Abstract
Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. 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. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss).
Highlights
Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies
A secondary electron puddle is characterized by its spatial location, its two-dimensional (2D) shape, and the pixel intensities within this shape
In reduction and compression scheme (ReCoDe) level L1, the sparsified signal pixel intensities are bit-packed into a dense format
Summary
Direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. While the size and shape of secondary electron puddles contain some information[1], localizing the entry point of the incident electron from its electron cloud already noticeably improves the spatial resolution of the image To accurately localize these electron puddles they must be spatiotemporally well separated (by increasing the frame rate or reducing the incident electron flux), thereby reducing the so-called coincidence loss[2]. At such high dose rates, the experimenter has to either sacrifice spatial resolution or be limited to atomic resolution only for radiation-hard samples None of these three options are ideal, especially since the vast majority of these high data loads are storing only the detector’s thermal and readout noise. If we stored only electron arrival events, we can enjoy high temporal and spatial resolution, while continuously acquiring movies of dose-sensitive samples at very low dose rates for practically hours, uninterrupted
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