{"id":4504,"date":"2025-08-07T15:42:38","date_gmt":"2025-08-07T13:42:38","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=4504"},"modified":"2026-03-11T12:03:30","modified_gmt":"2026-03-11T11:03:30","slug":"mikaia-first-steps","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-first-steps\/","title":{"rendered":"MIKAIA First Steps"},"content":{"rendered":"\n<p>New to MIKAIA<sup>\u00ae<\/sup>? This blog post will hopefully help you take the first steps.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Introduction video (10 min)<\/h2>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe title=\"MIKAIA\u00ae Introduction &amp; First Steps\" width=\"770\" height=\"433\" src=\"https:\/\/www.youtube.com\/embed\/CAS3G5uv7yM?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Important concepts<\/h2>\n\n\n\n<p>It is helpful to be aware of these concepts when working with MIKAIA<sup>\u00ae<\/sup>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/annotation-concepts-in-mikaia\/\">Annotation Concepts in MIKAIA<sup>\u00ae<\/sup> for Whole-Slide-Images<\/a><\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Where to get help?<\/h2>\n\n\n\n<p>The 100+ pages <strong>user manual<\/strong> is the most detailed resource. It is available from within MIKAIA<sup>\u00ae<\/sup>, by clicking in the main menu on &#8220;Help&#8221; and then &#8220;Open Manual&#8221;. The pdf is located in the MIKAIA<sup>\u00ae<\/sup> installation folder, and is available for download here: <a href=\"https:\/\/www.iis.fraunhofer.de\/en\/ff\/sse\/health\/medical-image-analysis\/mikaia\/manual.html\">Download MIKAIA<sup>\u00ae<\/sup> Manual<\/a><\/p>\n\n\n\n<p>The <strong>FAQs <\/strong>article contains a collection of important bits and pieces: <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/\">FAQs<\/a><\/p>\n\n\n\n<p>You have not found an answer to your question or want to discuss your project? You want to schedule a personal MIKAIA<sup>\u00ae<\/sup> training? <strong>Reach out at <a href=\"mailto:mikaia@iis.fraunhofer.de\">mikaia@iis.fraunhofer.de<\/a><\/strong>. We are here to help.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Image analysis<\/h2>\n\n\n\n<p>If you want to analyze <strong>fluorescence <\/strong>scans, regardless of 2plex, 20plex or 50plex, this article will give you a good overview about the typical analysis steps such as cell segmentation, cell typing and spatial analyses:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/overview-of-spatial-analysis-apps-for-mif-slides\/\">Overview of MIKAIA\u2019s Spatial Analysis Apps for Multiplexed Immunofluorescence Slides<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-mif-gallery\/\">mIF Cell AI Gallery<\/a><\/li>\n<\/ul>\n\n\n\n<p>Another widely used app is the <strong>Universal IHC Cell Detection AI<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ihc-cell-app-explained\/\">IHC Cell Detection App explained<\/a> (23min video tutorial, v2.4, Oct 2025)<\/li>\n\n\n\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a> Immune cell infiltration in tumor micro environment (TME) (June 2023)<\/li>\n\n\n\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ihc-cell-quantification-ai-gallery\/\">IHC Cell Quantification AI Gallery<\/a><\/li>\n<\/ul>\n\n\n\n<p>An introduction to using the <strong>AI Author App<\/strong> for analyzing your brightfield <strong>H&amp;E or IHC<\/strong> scans is available here:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology-batch-analysis-with-mikaia\/\">AI Author: Create New AI and Batch-analyze an Entire Dataset<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Evaluating MIKAIA <\/h2>\n\n\n\n<p>Contact <a href=\"mailto:mikaia@iis.fraunhofer.de\">mikaia@iis.fraunhofer.de<\/a> and ask for a set of one-time voucher codes that let you try out the Apps locked in MIKAIA lite. <br>Refer to this article for help on how to import the voucher codes: <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/activating-mikaia\/\">link<\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Activating MIKAIA after purchase<\/h2>\n\n\n\n<p>After a purchase you create a license request file that contains your computer&#8217;s unique fingerprint. Based on that, the activation file will be generated and returned to you. Refer to this article for a step by step guide: <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/activating-mikaia\/\">Getting Started: Activating MIKAIA<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>New to MIKAIA\u00ae? This blog post is here to help you get started on your first steps.<\/p>\n","protected":false},"author":2,"featured_media":4540,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,35,28,24],"tags":[114,7,29,108],"coauthors":[56],"class_list":["post-4504","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-digital-pathology","category-life-science","category-mikaia-university","category-spatial-biology","tag-getting-started","tag-mikaia","tag-mikaia-app-note","tag-video-tutorial"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>MIKAIA First Steps<\/title>\n<meta name=\"description\" content=\"Watch a 10-min introduction video and explore a collection of resources to help you get started analyzing your digital pathology or spatial biology dataset.\" \/>\n<meta name=\"robots\" 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