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Published on: October 14, 2011
Software tools for automated transmission electron microscopy
Martin Schorb1, Isabella Haberbosch2,3, Wim J H Hagen4
1Electron Microscopy Core Facility, EMBL, Heidelberg, Germany. martin.schorb@embl.de.
Abstract:
The demand for high-throughput data collection in electron microscopy is increasing for applications in structural and cellular biology. Here we present a combination of software tools that enable automated acquisition guided by image analysis for a variety of transmission electron microscopy acquisition schemes. SerialEM controls microscopes and detectors and can trigger automated tasks at multiple positions with high flexibility. Py-EM interfaces with SerialEM to enact specimen-specific image-analysis pipelines that enable feedback microscopy. As example applications, we demonstrate dose reduction in cryo-electron microscopy experiments, fully automated acquisition of every cell in a plastic section and automated targeting on serial sections for 3D volume imaging across multiple grids.
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