{"id":697,"date":"2022-11-20T13:06:09","date_gmt":"2022-11-20T11:06:09","guid":{"rendered":"https:\/\/phsites.technion.ac.il\/kkeren\/?page_id=697"},"modified":"2022-11-20T15:20:48","modified_gmt":"2022-11-20T13:20:48","slug":"fiber-orientation-analysis","status":"publish","type":"page","link":"https:\/\/phsites.technion.ac.il\/kkeren\/fiber-orientation-analysis\/","title":{"rendered":"Fiber Orientation Analysis"},"content":{"rendered":"\n

This is a simple version of our fiber orientation analysis software, adapted from https:\/\/github.com\/alilou63\/fingerprint<\/a> and published in https:\/\/doi.org\/10.1038\/s41567-020-01083-1<\/a>. The main script “runAnalysisSimple.m” calls two main functions, “FrameAnalysisSimple.m” which performs the analysis per movie frame, and “plotFrameAnalysis.m” which plots the results (but is not required for the calculations). Other subfunctions are included.
The raw data on which analysis is performed is assumed to be a set of 2D 16-bit images saved in a single folder, with each image having a matching 8-bit mask that defines the region for analysis. Masks are saved under the same name as their matching raw image in a separate folder for all masks.
Additional documentation can be found as comments in the script and in https:\/\/doi.org\/10.1038\/s41567-020-01083-1<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

This is a simple version of our fiber orientation analysis software, adapted from https:\/\/github.com\/alilou63\/fingerprint and published in https:\/\/doi.org\/10.1038\/s41567-020-01083-1. The main script “runAnalysisSimple.m” calls two main functions, “FrameAnalysisSimple.m” which performs the analysis per movie frame, and “plotFrameAnalysis.m” which plots the results (but is not required for the calculations). Other subfunctions are included.The raw data on which analysis is […]<\/p>\n","protected":false},"author":9999950,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","footnotes":""},"class_list":["post-697","page","type-page","status-publish","entry"],"yoast_head":"\nFiber Orientation Analysis - Self-organization of Biological systems<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/phsites.technion.ac.il\/kkeren\/fiber-orientation-analysis\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Fiber Orientation Analysis - Self-organization of Biological systems\" \/>\n<meta property=\"og:description\" content=\"This is a simple version of our fiber orientation analysis software, adapted from https:\/\/github.com\/alilou63\/fingerprint and published in https:\/\/doi.org\/10.1038\/s41567-020-01083-1. The main script “runAnalysisSimple.m” calls two main functions, “FrameAnalysisSimple.m” which performs the analysis per movie frame, and “plotFrameAnalysis.m” which plots the results (but is not required for the calculations). Other subfunctions are included.The raw data on which analysis is […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/phsites.technion.ac.il\/kkeren\/fiber-orientation-analysis\/\" \/>\n<meta property=\"og:site_name\" content=\"Self-organization of Biological systems\" \/>\n<meta property=\"article:modified_time\" content=\"2022-11-20T13:20:48+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/fiber-orientation-analysis\\\/\",\"url\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/fiber-orientation-analysis\\\/\",\"name\":\"Fiber Orientation Analysis - Self-organization of Biological systems\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/#website\"},\"datePublished\":\"2022-11-20T11:06:09+00:00\",\"dateModified\":\"2022-11-20T13:20:48+00:00\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/fiber-orientation-analysis\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/fiber-orientation-analysis\\\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/fiber-orientation-analysis\\\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Fiber Orientation Analysis\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/#website\",\"url\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/\",\"name\":\"Self-organization of Biological systems\",\"description\":\"Kinneret Keren\u2019s lab\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\\\/\\\/phsites.technion.ac.il\\\/kkeren\\\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Fiber Orientation Analysis - Self-organization of Biological systems","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/phsites.technion.ac.il\/kkeren\/fiber-orientation-analysis\/","og_locale":"en_US","og_type":"article","og_title":"Fiber Orientation Analysis - Self-organization of Biological systems","og_description":"This is a simple version of our fiber orientation analysis software, adapted from https:\/\/github.com\/alilou63\/fingerprint and published in https:\/\/doi.org\/10.1038\/s41567-020-01083-1. 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