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bioRxiv · 10.1101/289652

DSeg: A dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures

Zhang, H.·Soderholm, N.·Sandblad, L.·Wiklund, K.·Andersson, M.
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Abstract

MotivationQuantitative image analysis of growing filamentous fungi and prokaryotes are important to detect and evaluate morphological effects of growth conditions, compounds and mutations. However, analysis of time-series image data is often limited by the ability of the algorithms to accurately segment structures that are complicated or if an organism is within a crowded population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data as well as single images to find multiple filamentous structures e.g., filamentous prokaryotes, yeasts and molds using a dynamic segmentation approach. DSeg automatically segments and analyzes objects, includes drift correction, and outputs statistical data such as persistence length, growth rate and growth direction.\n\nAvailability and implementationDSeg is a free open-source program written in MATLAB. DSeg can be downloaded as a package from https://sourceforge.net/projects/dseg-software.\n\nContactmagnus.andersson@umu.se and hanqing.zhang@umu.se\n\nSupplementary informationSupplementary data are available at online.

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Zhang, H., Soderholm, N., Sandblad, L., Wiklund, K., Andersson, M.. 2018-03-27. DSeg: A dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures. https://doi.org/10.1101/289652

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