{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039748,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,7,11]],"date-time":"2020-07-11T00:00:00Z","timestamp":1594425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institutes of Health\/National Cancer Institute","award":["T32CA080621"],"award-info":[{"award-number":["T32CA080621"]}]},{"name":"National Institutes of Health\/Eunice Kennedy Shriver National Institute of Child Health and Human Development","award":["U54HD087351"],"award-info":[{"award-number":["U54HD087351"]}]},{"name":"University of Texas Southwestern Medical Center Wellstone Muscular Dystrophy Cooperative Research Center Training Pilot"},{"name":"National Institute of Health\/National Institute of General Medical Sciences","award":["R35 GM119619"],"award-info":[{"award-number":["R35 GM119619"]}]},{"name":"National Institute of Health\/National Institute of General Medical Sciences","award":["R01GM106023"],"award-info":[{"award-number":["R01GM106023"]}]},{"name":"National Institute of Health\/National Institute of General Medical Sciences","award":["P01GM096971"],"award-info":[{"award-number":["P01GM096971"]}]},{"DOI":"10.13039\/100004917","name":"Cancer Prevention and Research Institute of Texas","doi-asserted-by":"publisher","award":["R1216"],"award-info":[{"award-number":["R1216"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Texas Southwestern Medical Center Endowed Scholars"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Microscopy images of cytoskeletal, nucleoskeletal and other structures contain complex junctions of overlapping filaments with arbitrary geometry. Yet, state-of-the-art algorithms generally perform single orientation analysis to segment these structures, resulting in gaps near junctions, or assume particular junction geometries to detect them.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed a fully automated image analysis approach to address the challenge of determining the number of orientations and their values at each point in space to detect both lines and their junctions. Our approach does not assume any fixed number of orientations or any particular geometry in the case of multiple coincident orientations. It is based on analytically resolving coincident orientations revealed by steerable ridge filtering in an adaptive manner that balances orientation resolution and spatial localization. Combining this multiorientation resolution information with a generalization of the concept of non-maximum suppression allowed us to then identify the centers of lines and their junctions in an image. We validated our approach using a wide array of synthetic junctions and by comparison to manual segmentation. We also applied it to light microscopy images of cytoskeletal and nucleoskeletal networks.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/mkitti\/AdaptiveResolutionOrientationSpace.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary information is available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa627","type":"journal-article","created":{"date-parts":[[2020,7,3]],"date-time":"2020-07-03T15:35:32Z","timestamp":1593790532000},"page":"5093-5103","source":"Crossref","is-referenced-by-count":8,"title":["Adaptive multiorientation resolution analysis of complex filamentous network images"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9558-6248","authenticated-orcid":false,"given":"Mark","family":"Kittisopikul","sequence":"first","affiliation":[{"name":"Department of Biophysics, UT Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Department of Cell and Developmental Biology, Feinberg School of Medicine , Northwestern University, Chicago, IL 60611, USA"}]},{"given":"Amir","family":"Vahabikashi","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology, Feinberg School of Medicine , Northwestern University, Chicago, IL 60611, USA"}]},{"given":"Takeshi","family":"Shimi","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology, Feinberg School of Medicine , Northwestern University, Chicago, IL 60611, USA"},{"name":"World Research Hub Initiative Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama, Kanagawa 226-8503, Japan"}]},{"given":"Robert D","family":"Goldman","sequence":"additional","affiliation":[{"name":"Department of Cell and Developmental Biology, Feinberg School of Medicine , Northwestern University, Chicago, IL 60611, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3471-1911","authenticated-orcid":false,"given":"Khuloud","family":"Jaqaman","sequence":"additional","affiliation":[{"name":"Department of Biophysics, UT Southwestern Medical Center , Dallas, TX 75390, USA"},{"name":"Department of Bioinformatics, UT Southwestern Medical Center , Dallas, TX 75390, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,7,11]]},"reference":[{"key":"2023062408143869500_btaa627-B1","author":"Agamennoni","year":"2010"},{"key":"2023062408143869500_btaa627-B2","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.1093\/bioinformatics\/btx180","article-title":"Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification","volume":"33","author":"Arganda-Carreras","year":"2017","journal-title":"Bioinformatics"},{"key":"2023062408143869500_btaa627-B3","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1109\/34.969119","article-title":"Hierarchical decomposition of multiscale skeletons","volume":"23","author":"Borgefors","year":"2001","journal-title":"IEEE Trans. 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