy data storage and archival solutions. We have investigated what effects data compression and conversion to different file formats have on the ability to obtain high resolution cryoEM reconstructions. Standard lossless data compression strategies have a high impact on reducing the size of direct detector electron counting movie stacks, but provide more modest gains for aligned summed images. We show that EM images can be compressed using standard lossy methods to reduce file storage to 5-10% of the size of the original aligned sum or movie stack file and yet still retain enough information such that modern image processing pipelines will provide sub-2Å reconstructions from the compressed data.

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