{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T07:59:14Z","timestamp":1768291154927,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T00:00:00Z","timestamp":1725321600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Department of Biotechnology, Government of India","award":["DBT\/2018\/IISER-P\/1154"],"award-info":[{"award-number":["DBT\/2018\/IISER-P\/1154"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Quantification of microscopy time series of in vitro reconstituted motor-driven microtubule transport in \u201cgliding assays\u201d is typically performed using computational object tracking tools. However, these are limited to non-intersecting and rod-like filaments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we describe a novel computational image-analysis pipeline, KnotResolver, to track image time series of highly curved self-intersecting looped filaments (knots) by resolving cross-overs. The code integrates filament segmentation and cross-over or \u201cknot\u201d identification based on directed graph representation, where nodes represent cross-overs and edges represent the path connecting them. The graphs are mapped back to contours and the distance to a reference minimized. The accuracy of contour detection is sub-pixel with a robustness to noise. We demonstrate the utility of KnotResolver by automatically quantifying \u201cflagella-like\u201d curvature dynamics and wave-like oscillations of clamped microtubules in a \u201cgliding assay.\u201d<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The MATLAB-based source code is released as OpenSource and is available at https:\/\/github.com\/CyCelsLab\/MTKnotResolver.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae538","type":"journal-article","created":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T01:39:29Z","timestamp":1725413969000},"source":"Crossref","is-referenced-by-count":1,"title":["KnotResolver: tracking self-intersecting filaments in microscopy using directed 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