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A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs

O'Reilly, MT; Roth, A; Häusser, M; Griffin, LD; (2011) A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs. In: Sixth International Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), Heidelberg. Green open access

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Abstract

Recent developments in electron microscopy now permit the unambiguous reconstruction of even the smallest neural fibres by human experts. However, manual reconstruction of an interesting volume of neural tissue would take thousands of person-years. Techniques to automate such reconstruction are therefore highly desirable and currently under active development. Here we present a novel circle-based technique and assess its performance on classically stained electron micrographs of the molecular layer of mouse cerebellar cortex. We compare its performance to a recently published pixel-based classifier (ilastik), selected because a similar random forest classifier from the same group has shown promising results on images of neural tissue. The performance of our algorithm and that of ilastik are similar, achieving approximately 50% on an overlap-based f-measure.

Type: Proceedings paper
Title: A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs
Open access status: An open access version is available from UCL Discovery
Publisher version: http://www.miaab.org/miaab-2011-heidelberg-papers/...
Language: English
Keywords: basic image features; BIFs; electron microscopy; neural circuit reconstruction; connectomics; ilastik
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Medicine > Wolfson Inst for Biomedical Research
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Computer Science
URI: https://discovery.ucl.ac.uk/id/eprint/1395548
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