ReCoDe: A Data Reduction and Compression Description for High Throughput Time-Resolved Electron Microscopy

Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both high spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. The exception is when electron arrival events are spaced apart such that electron counting is possible. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both high spatial and temporal resolution for electron-counted data. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. Additionally, we discuss new electron microscopy modalities that will become possible with ReCoDe, including a noise-robust motion correction algorithm that succeeds with highly dose-fractionated, time-resolved electron-counted data.