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Sparse Scanning Electron Microscopy Data Acquisition and Deep Neural Networks for Automated Segmentation in Connectomics

Published online by Cambridge University Press:  07 April 2020

Pavel Potocek ,
Patrick Trampert ,
Maurice Peemen ,
Remco Schoenmakers  and
Tim Dahmen
Pavel Potocek
Affiliation:
Materials and Structural Analysis Thermo Fisher Scientific, Eindhoven, The Netherlands
Patrick Trampert
Affiliation:
German Research Center for Artificial Intelligence, DFKI, Saarbrücken, Germany Saarland University, Saarbrücken, Germany
Maurice Peemen
Affiliation:
Materials and Structural Analysis Thermo Fisher Scientific, Eindhoven, The Netherlands
Remco Schoenmakers
Affiliation:
Materials and Structural Analysis Thermo Fisher Scientific, Eindhoven, The Netherlands
Tim Dahmen*
Affiliation:
German Research Center for Artificial Intelligence, DFKI, Saarbrücken, Germany
*
*Author for correspondence: Tim Dahmen, E-mail: [email protected]
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Abstract

With the growing importance of three-dimensional and very large field of view imaging, acquisition time becomes a serious bottleneck. Additionally, dose reduction is of importance when imaging material like biological tissue that is sensitive to electron radiation. Random sparse scanning can be used in the combination with image reconstruction techniques to reduce the acquisition time or electron dose in scanning electron microscopy. In this study, we demonstrate a workflow that includes data acquisition on a scanning electron microscope, followed by a sparse image reconstruction based on compressive sensing or alternatively using neural networks. Neuron structures are automatically segmented from the reconstructed images using deep learning techniques. We show that the average dwell time per pixel can be reduced by a factor of 2–3, thereby providing a real-life confirmation of previous results on simulated data in one of the key segmentation applications in connectomics and thus demonstrating the feasibility and benefit of random sparse scanning techniques for a specific real-world scenario.

Keywords

connectomicsdeep learningscanning electron microscopysegmentationsparse scanning
Type
Software and Instrumentation
Information
Microscopy and Microanalysis , Volume 26 , Issue 3 , June 2020 , pp. 403 - 412
Copyright
Copyright © Microscopy Society of America 2020

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