{"id":3139,"date":"2025-02-03T18:56:07","date_gmt":"2025-02-03T17:56:07","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=3139"},"modified":"2025-11-07T20:14:12","modified_gmt":"2025-11-07T19:14:12","slug":"mikaia-faqs","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/","title":{"rendered":"MIKAIA FAQs"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Welcome to our MIKAIA FAQs. We know that navigating a flexible digital pathology &amp; spatial biology image analysis software like MIKAIA<sup>\u00ae <\/sup>can raise a lot of questions, and we&#8217;re here to help. Whether you&#8217;re looking for quick tips or detailed info, you\u2019ll find answers here. If you can\u2019t find what you\u2019re looking for or need a bit more help, don\u2019t hesitate to <a href=\"mailto: mikaia@iis.fraunhofer.de\">reach out<\/a> to us. We\u2019re just a message away!<br><\/p>\n\n\n\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_83 counter-hierarchy ez-toc-counter ez-toc-grey ez-toc-container-direction\">\n<div class=\"ez-toc-title-container\">\n<p class=\"ez-toc-title\" style=\"cursor:inherit\">Table of Contents<\/p>\n<span class=\"ez-toc-title-toggle\"><a href=\"#\" class=\"ez-toc-pull-right ez-toc-btn ez-toc-btn-xs ez-toc-btn-default ez-toc-toggle\" aria-label=\"Toggle Table of Content\"><span class=\"ez-toc-js-icon-con\"><span class=\"\"><span class=\"eztoc-hide\" style=\"display:none;\">Toggle<\/span><span class=\"ez-toc-icon-toggle-span\"><svg style=\"fill: #999;color:#999\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" class=\"list-377408\" width=\"20px\" height=\"20px\" viewBox=\"0 0 24 24\" fill=\"none\"><path d=\"M6 6H4v2h2V6zm14 0H8v2h12V6zM4 11h2v2H4v-2zm16 0H8v2h12v-2zM4 16h2v2H4v-2zm16 0H8v2h12v-2z\" fill=\"currentColor\"><\/path><\/svg><svg style=\"fill: #999;color:#999\" class=\"arrow-unsorted-368013\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" width=\"10px\" height=\"10px\" viewBox=\"0 0 24 24\" version=\"1.2\" baseProfile=\"tiny\"><path d=\"M18.2 9.3l-6.2-6.3-6.2 6.3c-.2.2-.3.4-.3.7s.1.5.3.7c.2.2.4.3.7.3h11c.3 0 .5-.1.7-.3.2-.2.3-.5.3-.7s-.1-.5-.3-.7zM5.8 14.7l6.2 6.3 6.2-6.3c.2-.2.3-.5.3-.7s-.1-.5-.3-.7c-.2-.2-.4-.3-.7-.3h-11c-.3 0-.5.1-.7.3-.2.2-.3.5-.3.7s.1.5.3.7z\"\/><\/svg><\/span><\/span><\/span><\/a><\/span><\/div>\n<nav><ul class='ez-toc-list ez-toc-list-level-1 ' ><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-1\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Good_to_know\" >Good to know<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-2\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#File_Formats_Storage\" >File Formats &amp; Storage<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-3\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Annotations\" >Annotations<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-4\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Analysis_Capabilities\" >Analysis Capabilities<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Performance_Features\" >Performance Features<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Required_Hardware_and_OS\" >Required Hardware and OS<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-7\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#AI_Integration\" >AI Integration<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Licensing_Pricing\" >Licensing &amp; Pricing<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-2'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#Compliance\" >Compliance<\/a><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Good_to_know\"><\/span>Good to know<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738916253582\"><strong class=\"schema-faq-question\">What are typical users of MIKAIA<sup>\u00ae<\/sup>?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> has always been designed for users in life science research and development, who want to be able realize heterogenous analyses without having to develop their own custom software. <br\/>Main user groups are academia, CROs, pharma, biotech and biobanks. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915963679\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> include AIs for the clinical routine?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> contains new AIs cleared for diagnostic use. We are happy to point you to a range of companys who focus on this: <br\/>&#8211; <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology-ais\/\">Digital Pathology AI Companies \u2014 List of Commercial AIs (CE-IVDR, FDA, RUO)<\/a> <br\/>&#8211; <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ims-vendors\/\">The Digital Pathologist\u2019s Cockpit: Image Management Systems (IMS) \u2013 Free Download of List of IMSes<\/a> <br\/>MIKAIA<sup>\u00ae<\/sup> has always been designed for users in life science research and development, who want to be able conduct heterogenous analyses without having to develop their own custom software. <br\/>Main user groups are academia, CROs, pharma, biotech, and biobanks. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738916337560\"><strong class=\"schema-faq-question\">Is MIKAIA<sup>\u00ae<\/sup> a software or a service?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> is a software that you can download and use by yourself in your lab or company.<br\/>If you prefer image analysis as a service, we do that too.<br\/>See <a href=\"http:\/\/www.iis.fraunhofer.de\/pharma-services \">http:\/\/www.iis.fraunhofer.de\/pharma-services <\/a> <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738916490778\"><strong class=\"schema-faq-question\">Do I purchase MIKAIA<sup>\u00ae<\/sup> studio from Fraunhofer?<\/strong> <p class=\"schema-faq-answer\">No, you can purchase it from one of the MIKAIA<sup>\u00ae<\/sup> distributors, who license MIKAIA<sup>\u00ae<\/sup> from Fraunhofer. We are happy to direct you to the most appropriate partner, based on your territory.<br\/><\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915716204\"><strong class=\"schema-faq-question\">How is MIKAIA<sup>\u00ae<\/sup> pronounced?<\/strong> <p class=\"schema-faq-answer\">[&#8216;mi:ka:ja:] or &#8220;MEE&#8221; &#8220;KAH&#8221; &#8220;YAH&#8221;<br\/>For Germans: Miekaja. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915770038\"><strong class=\"schema-faq-question\">Is MIKAIA<sup>\u00ae<\/sup> an acronym?<\/strong> <p class=\"schema-faq-answer\">Originally, MIKAIA<sup>\u00ae<\/sup> was called MICAIA. The spelling changed beginning of 2024. <br\/>MICAIA stands for <strong>Mic<\/strong>roscopy <strong>AI A<\/strong>nalysis. <br\/>The new spelling indicates the German origin: the German spelling is &#8220;Mi<strong>k<\/strong>roskop&#8221;. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915880550\"><strong class=\"schema-faq-question\">Are MIKAIA<sup>\u00ae<\/sup> and MICAIA the same?<\/strong> <p class=\"schema-faq-answer\">Until beginning of 2024, MIKAIA<sup>\u00ae<\/sup> was spelled MICAIA. We had to change the spelling to settle a dispute with the holder of a somewhat similar trademark.   <\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"File_Formats_Storage\"><\/span>File Formats &amp; Storage<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738342942362\"><strong class=\"schema-faq-question\">What file formats does MIKAIA<sup>\u00ae<\/sup> support?<\/strong> <p class=\"schema-faq-answer\">3DHistech MRXS, Leica SVS, Hamamatsu NDPI\/NDPIS, Zeiss CZI, Olympus VSI, DICOM, OME-TIFF (e.g Lunaphore), Akoya QPTIFF, BigTiff, Multifile TIFF (e.g. MACSima), JPG, PNG, TIF<br\/>See <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">WSI and Annotation File Format I\/O Support in MIKAIA<\/a> for more details.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343015263\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> work in the cloud or in the webbrowser?<\/strong> <p class=\"schema-faq-answer\">No, MIKAIA<sup>\u00ae<\/sup> is a native lightweight Windows software and does not even use a central database. You can easily install MIKAIA<sup>\u00ae<\/sup> on your computer or laptop, or use the portable version by simply unzipping it. Once installed (or unzipped), you can open slides by dragging and dropping them into the application or by importing one or multiple folders as workspaces.\u00a0These can be local or networkf folders.\u00a0<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343189432\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> store the annotations in a central database?<\/strong> <p class=\"schema-faq-answer\">No, MIKAIA<sup>\u00ae<\/sup> uses a decentral scheme: It stores annotations in an *.ano file next to the whole-slide-image file<em>. <\/em>An *.ano file is actually a zip file and it contains an XML file with the annotations.<br\/><br\/><img decoding=\"async\" width=\"480\" height=\"44\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image.png\" class=\"attachment-full size-full\" alt=\"\" style=\"max-width: 100%; height: auto;\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image.png 480w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-300x28.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-370x34.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-270x25.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-470x44.png 470w\" sizes=\"(max-width: 480px) 100vw, 480px\" \/><br\/><img decoding=\"async\" width=\"476\" height=\"43\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1.png\" class=\"attachment-full size-full\" alt=\"\" style=\"max-width: 100%; height: auto;\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1.png 476w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1-300x27.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1-370x33.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1-270x24.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-1-470x43.png 470w\" sizes=\"(max-width: 476px) 100vw, 476px\" \/><br\/><br\/>This is handy, because it enables users to move the slide (incl. *.ano file) into another folder and the connection between slide and annotation will not get broken. Users can also keep multiple versions of annotations, simply by creating copies of the *.ano file, or create backups of annotation files, for instance after they have created manual annotations.