Learning Guided Electron Microscopy with Active Acquisition

Lu Mi, Hao Wang, Yaron Meirovitch, Richard Schalek, Srinivas C. Turaga, Jeff W. Lichtman, Aravinthan D.T. Samuel, Nir Shavit

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Single-beam scanning electron microscopes (SEM) are widely used to acquire massive datasets for biomedical study, material analysis, and fabrication inspection. Datasets are typically acquired with uniform acquisition: applying the electron beam with the same power and duration to all image pixels, even if there is great variety in the pixels’ importance for eventual use. Many SEMs are now able to move the beam to any pixel in the field of view without delay, enabling them, in principle, to invest their time budget more effectively with non-uniform imaging. In this paper, we show how to use deep learning to accelerate and optimize single-beam SEM acquisition of images. Our algorithm rapidly collects an information-lossy image (e.g. low resolution) and then applies a novel learning method to identify a small subset of pixels to be collected at higher resolution based on a trade-off between the saliency and spatial diversity. We demonstrate the efficacy of this novel technique for active acquisition by speeding up the task of collecting connectomic datasets for neurobiology by up to an order of magnitude. Code is available at https://github.com/lumi9587/learning-guided-SEM.

Original languageEnglish (US)
Title of host publicationMedical Image Computing and Computer Assisted Intervention – MICCAI 2020 - 23rd International Conference, Proceedings
EditorsAnne L. Martel, Purang Abolmaesumi, Danail Stoyanov, Diana Mateus, Maria A. Zuluaga, S. Kevin Zhou, Daniel Racoceanu, Leo Joskowicz
PublisherSpringer Science and Business Media Deutschland GmbH
Pages77-87
Number of pages11
ISBN (Print)9783030597214
DOIs
StatePublished - 2020
Externally publishedYes
Event23rd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2020 - Lima, Peru
Duration: Oct 4 2020Oct 8 2020

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12265 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference23rd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2020
Country/TerritoryPeru
CityLima
Period10/4/2010/8/20

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Keywords

  • Active acquisition
  • Determinantal point process
  • Electron microscope

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