Superpixel-based segmentation of muscle fibers in multi-channel microscopy
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12918_2016_Article_372.pdf
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Author(s)
So, Peter T. C.
Heemskerk, Johannes Antonius
Tucker-Kellogg, Lisa
Nguyen, Binh P.
Date Issued
December 2016
Journal
BMC Systems Biology
Publisher
BioMed Central
Citation
Nguyen, Binh P., Hans Heemskerk, Peter T. C. So, and Lisa Tucker-Kellogg. “Superpixel-Based Segmentation of Muscle Fibers in Multi-Channel Microscopy.” BMC Systems Biology 10, no. S5 (December 2016): 39–50.
Version
Final published version
Abstract
Background
Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated muscle fibers in mice.
Results
We propose to integrate an edge detector into a superpixel algorithm and customize the method for multi-channel images. The enhanced superpixel method outperforms the original and another advanced superpixel algorithm in terms of both boundary recall and under-segmentation error. Our framework was applied to cross-section and lateral section images of regenerated muscle fibers from confetti-fluorescent mice. Compared with “ground-truth” segmentations, our framework yielded median Dice similarity coefficients of 0.92 and higher.
Conclusion
Our segmentation framework is flexible and provides very good segmentations of multi-color muscle fibers. We anticipate our methods will be useful for segmenting a variety of tissues in confetti fluorecent mice and in mice with similar multi-color labels.
MIT Department
Massachusetts Institute of Technology. Department of Mechanical Engineering
Massachusetts Institute of Technology. Research Laboratory of Electronics
Singapore-MIT Alliance in Research and Technology (SMART)
Singapore-MIT Alliance in Research and Technology (SMART)
Terms of Use
Creative Commons Attribution
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1186/s12918-016-0372-2