<br\/><br\/>If you want to store your analysis results separately from the scans, you can easily do that: Just create a shortcut to your original image file and then load the shortcut. MIKAIA will then put the *.ano file next to the shortcut.<br\/>When opening the shortcut, MIKAIA<sup>\u00ae<\/sup> will open the annotations located next to the shortcut instead of the annotation file located next to the original slide. This way, multiple annotation sets can be maintained, without having to duplicate the (large) WSIs. MIKAIA<sup>\u00ae<\/sup> has built-in dialogs that can be used to batch-create shortcuts or retarget existing shortcuts (in case the original WSIs have been relocated).<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915153741\"><strong class=\"schema-faq-question\">How can I analyze a dataset &#8220;out of place&#8221;, i.e., store the results in a different place? What if the folder with the images is readonle? <\/strong> <p class=\"schema-faq-answer\">You can create a separate folder and put shortcuts to your original scans into it. Then load the folder with the shortcuts into MIKAIA. When MIKAIA<sup>\u00ae<\/sup> loads an image via a shortcut, it will store annotations next to the shortcut.  <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915256758\"><strong class=\"schema-faq-question\">I worked with shortcuts and then moved my originial folders. Can I repair my zombie shortcuts? <\/strong> <p class=\"schema-faq-answer\">Yes, MIKAIA<sup>\u00ae<\/sup> includes a tool that lets you redirect to existing shortcuts to a new folder. It is available via main menu | <em>Annotations<\/em> | <em>Retarget shortcuts in folder<\/em>. You simply select 1) the folder with the zombie shortcuts and 2) the new folder where the scans have been moved. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738915455416\"><strong class=\"schema-faq-question\">Can I manage multiple versions of annotations file?<\/strong> <p class=\"schema-faq-answer\">Yes, when you&#8217;ve annotated or analyzed a set of image scans, the original image files will each have a sibling file with an *.ano extension. Copy all these *.ano files into a new folder. Then use the built-in MIKAIA<sup>\u00ae<\/sup> tool at main menu | <em>Annotations<\/em> | Add slide shortcuts next to *.ano files. You select the folder with the *.ano file copies and the original folder. MIKAIA will then automatically identify matches based on the file names and generate the shortcuts. You can then import the new folder containing the shortcuts + *.ano copies into MIKAIA<sup>\u00ae<\/sup>.<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Annotations\"><\/span>Annotations<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738311041716\"><strong class=\"schema-faq-question\">Can MIKAIA<sup>\u00ae<\/sup> import annotations from software XYZ?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> supports opening annotations in GeoJson format (used e.g. by QuPath), XML format (used by Leica Aperio), or 3DHistech *.dat format. You could also use the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-plugin-api\/\">REST API<\/a> to add annotations via a plugin, e.g. writtin in Python.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738313373731\"><strong class=\"schema-faq-question\">Can MIKAIA<sup>\u00ae<\/sup> export annotations to software XYZ?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> can export annotations to GeoJson format (used by QuPath), XML format (used by Leica Aperio), or CSV format. <br\/>Using the Annotation Image Export App or Tile Export App, you can also export images of annotations or export tiles along with masks (e.g., for AI training outside of MIKAIA<sup>\u00ae<\/sup>).<br\/>When you export a slide (e.g., in a different format, a crop, or at a lower resolution), you can also select to burn in the annotations. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1751474980305\"><strong class=\"schema-faq-question\">Can I use MIKAIA<sup>\u00ae<\/sup> to work on annotations collaboratively?<\/strong> <p class=\"schema-faq-answer\">Yes. Even though MIKAIA<sup>\u00ae<\/sup> is not a web-based software, it still can be used collaboratively: The free <strong>MIKAIA<sup>\u00ae<\/sup> lite <\/strong>edition can be used to create annotations manually, but it can also view annotations generated by an analysis conducted with <strong>MIKAIA<sup>\u00ae<\/sup> studio<\/strong>. In other words, <em>user A<\/em> can run an analysis with MIKAIA<sup>\u00ae<\/sup> studio on <em>computer A<\/em>, and later <em>users B-Z<\/em> can view the results on their own computers using the free MIKAIA<sup>\u00ae<\/sup> lite edition.<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Analysis_Capabilities\"><\/span>Analysis Capabilities<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738343415334\"><strong class=\"schema-faq-question\">Can I analyze H&amp;E staining?<\/strong> <p class=\"schema-faq-answer\">Yes, the Tissue Detection App works out of the box.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ai-authoring-app\/\">AI Author<\/a> can be used to train a tissue classifier, e.g., for masking tumor, necrosis, mucus, or any other tissue type.<br\/>The H&amp;E Cell AI can be used to segment and classify cells (learn more about <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-multiple-he-ais\/\">H&amp;E analysis using AIs<\/a>).<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-spatial-clustering-app\/\">Spatial Clustering App<\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-tile-export-app\/\">Tile Export App<\/a> or Annotation Image Export App can be used to export small images.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343454704\"><strong class=\"schema-faq-question\">Can I analyze IHC staining?<\/strong> <p class=\"schema-faq-answer\">Yes, the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a> supports segmenting both positive and negative cells. It can also grade cells based on staining intensity. It can detect nuclear, cytoplasmic, or membranous markers and is very flexibly configurable to support a broad variety of different markers.<br\/>The Mask-by-Color App can be used to mask regions based on pixel colors.\u00a0<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343500273\"><strong class=\"schema-faq-question\">Can I analyze mIF \/ FL \/ fluorescent scans?\u00a0<\/strong> <p class=\"schema-faq-answer\">Yes, analysis of IF scans is a popular and major use case in MIKAIA<sup>\u00ae<\/sup> &#8212; from low-plex scans with just one or two markers up to high-plex spatial proteomics scans.  <br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis App<\/a> can be used to segment and phenotype cells based on marker expression.\u00a0\u00a0<br\/>The Mask by Color App can be used to create a mask by thresholding an individual color channel or a combination of multiple color channels.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-spatial-clustering-app\/\">Spatial Clustering App<\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-tile-export-app\/\">Tile Export App<\/a> or Annotation Image Export App can be used to export small images.<br\/>Supported formats are Zeiss CZI, Olympus VSI, Hamamatsu NDPIS, QPTIFF (used by Akoya Biosciences), and OME-TIFF (used, e.g., by Lunaphore, Miltenyi MACSima, bioformats, and many other platforms; see <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">list of file formats<\/a>). You can also open flat images (e.g., JPG, PNG, or TIF) and select that each of the RGB color channels shall in fact be interpreted as a fluorescence channel.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343537134\"><strong class=\"schema-faq-question\">Does the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis App<\/a> support segmentation of the membrane?<\/strong> <p class=\"schema-faq-answer\">Yes, it can either be configured in different ways:<br\/>\u25cf The AI can segment nuclei (e.g., &#8220;DAPI&#8221;, &#8220;Hoechst&#8221;, or &#8220;DNA&#8221; channel) and then dilate them by a fixed radius.<br\/>\u25cf The AI can be fed both a nuclear and a membrane marker. It will then segment the membrane.<br\/>\u25cf The AI can be fed only a membrane or cytoplasmic marker. It will then segment the outer cell contours.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343568465\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> support analyzing hematology or cytology?<\/strong> <p class=\"schema-faq-answer\">It does not include apps specifically tailored to these domains. But the FL Cell Analysis App, for instance, can still be used to detect and phenotype cells in suspension. <\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343608979\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> support 3D-analysis or reconstruction?<\/strong> <p class=\"schema-faq-answer\">No, MIKAIA<sup>\u00ae<\/sup> supports z-levels (focus planes) and can analyze individual z-levels, but is a 2D analysis program.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343662241\"><strong class=\"schema-faq-question\">Are TMAs supported?<\/strong> <p class=\"schema-faq-answer\">Yes, the Tissue Detection App includes TMA-dearraying. Most apps, including the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">IHC Cell Detection<\/a> or <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis <\/a>Apps, will then group detected cells by core, so that per-core statistics are automatically generated.<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Performance_Features\"><\/span>Performance Features<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738343789579\"><strong class=\"schema-faq-question\">Does the viewer support 16 bit color depth?<\/strong> <p class=\"schema-faq-answer\">Yes.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343880104\"><strong class=\"schema-faq-question\">How many FL channels does the viewer support?<\/strong> <p class=\"schema-faq-answer\">We have not built in a fixed limit. Computer power and memory availability pose limits. We have had users analyze up to 50plexes, but more may be possible. We are happy to assist and provide voucher codes to users who want to experiment with even higher plexity.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738343921321\"><strong class=\"schema-faq-question\">Is it possible to convert a slide from format X into format Z?