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DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures

Published online by Cambridge University Press:  21 March 2019

Hanqing Zhang ,
Niklas Söderholm ,
Linda Sandblad ,
Krister Wiklund  and
Magnus Andersson Open the ORCID record for Magnus Andersson [Opens in a new window]
Hanqing Zhang
Affiliation:
Department of Physics, Umeå University, 901 87 Umeå, Sweden
Niklas Söderholm
Affiliation:
Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
Linda Sandblad
Affiliation:
Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
Krister Wiklund
Affiliation:
Department of Physics, Umeå University, 901 87 Umeå, Sweden
Magnus Andersson*
Affiliation:
Department of Physics, Umeå University, 901 87 Umeå, Sweden
*
*Author for correspondence: Magnus Andersson, E-mail: magnus.andersson@umu.se
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Abstract

Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.

Keywords

filamentoushyphaeimage segmentationMATLABsoftware
Type
Software and Instrumentation
Information
Microscopy and Microanalysis , Volume 25 , Issue 3 , June 2019 , pp. 711 - 719
Copyright
Copyright © Microscopy Society of America 2019 

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