{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T02:44:02Z","timestamp":1778899442634,"version":"3.51.4"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,11,22]],"date-time":"2023-11-22T00:00:00Z","timestamp":1700611200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Knowledge of soft tissue fiber structure is necessary for accurate characterization and modeling of their mechanical response. Fiber configuration and structure informs both our understanding of healthy tissue physiology and of pathological processes resulting from diseased states. This study develops an automatic algorithm to simultaneously estimate fiber global orientation, abundance, and waviness in an investigated image. To our best knowledge, this is the first validated algorithm which can reliably separate fiber waviness from its global orientation for considerably wavy fibers. This is much needed feature for biological tissue characterization. The algorithm is based on incremental movement of local regions of interest (ROI) and analyzes two-dimensional images. Pixels belonging to the fiber are identified in the ROI, and ROI movement is determined according to local orientation of fiber within the ROI. The algorithm is validated with artificial images and ten images of porcine trachea containing wavy fibers. In each image, 80\u2013120 fibers were tracked manually to serve as verification. The coefficient of determination R2 between curve lengths and histograms documenting the fiber waviness and global orientation were used as metrics for analysis. Verification-confirmed results were independent of image rotation and degree of fiber waviness, with curve length accuracy demonstrated to be below 1% of fiber curved length. Validation-confirmed median and interquartile range of R2, respectively, were 0.90 and 0.05 for curved length, 0.92 and 0.07 for waviness, and 0.96 and 0.04 for global orientation histograms. Software constructed from the proposed algorithm was able to track one fiber in about 1.1\u2005s using a typical office computer. The proposed algorithm can reliably and accurately estimate fiber waviness, curve length, and global orientation simultaneously, moving beyond the limitations of prior methods.<\/jats:p>","DOI":"10.1093\/micmic\/ozad117","type":"journal-article","created":{"date-parts":[[2023,11,22]],"date-time":"2023-11-22T20:36:18Z","timestamp":1700685378000},"page":"2108-2126","source":"Crossref","is-referenced-by-count":7,"title":["MATLAB-Based Algorithm and Software for Analysis of Wavy Collagen Fibers"],"prefix":"10.1093","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5439-2009","authenticated-orcid":false,"given":"Stanislav","family":"Polzer","sequence":"first","affiliation":[{"name":"Department of Applied Mechanics, VSB-Technical University of Ostrava , 17.listopadu 2172\/15, 708 00 Ostrava , Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Thompson","sequence":"additional","affiliation":[{"name":"Department of Mechanical Engineering, University of California at Riverside , 3401 Watkins Drive, Riverside CA 92521 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Swathi","family":"Vittalbabu","sequence":"additional","affiliation":[{"name":"Department of Mechanical Engineering, University of California at Riverside , 3401 Watkins Drive, Riverside CA 92521 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arzu","family":"Ulu","sequence":"additional","affiliation":[{"name":"BREATHE Center School of Medicine, University of California at Riverside , 3401 Watkins Drive, Riverside CA 92521 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Carter","sequence":"additional","affiliation":[{"name":"Molecular Cell and Systems Biology, University of California at Riverside, 900 University Ave, Riverside CA 92521 , 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