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> can export any brightfield scan that it supports to either SVS, BigTiff, ZIF, or DeepZoom. Learn more about WSI and annotation file formats <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">here<\/a>.<br\/>We are working on exporting to OME-TIFF as well.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738344056732\"><strong class=\"schema-faq-question\">Is it possible to compute resolution levels \/ pyramid levels for a large flat scan?<\/strong> <p class=\"schema-faq-answer\">No, not at this point. We plan to add this feature soon.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738344083628\"><strong class=\"schema-faq-question\">Is MIKAIA<sup>\u00ae<\/sup> compatible with any Image Management System (IMS)<\/strong> <p class=\"schema-faq-answer\">No, not at this point. MIKAIA<sup>\u00ae<\/sup> must have direct access to the image scan files.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738344123596\"><strong class=\"schema-faq-question\">Does MIKAIA<sup>\u00ae<\/sup> support batch analysis?<\/strong> <p class=\"schema-faq-answer\">Yes, you can multi-select slides in the MIKAIA<sup>\u00ae<\/sup> workspace. As soon as you select more than one slide, the analyze-&#8220;Slide&#8221; button turns into the analyze-&#8220;Batch&#8221; button. Once you select more than one slide, the &#8220;Analyze Slide&#8221; button changes to &#8220;Analyze Batch.&#8221; You can also create a *.micbat file (refer to the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-university\/\">user manual<\/a>) that lists the apps to be used, the app configuration file, and the selected slides. To start a batch process, simply open this *.micbat text file. All results, including a combined CSV file with results from all slides, will be saved in an export folder.<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Required_Hardware_and_OS\"><\/span>Required Hardware and OS<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738570465325\"><strong class=\"schema-faq-question\">What computer hardware do I need? Do I need a GPU?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> runs on a Windows laptop or PC. The AI based analysis apps benefit strongly from the presence of a CUDA-enabled <strong>GPU <\/strong>(CUDA 8 or newer &#8212; see below: &#8220;What GPU do I need for fast AI interference?&#8221;). They do fallback to CPU when no compatible GPU is available, but the apps that use quite large AI models (H&amp;E Cell AI, HE Crypt Segmentation) are really slow in CPU-mode.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a>, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology\/mikaia-fl-colocalization-app\/\">FL Cell Segmentation App<\/a>, or <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ai\/mikaia-ai-authoring-app\/\">AI Author<\/a> are fairly usable in CPU mode, but again, they are faster when a CUDA-enabled GPU is available.\u00a0<br\/>Due to the large size of whole-slide-images, it is recommended to have <strong>16 GB RAM<\/strong> or more.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570519807\"><strong class=\"schema-faq-question\">What GPU do I need for fast AI inference?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> only supports CUDA-enabled NVIDIA GPUs. GPUs by other vendors are not supported as AI co-processors. MIKAIA<sup>\u00ae<\/sup> does not require a professional series GPU, but is also compatible with consumer-level gaming GPUs (NVIDIA GeForce).<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570490401\"><strong class=\"schema-faq-question\">Is MIKAIA<sup>\u00ae<\/sup> available for Mac \/ Apple?<\/strong> <p class=\"schema-faq-answer\">No, sorry. Only for Windows.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570500577\"><strong class=\"schema-faq-question\">Is MIKAIA<sup>\u00ae<\/sup> available for Linux?<\/strong> <p class=\"schema-faq-answer\">No, sorry. Only for Windows.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570538447\"><strong class=\"schema-faq-question\">Does the license server have to be a Windows computer?<\/strong> <p class=\"schema-faq-answer\">No, it can be a Linux or Mac. You just need to be able to install the WIBU CodeMeter runtime (the copy protection framework used by MIKAIA<sup>\u00ae<\/sup>), which is <a href=\"https:\/\/www.wibu.com\/support\/user\/user-software.html?tx_wibudownloads_downloadlist%5Baction%5D=index&amp;tx_wibudownloads_downloadlist%5Bcontroller%5D=DownloadList&amp;cHash=9589e4298c76dfab073014d6aabdb48b\">available for download at the WIBU website<\/a>.\u00a0<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1746615140837\"><strong class=\"schema-faq-question\">What are the initial steps to set up MIKAIA<sup>\u00ae<\/sup> on my system?<\/strong> <p class=\"schema-faq-answer\">We offer both an\u00a0<strong>installer<\/strong>\u00a0and a\u00a0<strong>portable version<\/strong>. The installer is an *.exe file and it requires\u00a0<strong>admin rights<\/strong>\u00a0for installation. The portable version is a ZIP file that must be manually extracted and then MIKAIA.exe can be started from there. This process does not require admin rights.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1746615215749\"><strong class=\"schema-faq-question\">What display resolutions and input devices are supported by MIKAIA<sup>\u00ae<\/sup>?<\/strong> <p class=\"schema-faq-answer\">Both 2K and 4K displays are supported. MIKAIA<sup>\u00ae<\/sup> has also good <strong>touch-support<\/strong>. For creating accurate annotations, we recommend using a <strong>tablet<\/strong> with a stylus pen (we use WACOM tablets). At exhibitions, we sometimes show MIKAIA<sup>\u00ae<\/sup> on a touch-enabled digital whiteboard (we use a Samsung Flip 2).<br\/><br\/><img decoding=\"async\" width=\"4844\" height=\"1766\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2.png\" class=\"attachment-full size-full\" alt=\"\" style=\"max-width: 100%; height: auto;\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2.png 4844w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-300x109.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-1024x373.png 1024w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-768x280.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-1536x560.png 1536w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-2048x747.png 2048w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-370x135.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-270x98.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-570x208.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/11\/image-2-740x270.png 740w\" sizes=\"(max-width: 4844px) 100vw, 4844px\" \/><\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"AI_Integration\"><\/span>AI Integration<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738570709683\"><strong class=\"schema-faq-question\">Can I plug my own AI into MIKAIA<sup><sup>\u00ae<\/sup><\/sup>?<\/strong> <p class=\"schema-faq-answer\">Yes, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ai\/mikaia-ai-authoring-app\/\">MIKAIA<sup><sup>\u00ae<\/sup><\/sup> has a REST API<\/a>. You can easily integrate your own scripts in any scripting language. We provide Python examples that show how to integrate your own AI as well as a Python API that simplifies calling the MIKAIA<sup><sup>\u00ae<\/sup><\/sup> REST API. A plugin can even run in a Docker or on another computer (even Mac or Linux).<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570724503\"><strong class=\"schema-faq-question\">Can my AI use TensorFlow, PyTorch, or XYZ framework?<\/strong> <p class=\"schema-faq-answer\">Your plugin can use any framework as using the AI model is entirely handled by the plugin and not by MIKAIA<sup><sup>\u00ae<\/sup><\/sup>. This gives the plugin complete freedom in terms of pre- or post-processing the AI input and output.\u00a0<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Licensing_Pricing\"><\/span>Licensing &amp; Pricing<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738570828729\"><strong class=\"schema-faq-question\">What is difference between MIKAIA<sup>\u00ae<\/sup> lite and MIKAIA<sup>\u00ae<\/sup> studio?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> lite is free. Most image analysis capabilities are locked in MIKAIA<sup>\u00ae<\/sup> lite, though. They are only available in MIKAIA<sup>\u00ae<\/sup> studio. Many, but not all apps are included in MIKAIA<sup>\u00ae<\/sup> studio \u2013 some require purchasing an optional add-on bundle. Browse the editions <a href=\"https:\/\/www.iis.fraunhofer.de\/en\/ff\/sse\/health\/medical-image-analysis\/mikaia\/mikaia-apps-and-ais.html\">here<\/a><strong>.<\/strong>\u00a0<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570849804\"><strong class=\"schema-faq-question\">Can I evaluate the features that are locked in MIKAIA<sup>\u00ae<\/sup> lite?<\/strong> <p class=\"schema-faq-answer\">Yes, get in touch (<a href=\"mailto:mikaia@iis.fraunhofer.de\">mikaia@iis.fraunhofer.de<\/a>) and we are happy to provide voucher codes that let you temporarily use the locked features.<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738570953643\"><strong class=\"schema-faq-question\">What is the price of MIKAIA<sup>\u00ae<\/sup> studio?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup>\u00ae<\/sup> has a very fair price. We are happy to put you in touch with one of our distributors, who can give information on pricing or issue a quotation.<br\/>The default is a perpetual node-locked license for a one-time up-front free that includes one year of updates &amp; support. We also offer floating or multi-user network licenses.\u00a0<\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1751474371673\"><strong class=\"schema-faq-question\">What types of licenses are offered for MIKAIA<sup>\u00ae<\/sup>?<\/strong> <p class=\"schema-faq-answer\">By default, we offer <strong>perpetual licenses<\/strong>, i.e., once activated, features are available forever, without any follow-up costs.