Journal
JOURNAL OF BIOPHOTONICS
Volume 15, Issue 12, Pages -Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/jbio.202200191
Keywords
collagen; convolutional neural network; image segmentation; second harmonic generation
Categories
Funding
- Arkansas Biosciences Institute
- National Institute of Biomedical Imaging and Bioengineering [R00EB017723, R01EB031032]
- National Institute of General Medical Sciences [P20GM139768]
- National Institute on Aging [R01AG056560]
- National Science Foundation [1846853]
- Directorate For Engineering
- Div Of Chem, Bioeng, Env, & Transp Sys [1846853] Funding Source: National Science Foundation
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Collagen fibers play a vital role in various tissues, but accurate segmentation is challenging due to variable imaging depths. This study employed a U-Net convolutional neural network for precise segmentation of collagen fibers and demonstrated superior performance compared to other thresholding techniques, particularly at deeper imaging depths.
Collagen fibers play an important role in both the structure and function of various tissues in the human body. Visualization and quantitative measurements of collagen fibers are possible through imaging modalities such as second harmonic generation (SHG), but accurate segmentation of collagen fibers is difficult for datasets involving variable imaging depths due to the effects of scattering and absorption. Therefore, an objective approach to segmentation is needed for datasets with images of variable SHG intensity. In this study, a U-Net convolutional neural network (CNN) was trained to accurately segment collagen-positive pixels throughout SHG z-stacks. CNN performance was benchmarked against other common thresholding techniques, and was found to outperform intensity-based segmentation algorithms within an independent dataset, particularly at deeper imaging depths. These results indicate that a trained CNN can accurately segment collagen-positive pixels within a wide range of imaging depths, which is useful for quantitative SHG imaging in thick tissues.
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