CytoSeg 2.0: automated extraction of actin filaments

Nowak, J.; Gennermann, Kristin; Persson, Staffan; Nikoloski, Z.

doi:10.1093/bioinformatics/btaa035

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CytoSeg 2.0: automated extraction of actin filaments

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Nowak, J.
Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Nikoloski, Z.
Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society;

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Nowak, J., Gennermann, K., Persson, S., & Nikoloski, Z. (2020). CytoSeg 2.0: automated extraction of actin filaments. Bioinformatics, 36(9), 2950-2951. doi:10.1093/bioinformatics/btaa035.

Cite as: https://hdl.handle.net/21.11116/0000-0006-5D0B-7

Abstract

Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task.We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community.CytoSeg 2.0 is open-source software under the GPL and is available on Github: https://github.com/jnowak90/CytoSeg2.0.nowakj@student.unimelb.edu.auSupplementary data are available at Bioinformatics online.