<br\/>A license can be <strong>node-locked<\/strong>, which means it is locked to a particular PC, or alternatively, we offer <strong>single-user or multi-user floating licenses<\/strong>. Here, the activation file is imported on a server in your network. MIKAIA<sup>\u00ae<\/sup> can then be installed on any computer in your network or on a (VPN-connected) <strong>home office<\/strong> laptop. At startup, MIKAIA<sup>\u00ae<\/sup> will automatically detect the license server and, if a user-slot of the single- or multi-user license is currently free, it will start up as MIKAIA<sup>\u00ae<\/sup> studio, else as MIKAIA<sup>\u00ae<\/sup> lite. The licensing modes are also illustrated in the <a href=\"https:\/\/www.iis.fraunhofer.de\/content\/dam\/iis\/en\/doc\/il\/bmt\/MIKAIA_Brochure.pdf\"><strong>MIKAIA<\/strong><\/a><strong><a href=\"https:\/\/www.iis.fraunhofer.de\/content\/dam\/iis\/en\/doc\/il\/bmt\/MIKAIA_Brochure.pdf\"><sup>\u00ae<\/sup>\u00a0product brochure<\/a><\/strong>.<\/p> <\/div> <\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Compliance\"><\/span>Compliance<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<div class=\"schema-faq wp-block-yoast-faq-block\"><div class=\"schema-faq-section\" id=\"faq-question-1738570983195\"><strong class=\"schema-faq-question\">Is MIKAIA<sup><sup>\u00ae<\/sup><\/sup> CE-IVD, CE-IVDR, or FDA cleared?<\/strong> <p class=\"schema-faq-answer\">No, MIKAIA<sup><sup>\u00ae<\/sup><\/sup> is designed for life science researchers. Most apps are quite generically usable. The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ai-authoring-app\/\">AI Author<\/a> is a good example: <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology-batch-analysis-with-mikaia\/\">Users can train their own AIs directly in MIKAIA<sup><sup>\u00ae<\/sup><\/sup><\/a>.<br\/><strong>MIKAIA<sup><sup>\u00ae<\/sup><\/sup><\/strong>, <strong>incl. all apps, i<\/strong>s <strong>for research use only (RUO).<\/strong><\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738580265149\"><strong class=\"schema-faq-question\">Can MIKAIA<sup><sup>\u00ae<\/sup><\/sup> be used in a GLP setting?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup><sup>\u00ae<\/sup><\/sup> contains a funtionality that helps with documentation and ensures repeatability. When batch-analysing a cohort, the results folder will contain shortcuts to the analyzed slides, the app settings file that contains all parameters that were used in the particular anylsis, a *.micbat file that lists the entire batch job (and can later be executed again), and the CSV file with all quantitative results. This additionally states the software version, computer and user name, and date.<br\/><\/p> <\/div> <div class=\"schema-faq-section\" id=\"faq-question-1738580619053\"><strong class=\"schema-faq-question\">Does MIKAIA<sup><sup>\u00ae<\/sup><\/sup> communicate with the cloud?<\/strong> <p class=\"schema-faq-answer\">MIKAIA<sup><sup>\u00ae<\/sup><\/sup> works offline. The only communication is at startup, when by default, MIKAIA<sup><sup>\u00ae<\/sup><\/sup> checks with a Fraunhofer server if a new version is available and, if that is the case, then shows a notification dialog. This check can optionally be disabled and has no further impact of the functionality of MIKAIA<sup><sup>\u00ae<\/sup><\/sup>. <\/p> <\/div> <\/div>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Welcome to our MIKAIA FAQs. We know that navigating a flexible digital pathology &amp; spatial biology image analysis software like MIKAIA\u00ae can raise a lot of questions, and we&#8217;re here to help. Whether you&#8217;re looking for quick tips or detailed info, you\u2019ll find answers here. If you can\u2019t find what you\u2019re looking for or need [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":4468,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,28],"tags":[114,7],"coauthors":[56],"class_list":["post-3139","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-digital-pathology","category-mikaia-university","tag-getting-started","tag-mikaia"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>MIKAIA FAQs - SMART SENSING insights<\/title>\n<meta name=\"description\" content=\"Discover the MIKAIA FAQs to get answers to your questions about our digital pathology software. 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Explore tips, troubleshooting, and helpful resources.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/\" \/>\n<meta property=\"og:site_name\" content=\"SMART SENSING insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/FraunhoferIIS\" \/>\n<meta property=\"article:published_time\" content=\"2025-02-03T17:56:07+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-11-07T19:14:12+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/02\/FAQ-Header-scaled.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"2560\" \/>\n\t<meta property=\"og:image:height\" content=\"853\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Volker Bruns\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Volker Bruns\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"14 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/\"},\"author\":{\"name\":\"Volker Bruns\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#\\\/schema\\\/person\\\/fd37d35c4d3576840cf0bc3f74eafb98\"},\"headline\":\"MIKAIA FAQs\",\"datePublished\":\"2025-02-03T17:56:07+00:00\",\"dateModified\":\"2025-11-07T19:14:12+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/\"},\"wordCount\":2886,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#organization\"},\"image\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/wp-content\\\/uploads\\\/2025\\\/02\\\/FAQ-Header-scaled.jpg\",\"keywords\":[\"Getting Started\",\"MIKAIA\u00ae\"],\"articleSection\":[\"Digital Pathology\",\"MIKAIA University\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#respond\"]}]},{\"@type\":[\"WebPage\",\"FAQPage\"],\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/\",\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/\",\"name\":\"MIKAIA FAQs - SMART SENSING insights\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/wp-content\\\/uploads\\\/2025\\\/02\\\/FAQ-Header-scaled.jpg\",\"datePublished\":\"2025-02-03T17:56:07+00:00\",\"dateModified\":\"2025-11-07T19:14:12+00:00\",\"description\":\"Discover the MIKAIA FAQs to get answers to your questions about our digital pathology software. 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We had to change the spelling to settle a dispute with the holder of a somewhat similar trademark.   \",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738342942362\",\"position\":8,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738342942362\",\"name\":\"What file formats does MIKAIA\u00ae support?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"3DHistech MRXS, Leica SVS, Hamamatsu NDPI\\\/NDPIS, Zeiss CZI, Olympus VSI, DICOM, OME-TIFF (e.g Lunaphore), Akoya QPTIFF, BigTiff, Multifile TIFF (e.g. MACSima), JPG, PNG, TIF<br\\\/>See <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\\\">WSI and Annotation File Format I\\\/O Support in MIKAIA<\\\/a> for more details.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343015263\",\"position\":9,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343015263\",\"name\":\"Does MIKAIA\u00ae work in the cloud or in the webbrowser?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, MIKAIA\u00ae is a native lightweight Windows software and does not even use a central database. You can easily install MIKAIA\u00ae on your computer or laptop, or use the portable version by simply unzipping it. Once installed (or unzipped), you can open slides by dragging and dropping them into the application or by importing one or multiple folders as workspaces.\u00a0These can be local or networkf folders.\u00a0\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343189432\",\"position\":10,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343189432\",\"name\":\"Does MIKAIA\u00ae store the annotations in a central database?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, MIKAIA\u00ae uses a decentral scheme: It stores annotations in an *.ano file next to the whole-slide-image file<em>. <\\\/em>An *.ano file is actually a zip file and it contains an XML file with the annotations.<br\\\/><br\\\/><br\\\/><br\\\/><br\\\/>This is handy, because it enables users to move the slide (incl. *.ano file) into another folder and the connection between slide and annotation will not get broken. Users can also keep multiple versions of annotations, simply by creating copies of the *.ano file, or create backups of annotation files, for instance after they have created manual annotations.<br\\\/><br\\\/>If you want to store your analysis results separately from the scans, you can easily do that: Just create a shortcut to your original image file and then load the shortcut. MIKAIA will then put the *.ano file next to the shortcut.<br\\\/>When opening the shortcut, MIKAIA\u00ae will open the annotations located next to the shortcut instead of the annotation file located next to the original slide. This way, multiple annotation sets can be maintained, without having to duplicate the (large) WSIs. MIKAIA\u00ae has built-in dialogs that can be used to batch-create shortcuts or retarget existing shortcuts (in case the original WSIs have been relocated).\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915153741\",\"position\":11,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915153741\",\"name\":\"How can I analyze a dataset \\\"out of place\\\", i.e., store the results in a different place? What if the folder with the images is readonle?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"You can create a separate folder and put shortcuts to your original scans into it. Then load the folder with the shortcuts into MIKAIA. When MIKAIA\u00ae loads an image via a shortcut, it will store annotations next to the shortcut.  \",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915256758\",\"position\":12,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915256758\",\"name\":\"I worked with shortcuts and then moved my originial folders. Can I repair my zombie shortcuts?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, MIKAIA\u00ae includes a tool that lets you redirect to existing shortcuts to a new folder. It is available via main menu | <em>Annotations<\\\/em> | <em>Retarget shortcuts in folder<\\\/em>. You simply select 1) the folder with the zombie shortcuts and 2) the new folder where the scans have been moved. \",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915455416\",\"position\":13,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738915455416\",\"name\":\"Can I manage multiple versions of annotations file?