{"id":891,"date":"2014-03-07T14:36:41","date_gmt":"2014-03-07T13:36:41","guid":{"rendered":"http:\/\/wp.unil.ch\/hardtkelab\/?p=891"},"modified":"2014-03-07T14:43:37","modified_gmt":"2014-03-07T13:43:37","slug":"code-for-sankar-et-al-2014","status":"publish","type":"post","link":"https:\/\/wp.unil.ch\/hardtkelab\/2014\/03\/code-for-sankar-et-al-2014\/","title":{"rendered":"Code for Sankar et al. 2014"},"content":{"rendered":"<p>The code for the<a href=\"https:\/\/elife.elifesciences.org\/content\/3\/e01567\" target=\"_blank\"> Automated Quantitative Histology<\/a> approach described in <a href=\"https:\/\/elife.elifesciences.org\/content\/3\/e01567\" target=\"_blank\">Sankar, Nieminen &amp; Ragni et al. 2014<\/a> is available in the following files that are contained in this\u00a0<a href=\"https:\/\/wp.unil.ch\/hardtkelab\/files\/2014\/03\/Sankar_et_al_2014_code.zip\" target=\"_blank\">linked archive<\/a>:<\/p>\n<pre><i>-\u00a0<\/i><i>IPFactory.py: <\/i>this file\u00a0is the pipeline for automated image processing and information extraction.<\/pre>\n<pre>-\u00a0<i>halfdawn_function.R: <\/i>t<span style=\"letter-spacing: 0.05em;line-height: 1.6875\">his file<i>\u00a0<\/i><\/span><span style=\"letter-spacing: 0.05em;line-height: 1.6875\">contains the list of functions for image pre-processing in order to get the binary pictures<\/span><i style=\"letter-spacing: 0.05em;line-height: 1.6875\">.<\/i><\/pre>\n<pre><i style=\"letter-spacing: 0.05em;line-height: 1.6875\"><\/i><i>-\u00a0<\/i><i>runGetBinarized.R: <\/i>this file contains the call to the wrapper function<i>\u00a0*<\/i>getBinImages* used inside the pipeline.<\/pre>\n<pre>- <i>postSeg_function.R: <\/i>this file\u00a0contains the list of functions for feature extraction and segmentation data processing (color circle map generation, incline angle calculation, etc.)<\/pre>\n<pre>-\u00a0<i>runGetFeatures.R: <\/i>this file\u00a0contains the call to the wrapper function<i>\u00a0*<\/i>getFeaturesOverall* used inside the pipeline.<\/pre>\n<pre>-\u00a0<i>runSaveOverlayedImage.R: <\/i>this file\u00a0contains the call to the function *saveOverlayImage* used in the pipeline.<\/pre>\n<pre>- <i>ML_function.R: <\/i>this file\u00a0contains a collection of functions for the machine learning.<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>The code for the Automated Quantitative Histology approach described in Sankar, Nieminen &amp; Ragni et al. 2014 is available in the following files that are contained in this\u00a0linked archive: &#8211;\u00a0IPFactory.py: &hellip; <\/p>\n","protected":false},"author":1001,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"categories":[54534],"tags":[52949,54536,54535,54523],"class_list":{"0":"post-891","1":"post","2":"type-post","3":"status-publish","4":"format-standard","6":"category-resources","7":"tag-arabidopsis","8":"tag-computational-biology","9":"tag-histology","10":"tag-secondary-growth"},"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/posts\/891","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/users\/1001"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/comments?post=891"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/posts\/891\/revisions"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/media?parent=891"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/categories?post=891"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/wp.unil.ch\/hardtkelab\/wp-json\/wp\/v2\/tags?post=891"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}