{"id":3721,"date":"2023-05-04T16:26:20","date_gmt":"2023-05-04T20:26:20","guid":{"rendered":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/?page_id=3721"},"modified":"2026-02-06T17:31:10","modified_gmt":"2026-02-06T22:31:10","slug":"image-analysis-resources","status":"publish","type":"page","link":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/image-analysis-resources\/","title":{"rendered":"Image Analysis"},"content":{"rendered":"<div id=\"pl-3721\"  class=\"panel-layout\" ><div id=\"pg-3721-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-0-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3721-0-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child panel-last-child\" data-index=\"0\" ><div class=\"textwidget\"><h2>Quantitative Bioimaging Reference Articles<\/h2>\n<p><a href=\"https:\/\/www.bioimagingguide.org\/welcome.html#\" target=\"_blank\" rel=\"noopener\">Bioimaging Guide<\/a> - Online companion website to the paper \"<a href=\"https:\/\/zenodo.org\/record\/7810631#.ZGZUB3bMJ9M\" target=\"_blank\" rel=\"noopener\">A biologist's guide to the field of quantitative bioimaging<\/a>.\"<\/p>\n<p class=\"title mathjax\">Checklist for publishing images and image analysis developed by the <a href=\"https:\/\/quarep.org\/\" target=\"_blank\" rel=\"noopener\">QUAREP<\/a> community - <a href=\"https:\/\/arxiv.org\/abs\/2302.07005\" target=\"_blank\" rel=\"noopener\">Community-developed checklists for publishing images and image analysis<\/a><\/p>\n<p>&nbsp;<\/p>\n<h2>Recommended Analysis Software<\/h2>\n<ul>\n<li><a href=\"https:\/\/imagej.net\/software\/fiji\/downloads\" target=\"_blank\" rel=\"noopener\">FIJI\/ImageJ<\/a><\/li>\n<li><a href=\"https:\/\/imaris.oxinst.com\/learning\/view\/article\/create-eye-catching-animations-and-snapshots-using-imaris\" target=\"_blank\" rel=\"noopener\">Imaris 3D\/4D Visualization and Analysis Software<\/a><\/li>\n<li><a href=\"https:\/\/www.ilastik.org\/\" target=\"_blank\" rel=\"noopener\">ilastik Interactive learning and segmentation toolkit<\/a><\/li>\n<\/ul>\n<\/div><\/div><\/div><\/div><div id=\"pg-3721-1\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-1-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3721-1-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child panel-last-child\" data-index=\"1\" ><div class=\"textwidget\"><h2 style=\"text-align: left;\">Shading Correction Using BASiC Plugin from FIJI<\/h2>\n<p>&nbsp;<\/p>\n<p>In this short video, you will learn how to use the BASiC Plugin to remove uneven shading from a phase microscope image. This is a fairly common practice when capturing microscope images and can be quickly and easily performed with this plugin.<\/p>\n<p>&nbsp;<\/p>\n<p><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/06\/FIJI-Shading-CorrectionCC.mp4\" target=\"_blank\" rel=\"noopener\">Closed Caption Version of Video (14 MB)<\/a><\/p>\n<\/div><\/div><\/div><\/div><div id=\"pg-3721-2\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-2-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3721-2-0-0\" class=\"so-panel widget widget_media_video panel-first-child panel-last-child\" data-index=\"2\" ><div style=\"width:100%;\" class=\"wp-video\"><!--[if lt IE 9]><script>document.createElement('video');<\/script><![endif]-->\n<video class=\"wp-video-shortcode\" id=\"video-3721-1\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/mp4\" src=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/06\/FIJI-Shading-Correction.mp4?_=1\" \/><source type=\"video\/mp4\" src=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/06\/FIJI-Shading-Correction.mp4?_=1\" \/><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/06\/FIJI-Shading-Correction.mp4\">https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/06\/FIJI-Shading-Correction.mp4<\/a><\/video><\/div><\/div><\/div><\/div><div id=\"pg-3721-3\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-3-0\"  class=\"panel-grid-cell panel-grid-cell-empty\" ><\/div><\/div><div id=\"pg-3721-4\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-4-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3721-4-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child panel-last-child\" data-index=\"3\" ><div class=\"textwidget\"><h2 style=\"text-align: left;\">Drift Correction Using the Correct 3D Drift Plugin from FIJI<\/h2>\n<p>&nbsp;<\/p>\n<p>Drift can arise from various sources and is ultimately a distraction to visualizing and analyzing your data.\u00a0In this video, you will learn how to use the Correct 3D Drift Plugin in order to minimize the drift observed during the acquisition of a time series experiment.<\/p>\n<p><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/05\/Drift-Correction-CCb.mp4\" target=\"_blank\" rel=\"noopener\">Closed Caption Version of\u00a0 Video (24 MB)<\/a><\/p>\n<\/div><\/div><\/div><\/div><div id=\"pg-3721-5\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3721-5-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3721-5-0-0\" class=\"so-panel widget widget_media_video panel-first-child panel-last-child\" data-index=\"4\" ><div style=\"width:100%;\" class=\"wp-video\"><video class=\"wp-video-shortcode\" id=\"video-3721-2\" preload=\"metadata\" controls=\"controls\"><source type=\"video\/mp4\" src=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/05\/Drift-Correction-CC.mp4?_=2\" \/><source type=\"video\/mp4\" src=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/05\/Drift-Correction-CC.mp4?_=2\" \/><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/05\/Drift-Correction-CC.mp4\">https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2023\/05\/Drift-Correction-CC.mp4<\/a><\/video><\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>Quantitative Bioimaging Reference Articles Bioimaging Guide &#8211; Online companion website to the paper &#8220;A biologist&#8217;s guide to the field of quantitative bioimaging.&#8221; Checklist for publishing images and image analysis developed by the QUAREP community &#8211; Community-developed checklists for publishing images and image analysis &nbsp; Recommended Analysis Software FIJI\/ImageJ Imaris 3D\/4D Visualization and Analysis Software ilastik [&hellip;]<\/p>\n","protected":false},"author":283,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-04-20 02:08:27","action":"change-status","newStatus":"draft","terms":[],"taxonomy":""},"_links":{"self":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3721"}],"collection":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/users\/283"}],"replies":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/comments?post=3721"}],"version-history":[{"count":22,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3721\/revisions"}],"predecessor-version":[{"id":5071,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3721\/revisions\/5071"}],"wp:attachment":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/media?parent=3721"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}