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, when you've annotated or analyzed a set of image scans, the original image files will each have a sibling file with an *.ano extension. Copy all these *.ano files into a new folder. Then use the built-in MIKAIA\u00ae tool at main menu | <em>Annotations<\\\/em> | Add slide shortcuts next to *.ano files. You select the folder with the *.ano file copies and the original folder. MIKAIA will then automatically identify matches based on the file names and generate the shortcuts. You can then import the new folder containing the shortcuts + *.ano copies into MIKAIA\u00ae.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738311041716\",\"position\":14,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738311041716\",\"name\":\"Can MIKAIA\u00ae import annotations from software XYZ?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae supports opening annotations in GeoJson format (used e.g. by QuPath), XML format (used by Leica Aperio), or 3DHistech *.dat format. You could also use the <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-plugin-api\\\/\\\">REST API<\\\/a> to add annotations via a plugin, e.g. writtin in Python.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738313373731\",\"position\":15,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738313373731\",\"name\":\"Can MIKAIA\u00ae export annotations to software XYZ?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae can export annotations to GeoJson format (used by QuPath), XML format (used by Leica Aperio), or CSV format. <br\\\/>Using the Annotation Image Export App or Tile Export App, you can also export images of annotations or export tiles along with masks (e.g., for AI training outside of MIKAIA\u00ae).<br\\\/>When you export a slide (e.g., in a different format, a crop, or at a lower resolution), you can also select to burn in the annotations. \",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1751474980305\",\"position\":16,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1751474980305\",\"name\":\"Can I use MIKAIA\u00ae to work on annotations collaboratively?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes. Even though MIKAIA\u00ae is not a web-based software, it still can be used collaboratively: The free <strong>MIKAIA\u00ae lite <\\\/strong>edition can be used to create annotations manually, but it can also view annotations generated by an analysis conducted with <strong>MIKAIA\u00ae studio<\\\/strong>. In other words, <em>user A<\\\/em> can run an analysis with MIKAIA\u00ae studio on <em>computer A<\\\/em>, and later <em>users B-Z<\\\/em> can view the results on their own computers using the free MIKAIA\u00ae lite edition.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343415334\",\"position\":17,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343415334\",\"name\":\"Can I analyze H&amp;E staining?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, the Tissue Detection App works out of the box.<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-ai-authoring-app\\\/\\\">AI Author<\\\/a> can be used to train a tissue classifier, e.g., for masking tumor, necrosis, mucus, or any other tissue type.<br\\\/>The H&amp;E Cell AI can be used to segment and classify cells (learn more about <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-multiple-he-ais\\\/\\\">H&amp;E analysis using AIs<\\\/a>).<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-spatial-clustering-app\\\/\\\">Spatial Clustering App<\\\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-tile-export-app\\\/\\\">Tile Export App<\\\/a> or Annotation Image Export App can be used to export small images.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343454704\",\"position\":18,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343454704\",\"name\":\"Can I analyze IHC staining?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, the <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-ihc-cell-detection-app\\\/\\\">IHC Cell Detection App<\\\/a> supports segmenting both positive and negative cells. It can also grade cells based on staining intensity. It can detect nuclear, cytoplasmic, or membranous markers and is very flexibly configurable to support a broad variety of different markers.<br\\\/>The Mask-by-Color App can be used to mask regions based on pixel colors.\u00a0\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343500273\",\"position\":19,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343500273\",\"name\":\"Can I analyze mIF \\\/ FL \\\/ fluorescent scans?\u00a0\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, analysis of IF scans is a popular and major use case in MIKAIA\u00ae -- from low-plex scans with just one or two markers up to high-plex spatial proteomics scans.  <br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-fl-colocalization-app\\\/\\\">FL Cell Analysis App<\\\/a> can be used to segment and phenotype cells based on marker expression.\u00a0\u00a0<br\\\/>The Mask by Color App can be used to create a mask by thresholding an individual color channel or a combination of multiple color channels.<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-spatial-clustering-app\\\/\\\">Spatial Clustering App<\\\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-tile-export-app\\\/\\\">Tile Export App<\\\/a> or Annotation Image Export App can be used to export small images.<br\\\/>Supported formats are Zeiss CZI, Olympus VSI, Hamamatsu NDPIS, QPTIFF (used by Akoya Biosciences), and OME-TIFF (used, e.g., by Lunaphore, Miltenyi MACSima, bioformats, and many other platforms; see <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\\\">list of file formats<\\\/a>). You can also open flat images (e.g., JPG, PNG, or TIF) and select that each of the RGB color channels shall in fact be interpreted as a fluorescence channel.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343537134\",\"position\":20,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343537134\",\"name\":\"Does the FL Cell Analysis App support segmentation of the membrane?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, it can either be configured in different ways:<br\\\/>\u25cf The AI can segment nuclei (e.g., \\\"DAPI\\\", \\\"Hoechst\\\", or \\\"DNA\\\" channel) and then dilate them by a fixed radius.<br\\\/>\u25cf The AI can be fed both a nuclear and a membrane marker. It will then segment the membrane.<br\\\/>\u25cf The AI can be fed only a membrane or cytoplasmic marker. It will then segment the outer cell contours.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343568465\",\"position\":21,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343568465\",\"name\":\"Does MIKAIA\u00ae support analyzing hematology or cytology?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"It does not include apps specifically tailored to these domains. But the FL Cell Analysis App, for instance, can still be used to detect and phenotype cells in suspension. \",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343608979\",\"position\":22,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343608979\",\"name\":\"Does MIKAIA\u00ae support 3D-analysis or reconstruction?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, MIKAIA\u00ae supports z-levels (focus planes) and can analyze individual z-levels, but is a 2D analysis program.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343662241\",\"position\":23,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343662241\",\"name\":\"Are TMAs supported?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, the Tissue Detection App includes TMA-dearraying. Most apps, including the <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-fl-colocalization-app\\\/\\\">IHC Cell Detection<\\\/a> or <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-fl-colocalization-app\\\/\\\">FL Cell Analysis <\\\/a>Apps, will then group detected cells by core, so that per-core statistics are automatically generated.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343789579\",\"position\":24,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343789579\",\"name\":\"Does the viewer support 16 bit color depth?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343880104\",\"position\":25,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343880104\",\"name\":\"How many FL channels does the viewer support?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"We have not built in a fixed limit. Computer power and memory availability pose limits. We have had users analyze up to 50plexes, but more may be possible. We are happy to assist and provide voucher codes to users who want to experiment with even higher plexity.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343921321\",\"position\":26,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738343921321\",\"name\":\"Is it possible to convert a slide from format X into format Z?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae can export any brightfield scan that it supports to either SVS, BigTiff, ZIF, or DeepZoom. Learn more about WSI and annotation file formats <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\\\">here<\\\/a>.<br\\\/>We are working on exporting to OME-TIFF as well.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344056732\",\"position\":27,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344056732\",\"name\":\"Is it possible to compute resolution levels \\\/ pyramid levels for a large flat scan?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, not at this point. We plan to add this feature soon.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344083628\",\"position\":28,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344083628\",\"name\":\"Is MIKAIA\u00ae compatible with any Image Management System (IMS)\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, not at this point. MIKAIA\u00ae must have direct access to the image scan files.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344123596\",\"position\":29,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738344123596\",\"name\":\"Does MIKAIA\u00ae support batch analysis?