{"id":430,"date":"2010-08-07T02:24:04","date_gmt":"2010-08-07T02:24:04","guid":{"rendered":"http:\/\/labrigger.com\/blog\/?p=430"},"modified":"2010-08-07T02:24:04","modified_gmt":"2010-08-07T02:24:04","slug":"trees-matlab-toolbox","status":"publish","type":"post","link":"http:\/\/labrigger.com\/blog\/2010\/08\/07\/trees-matlab-toolbox\/","title":{"rendered":"TREES: MATLAB toolbox"},"content":{"rendered":"<p align=\"center\"><a href=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees4.png\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees4.png\" alt=\"\" title=\"trees4\" width=\"433\" height=\"340\" class=\"aligncenter size-full wp-image-438\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees4.png 433w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees4-300x235.png 300w\" sizes=\"auto, (max-width: 433px) 100vw, 433px\" \/><\/a><\/p>\n<p>A <a href=\"http:\/\/www.ploscompbiol.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000877\">new paper<\/a> in PLoS Computation Biology proposes an elegant formalism for describing neuronal morphology. The reason I&#8217;m highlighting it on Labrigger is because the authors have simultaneously released a very extensive, impressive MATLAB toolbox for studying neuronal morphology, including reconstructing neurons from image stacks: the <a href=\"http:\/\/www.treestoolbox.org\/index.html\">TREES toolbox<\/a>.<\/p>\n<p>What you&#8217;ll find in the TREES toolbox:<\/p>\n<blockquote><p>\no Tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees.<\/p>\n<p>o The basic tools to edit, visualize and analyze dendritic and axonal trees.<\/p>\n<p>o Methods for quantitatively comparing branching structures between neurons.<\/p>\n<p>o Tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distance.<\/p><\/blockquote>\n<p>To get an idea of what this toolbox is capable of, look through the extensive <a href=\"http:\/\/www.treestoolbox.org\/downloads\/TREES_manual_hres.pdf\">manual<\/a>.<\/p>\n<p align=\"center\"><a href=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees3.png\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees3.png\" alt=\"\" title=\"trees3\" width=\"458\" height=\"242\" class=\"aligncenter size-full wp-image-439\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees3.png 458w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees3-300x158.png 300w\" sizes=\"auto, (max-width: 458px) 100vw, 458px\" \/><\/a><br \/>\n<a href=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees1.png\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees1.png\" alt=\"\" title=\"trees1\" width=\"630\" height=\"219\" class=\"aligncenter size-full wp-image-440\" srcset=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees1.png 630w, http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees1-300x104.png 300w\" sizes=\"auto, (max-width: 630px) 100vw, 630px\" \/><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p align=\"center\"><a href=\"http:\/\/labrigger.com\/blog\/wp-content\/uploads\/2010\/08\/trees4.png\"><\/a><\/p>\n<p>A <a href=\"http:\/\/www.ploscompbiol.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000877\">new paper<\/a> in PLoS Computation Biology proposes an elegant formalism for describing neuronal morphology. The reason I&#8217;m highlighting it on Labrigger is because the authors have simultaneously released a very extensive,&#8230;<\/p>\n<div class=\"read-more\"><a href=\"http:\/\/labrigger.com\/blog\/2010\/08\/07\/trees-matlab-toolbox\/\">Read More<\/a><\/div><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[25],"class_list":["post-430","post","type-post","status-publish","format-standard","hentry","category-software","tag-analysis"],"_links":{"self":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/430","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/comments?post=430"}],"version-history":[{"count":9,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/430\/revisions"}],"predecessor-version":[{"id":442,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/posts\/430\/revisions\/442"}],"wp:attachment":[{"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/media?parent=430"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/categories?post=430"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/labrigger.com\/blog\/wp-json\/wp\/v2\/tags?post=430"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}