High resolution segmentation of neuronal tissues from low depth-resolution EM imagery

  • Authors:
  • Daniel Glasner;Tao Hu;Juan Nunez-Iglesias;Lou Scheffer;Shan Xu;Harald Hess;Richard Fetter;Dmitri Chklovskii;Ronen Basri

  • Affiliations:
  • Howard Hughes Medical Institute and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute;Howard Hughes Medical Institute and Department of Computer Science and Applied Mathematics, Weizmann Institute of Science

  • Venue:
  • EMMCVPR'11 Proceedings of the 8th international conference on Energy minimization methods in computer vision and pattern recognition
  • Year:
  • 2011

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Abstract

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.