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, you can multi-select slides in the MIKAIA\u00ae workspace. As soon as you select more than one slide, the analyze-\\\"Slide\\\" button turns into the analyze-\\\"Batch\\\" button. Once you select more than one slide, the \\\"Analyze Slide\\\" button changes to \\\"Analyze Batch.\\\" You can also create a *.micbat file (refer to the <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-university\\\/\\\">user manual<\\\/a>) that lists the apps to be used, the app configuration file, and the selected slides. To start a batch process, simply open this *.micbat text file. All results, including a combined CSV file with results from all slides, will be saved in an export folder.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570465325\",\"position\":30,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570465325\",\"name\":\"What computer hardware do I need? Do I need a GPU?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae runs on a Windows laptop or PC. The AI based analysis apps benefit strongly from the presence of a CUDA-enabled <strong>GPU <\\\/strong>(CUDA 8 or newer -- see below: \\\"What GPU do I need for fast AI interference?\\\"). They do fallback to CPU when no compatible GPU is available, but the apps that use quite large AI models (H&amp;E Cell AI, HE Crypt Segmentation) are really slow in CPU-mode.<br\\\/>The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/digital-pathology\\\/mikaia-ihc-cell-detection-app\\\/\\\">IHC Cell Detection App<\\\/a>, <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/digital-pathology\\\/mikaia-fl-colocalization-app\\\/\\\">FL Cell Segmentation App<\\\/a>, or <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/ai\\\/mikaia-ai-authoring-app\\\/\\\">AI Author<\\\/a> are fairly usable in CPU mode, but again, they are faster when a CUDA-enabled GPU is available.\u00a0<br\\\/>Due to the large size of whole-slide-images, it is recommended to have <strong>16 GB RAM<\\\/strong> or more.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570519807\",\"position\":31,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570519807\",\"name\":\"What GPU do I need for fast AI inference?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae only supports CUDA-enabled NVIDIA GPUs. GPUs by other vendors are not supported as AI co-processors. MIKAIA\u00ae does not require a professional series GPU, but is also compatible with consumer-level gaming GPUs (NVIDIA GeForce).\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570490401\",\"position\":32,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570490401\",\"name\":\"Is MIKAIA\u00ae available for Mac \\\/ Apple?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, sorry. Only for Windows.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570500577\",\"position\":33,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570500577\",\"name\":\"Is MIKAIA\u00ae available for Linux?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, sorry. Only for Windows.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570538447\",\"position\":34,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570538447\",\"name\":\"Does the license server have to be a Windows computer?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, it can be a Linux or Mac. You just need to be able to install the WIBU CodeMeter runtime (the copy protection framework used by MIKAIA\u00ae), which is <a href=\\\"https:\\\/\\\/www.wibu.com\\\/support\\\/user\\\/user-software.html?tx_wibudownloads_downloadlist%5Baction%5D=index&amp;tx_wibudownloads_downloadlist%5Bcontroller%5D=DownloadList&amp;cHash=9589e4298c76dfab073014d6aabdb48b\\\">available for download at the WIBU website<\\\/a>.\u00a0\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1746615140837\",\"position\":35,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1746615140837\",\"name\":\"What are the initial steps to set up MIKAIA\u00ae on my system?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"We offer both an\u00a0<strong>installer<\\\/strong>\u00a0and a\u00a0<strong>portable version<\\\/strong>. 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Browse the editions <a href=\\\"https:\\\/\\\/www.iis.fraunhofer.de\\\/en\\\/ff\\\/sse\\\/health\\\/medical-image-analysis\\\/mikaia\\\/mikaia-apps-and-ais.html\\\">here<\\\/a><strong>.<\\\/strong>\u00a0\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570849804\",\"position\":40,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570849804\",\"name\":\"Can I evaluate the features that are locked in MIKAIA\u00ae lite?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"Yes, get in touch (<a href=\\\"mailto:mikaia@iis.fraunhofer.de\\\">mikaia@iis.fraunhofer.de<\\\/a>) and we are happy to provide voucher codes that let you temporarily use the locked features.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570953643\",\"position\":41,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570953643\",\"name\":\"What is the price of MIKAIA\u00ae studio?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae has a very fair price. We are happy to put you in touch with one of our distributors, who can give information on pricing or issue a quotation.<br\\\/>The default is a perpetual node-locked license for a one-time up-front free that includes one year of updates &amp; support. 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The licensing modes are also illustrated in the <a href=\\\"https:\\\/\\\/www.iis.fraunhofer.de\\\/content\\\/dam\\\/iis\\\/en\\\/doc\\\/il\\\/bmt\\\/MIKAIA_Brochure.pdf\\\"><strong>MIKAIA<\\\/strong><\\\/a><strong><a href=\\\"https:\\\/\\\/www.iis.fraunhofer.de\\\/content\\\/dam\\\/iis\\\/en\\\/doc\\\/il\\\/bmt\\\/MIKAIA_Brochure.pdf\\\">\u00ae\u00a0product brochure<\\\/a><\\\/strong>.\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570983195\",\"position\":43,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738570983195\",\"name\":\"Is MIKAIA\u00ae CE-IVD, CE-IVDR, or FDA cleared?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"No, MIKAIA\u00ae is designed for life science researchers. Most apps are quite generically usable. The <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-ai-authoring-app\\\/\\\">AI Author<\\\/a> is a good example: <a href=\\\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/digital-pathology-batch-analysis-with-mikaia\\\/\\\">Users can train their own AIs directly in MIKAIA\u00ae<\\\/a>.<br\\\/><strong>MIKAIA\u00ae<\\\/strong>, <strong>incl. all apps, i<\\\/strong>s <strong>for research use only (RUO).<\\\/strong>\",\"inLanguage\":\"en-US\"},\"inLanguage\":\"en-US\"},{\"@type\":\"Question\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738580265149\",\"position\":44,\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-faqs\\\/#faq-question-1738580265149\",\"name\":\"Can MIKAIA\u00ae be used in a GLP setting?\",\"answerCount\":1,\"acceptedAnswer\":{\"@type\":\"Answer\",\"text\":\"MIKAIA\u00ae contains a funtionality that helps with documentation and ensures repeatability. 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Bruns","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/05\/cropped-cropped-Bruns_Volker_DSC1679_Pulkert-scaled-1-96x96.jpg6283dd75b937ac114f8ae92ee4dbfc95","url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/05\/cropped-cropped-Bruns_Volker_DSC1679_Pulkert-scaled-1-96x96.jpg","contentUrl":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2023\/05\/cropped-cropped-Bruns_Volker_DSC1679_Pulkert-scaled-1-96x96.jpg","caption":"Volker Bruns"},"description":"Volker is a digital pathology and spatial biology enthusiast with a computer science background. Volker and his team develop commercial image analysis software for digital pathology and offer contract development, as well as image analysis as a service in the life sciences.","sameAs":["https:\/\/orcid.org\/0000-0001-7693-3542","https:\/\/www.linkedin.com\/in\/volker-bruns\/","https:\/\/www.youtube.com\/playlist?list=PL1xbox4kZP0OL7PskwG_xYgmu9iV_N5Fd"],"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/author\/volker-brunsiis-fraunhofer-de\/"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916253582","position":1,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916253582","name":"What are typical users of MIKAIA\u00ae?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae has always been designed for users in life science research and development, who want to be able realize heterogenous analyses without having to develop their own custom software. <br\/>Main user groups are academia, CROs, pharma, biotech and biobanks. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915963679","position":2,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915963679","name":"Does MIKAIA\u00ae include AIs for the clinical routine?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae contains new AIs cleared for diagnostic use. We are happy to point you to a range of companys who focus on this: <br\/>- <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology-ais\/\">Digital Pathology AI Companies \u2014 List of Commercial AIs (CE-IVDR, FDA, RUO)<\/a> <br\/>- <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ims-vendors\/\">The Digital Pathologist\u2019s Cockpit: Image Management Systems (IMS) \u2013 Free Download of List of IMSes<\/a> <br\/>MIKAIA\u00ae has always been designed for users in life science research and development, who want to be able conduct heterogenous analyses without having to develop their own custom software. <br\/>Main user groups are academia, CROs, pharma, biotech, and biobanks. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916337560","position":3,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916337560","name":"Is MIKAIA\u00ae a software or a service?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae is a software that you can download and use by yourself in your lab or company.<br\/>If you prefer image analysis as a service, we do that too.<br\/>See <a href=\"http:\/\/www.iis.fraunhofer.de\/pharma-services \">http:\/\/www.iis.fraunhofer.de\/pharma-services <\/a> ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916490778","position":4,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738916490778","name":"Do I purchase MIKAIA\u00ae studio from Fraunhofer?