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Fast, direct electron detectors have significantly improved thespatio-temporal resolution of electron microscopy movies. Preserving bothspatial and temporal resolution in extended observations, however, requiresstoring prohibitively large amounts of data. Here, we describe an efficient andflexible data reduction and compression scheme (ReCoDe) that retains bothspatial and temporal resolution by preserving individual electron events.Running ReCoDe on a workstation we demonstrate on-the-fly reduction andcompression of raw data streaming off a detector at 3 GB/s, for hours ofuninterrupted data collection. The output was 100-fold smaller than the rawdata and saved directly onto network-attached storage drives over a 10 GbEconnection. We discuss calibration techniques that support electron detectionand counting (e.g. estimate electron backscattering rates, false positiverates, and data compressibility), and novel data analysis methods enabled byReCoDe (e.g. recalibration of data post acquisition, and accurate estimation ofcoincidence loss).

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