Ct3d
Computational Tool
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General Information
DescriptionTracking microglia motility in 3D using a novel cosegmentation approach
Homepagehttp://www.picb.ac.cn/patterns/Software/ct3d
Publications
Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach
Hang Xiao; Ying Li; Jiulin Du; Axel Mosig
Motivation: Cell tracking is an important method to quantitatively analyze time-lapse microscopy data. While numerous methods and tools exist for tracking cells in 2D time-lapse images, only few and very application-specific tracking tools are available for 3D time-lapse images, which is of high relevance in immunoimaging, in particular for studying the motility of microglia in vivo.
Results: We introduce a novel algorithm for tracking cells in 3D time-lapse microscopy data, based on computing cosegmentations between component trees representing individual time frames using the so-called tree-assignments. For the first time, our method allows to track microglia in three dimensional confocal time-lapse microscopy images. We also evaluate our method on synthetically generated data, demonstrating that our algorithm is robust even in the presence of different types of inhomogeneous background noise.
Availability: Our algorithm is implemented in the ct3d package, which is available under http://www.picb.ac.cn/patterns/Software/ct3d; supplementary videos are available from http://www.picb.ac.cn/patterns/Supplements/ct3d.
Contact: axel@picb.ac.cn; forestdu@ion.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btq691
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