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, you can purchase it from one of the MIKAIA\u00ae distributors, who license MIKAIA\u00ae from Fraunhofer. We are happy to direct you to the most appropriate partner, based on your territory.<br\/>","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915716204","position":5,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915716204","name":"How is MIKAIA\u00ae pronounced?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"['mi:ka:ja:] or \"MEE\" \"KAH\" \"YAH\"<br\/>For Germans: Miekaja. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915770038","position":6,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915770038","name":"Is MIKAIA\u00ae an acronym?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Originally, MIKAIA\u00ae was called MICAIA. The spelling changed beginning of 2024. <br\/>MICAIA stands for <strong>Mic<\/strong>roscopy <strong>AI A<\/strong>nalysis. <br\/>The new spelling indicates the German origin: the German spelling is \"Mi<strong>k<\/strong>roskop\". ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915880550","position":7,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915880550","name":"Are MIKAIA\u00ae and MICAIA the same?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Until beginning of 2024, MIKAIA\u00ae was spelled MICAIA. We had to change the spelling to settle a dispute with the holder of a somewhat similar trademark.   ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738342942362","position":8,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738342942362","name":"What file formats does MIKAIA\u00ae support?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"3DHistech MRXS, Leica SVS, Hamamatsu NDPI\/NDPIS, Zeiss CZI, Olympus VSI, DICOM, OME-TIFF (e.g Lunaphore), Akoya QPTIFF, BigTiff, Multifile TIFF (e.g. MACSima), JPG, PNG, TIF<br\/>See <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">WSI and Annotation File Format I\/O Support in MIKAIA<\/a> for more details.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343015263","position":9,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343015263","name":"Does MIKAIA\u00ae work in the cloud or in the webbrowser?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, MIKAIA\u00ae is a native lightweight Windows software and does not even use a central database. You can easily install MIKAIA\u00ae on your computer or laptop, or use the portable version by simply unzipping it. Once installed (or unzipped), you can open slides by dragging and dropping them into the application or by importing one or multiple folders as workspaces.\u00a0These can be local or networkf folders.\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343189432","position":10,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343189432","name":"Does MIKAIA\u00ae store the annotations in a central database?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, MIKAIA\u00ae uses a decentral scheme: It stores annotations in an *.ano file next to the whole-slide-image file<em>. <\/em>An *.ano file is actually a zip file and it contains an XML file with the annotations.<br\/><br\/><br\/><br\/><br\/>This is handy, because it enables users to move the slide (incl. *.ano file) into another folder and the connection between slide and annotation will not get broken. Users can also keep multiple versions of annotations, simply by creating copies of the *.ano file, or create backups of annotation files, for instance after they have created manual annotations.<br\/><br\/>If you want to store your analysis results separately from the scans, you can easily do that: Just create a shortcut to your original image file and then load the shortcut. MIKAIA will then put the *.ano file next to the shortcut.<br\/>When opening the shortcut, MIKAIA\u00ae will open the annotations located next to the shortcut instead of the annotation file located next to the original slide. This way, multiple annotation sets can be maintained, without having to duplicate the (large) WSIs. MIKAIA\u00ae has built-in dialogs that can be used to batch-create shortcuts or retarget existing shortcuts (in case the original WSIs have been relocated).","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915153741","position":11,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915153741","name":"How can I analyze a dataset \"out of place\", i.e., store the results in a different place? What if the folder with the images is readonle?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"You can create a separate folder and put shortcuts to your original scans into it. Then load the folder with the shortcuts into MIKAIA. When MIKAIA\u00ae loads an image via a shortcut, it will store annotations next to the shortcut.  ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915256758","position":12,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915256758","name":"I worked with shortcuts and then moved my originial folders. Can I repair my zombie shortcuts?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, MIKAIA\u00ae includes a tool that lets you redirect to existing shortcuts to a new folder. It is available via main menu | <em>Annotations<\/em> | <em>Retarget shortcuts in folder<\/em>. You simply select 1) the folder with the zombie shortcuts and 2) the new folder where the scans have been moved. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915455416","position":13,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738915455416","name":"Can I manage multiple versions of annotations file?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, when you've annotated or analyzed a set of image scans, the original image files will each have a sibling file with an *.ano extension. Copy all these *.ano files into a new folder. Then use the built-in MIKAIA\u00ae tool at main menu | <em>Annotations<\/em> | Add slide shortcuts next to *.ano files. You select the folder with the *.ano file copies and the original folder. MIKAIA will then automatically identify matches based on the file names and generate the shortcuts. You can then import the new folder containing the shortcuts + *.ano copies into MIKAIA\u00ae.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738311041716","position":14,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738311041716","name":"Can MIKAIA\u00ae import annotations from software XYZ?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae supports opening annotations in GeoJson format (used e.g. by QuPath), XML format (used by Leica Aperio), or 3DHistech *.dat format. You could also use the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-plugin-api\/\">REST API<\/a> to add annotations via a plugin, e.g. writtin in Python.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738313373731","position":15,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738313373731","name":"Can MIKAIA\u00ae export annotations to software XYZ?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae can export annotations to GeoJson format (used by QuPath), XML format (used by Leica Aperio), or CSV format. <br\/>Using the Annotation Image Export App or Tile Export App, you can also export images of annotations or export tiles along with masks (e.g., for AI training outside of MIKAIA\u00ae).<br\/>When you export a slide (e.g., in a different format, a crop, or at a lower resolution), you can also select to burn in the annotations. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1751474980305","position":16,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1751474980305","name":"Can I use MIKAIA\u00ae to work on annotations collaboratively?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes. Even though MIKAIA\u00ae is not a web-based software, it still can be used collaboratively: The free <strong>MIKAIA\u00ae lite <\/strong>edition can be used to create annotations manually, but it can also view annotations generated by an analysis conducted with <strong>MIKAIA\u00ae studio<\/strong>. In other words, <em>user A<\/em> can run an analysis with MIKAIA\u00ae studio on <em>computer A<\/em>, and later <em>users B-Z<\/em> can view the results on their own computers using the free MIKAIA\u00ae lite edition.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343415334","position":17,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343415334","name":"Can I analyze H&amp;E staining?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, the Tissue Detection App works out of the box.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ai-authoring-app\/\">AI Author<\/a> can be used to train a tissue classifier, e.g., for masking tumor, necrosis, mucus, or any other tissue type.<br\/>The H&amp;E Cell AI can be used to segment and classify cells (learn more about <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-multiple-he-ais\/\">H&amp;E analysis using AIs<\/a>).<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-spatial-clustering-app\/\">Spatial Clustering App<\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-tile-export-app\/\">Tile Export App<\/a> or Annotation Image Export App can be used to export small images.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343454704","position":18,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343454704","name":"Can I analyze IHC staining?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a> supports segmenting both positive and negative cells. It can also grade cells based on staining intensity. It can detect nuclear, cytoplasmic, or membranous markers and is very flexibly configurable to support a broad variety of different markers.<br\/>The Mask-by-Color App can be used to mask regions based on pixel colors.\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343500273","position":19,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343500273","name":"Can I analyze mIF \/ FL \/ fluorescent scans?\u00a0","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, analysis of IF scans is a popular and major use case in MIKAIA\u00ae -- from low-plex scans with just one or two markers up to high-plex spatial proteomics scans.  <br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis App<\/a> can be used to segment and phenotype cells based on marker expression.\u00a0\u00a0<br\/>The Mask by Color App can be used to create a mask by thresholding an individual color channel or a combination of multiple color channels.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-spatial-clustering-app\/\">Spatial Clustering App<\/a>, Cell-Cell-Connection App, Cellular Neighborhood App, or Proximity Analysis App can be used to analyze spatial layout of detected cells.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-tile-export-app\/\">Tile Export App<\/a> or Annotation Image Export App can be used to export small images.<br\/>Supported formats are Zeiss CZI, Olympus VSI, Hamamatsu NDPIS, QPTIFF (used by Akoya Biosciences), and OME-TIFF (used, e.g., by Lunaphore, Miltenyi MACSima, bioformats, and many other platforms; see <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">list of file formats<\/a>). You can also open flat images (e.g., JPG, PNG, or TIF) and select that each of the RGB color channels shall in fact be interpreted as a fluorescence channel.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343537134","position":20,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343537134","name":"Does the FL Cell Analysis App support segmentation of the membrane?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, it can either be configured in different ways:<br\/>\u25cf The AI can segment nuclei (e.g., \"DAPI\", \"Hoechst\", or \"DNA\" channel) and then dilate them by a fixed radius.<br\/>\u25cf The AI can be fed both a nuclear and a membrane marker. It will then segment the membrane.<br\/>\u25cf The AI can be fed only a membrane or cytoplasmic marker. It will then segment the outer cell contours.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343568465","position":21,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343568465","name":"Does MIKAIA\u00ae support analyzing hematology or cytology?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"It does not include apps specifically tailored to these domains. But the FL Cell Analysis App, for instance, can still be used to detect and phenotype cells in suspension. ","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343608979","position":22,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343608979","name":"Does MIKAIA\u00ae support 3D-analysis or reconstruction?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, MIKAIA\u00ae supports z-levels (focus planes) and can analyze individual z-levels, but is a 2D analysis program.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343662241","position":23,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343662241","name":"Are TMAs supported?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, the Tissue Detection App includes TMA-dearraying. Most apps, including the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">IHC Cell Detection<\/a> or <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis <\/a>Apps, will then group detected cells by core, so that per-core statistics are automatically generated.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343789579","position":24,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343789579","name":"Does the viewer support 16 bit color depth?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343880104","position":25,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343880104","name":"How many FL channels does the viewer support?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"We have not built in a fixed limit. Computer power and memory availability pose limits. We have had users analyze up to 50plexes, but more may be possible. We are happy to assist and provide voucher codes to users who want to experiment with even higher plexity.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343921321","position":26,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738343921321","name":"Is it possible to convert a slide from format X into format Z?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae can export any brightfield scan that it supports to either SVS, BigTiff, ZIF, or DeepZoom. Learn more about WSI and annotation file formats <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\">here<\/a>.<br\/>We are working on exporting to OME-TIFF as well.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344056732","position":27,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344056732","name":"Is it possible to compute resolution levels \/ pyramid levels for a large flat scan?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, not at this point. We plan to add this feature soon.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344083628","position":28,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344083628","name":"Is MIKAIA\u00ae compatible with any Image Management System (IMS)","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, not at this point. MIKAIA\u00ae must have direct access to the image scan files.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344123596","position":29,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738344123596","name":"Does MIKAIA\u00ae support batch analysis?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, you can multi-select slides in the MIKAIA\u00ae workspace. As soon as you select more than one slide, the analyze-\"Slide\" button turns into the analyze-\"Batch\" button. Once you select more than one slide, the \"Analyze Slide\" button changes to \"Analyze Batch.\" You can also create a *.micbat file (refer to the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-university\/\">user manual<\/a>) that lists the apps to be used, the app configuration file, and the selected slides. To start a batch process, simply open this *.micbat text file. All results, including a combined CSV file with results from all slides, will be saved in an export folder.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570465325","position":30,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570465325","name":"What computer hardware do I need? Do I need a GPU?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae runs on a Windows laptop or PC. The AI based analysis apps benefit strongly from the presence of a CUDA-enabled <strong>GPU <\/strong>(CUDA 8 or newer -- see below: \"What GPU do I need for fast AI interference?\"). They do fallback to CPU when no compatible GPU is available, but the apps that use quite large AI models (H&amp;E Cell AI, HE Crypt Segmentation) are really slow in CPU-mode.<br\/>The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a>, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology\/mikaia-fl-colocalization-app\/\">FL Cell Segmentation App<\/a>, or <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ai\/mikaia-ai-authoring-app\/\">AI Author<\/a> are fairly usable in CPU mode, but again, they are faster when a CUDA-enabled GPU is available.\u00a0<br\/>Due to the large size of whole-slide-images, it is recommended to have <strong>16 GB RAM<\/strong> or more.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570519807","position":31,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570519807","name":"What GPU do I need for fast AI inference?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae only supports CUDA-enabled NVIDIA GPUs. GPUs by other vendors are not supported as AI co-processors. MIKAIA\u00ae does not require a professional series GPU, but is also compatible with consumer-level gaming GPUs (NVIDIA GeForce).","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570490401","position":32,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570490401","name":"Is MIKAIA\u00ae available for Mac \/ Apple?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, sorry. Only for Windows.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570500577","position":33,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570500577","name":"Is MIKAIA\u00ae available for Linux?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, sorry. Only for Windows.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570538447","position":34,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570538447","name":"Does the license server have to be a Windows computer?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, it can be a Linux or Mac. You just need to be able to install the WIBU CodeMeter runtime (the copy protection framework used by MIKAIA\u00ae), which is <a href=\"https:\/\/www.wibu.com\/support\/user\/user-software.html?tx_wibudownloads_downloadlist%5Baction%5D=index&amp;tx_wibudownloads_downloadlist%5Bcontroller%5D=DownloadList&amp;cHash=9589e4298c76dfab073014d6aabdb48b\">available for download at the WIBU website<\/a>.\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1746615140837","position":35,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1746615140837","name":"What are the initial steps to set up MIKAIA\u00ae on my system?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"We offer both an\u00a0<strong>installer<\/strong>\u00a0and a\u00a0<strong>portable version<\/strong>. The installer is an *.exe file and it requires\u00a0<strong>admin rights<\/strong>\u00a0for installation. The portable version is a ZIP file that must be manually extracted and then MIKAIA.exe can be started from there. This process does not require admin rights.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1746615215749","position":36,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1746615215749","name":"What display resolutions and input devices are supported by MIKAIA\u00ae?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Both 2K and 4K displays are supported. MIKAIA\u00ae has also good <strong>touch-support<\/strong>. For creating accurate annotations, we recommend using a <strong>tablet<\/strong> with a stylus pen (we use WACOM tablets). At exhibitions, we sometimes show MIKAIA\u00ae on a touch-enabled digital whiteboard (we use a Samsung Flip 2).<br\/><br\/>","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570709683","position":37,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570709683","name":"Can I plug my own AI into MIKAIA\u00ae?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ai\/mikaia-ai-authoring-app\/\">MIKAIA\u00ae has a REST API<\/a>. You can easily integrate your own scripts in any scripting language. We provide Python examples that show how to integrate your own AI as well as a Python API that simplifies calling the MIKAIA\u00ae REST API. A plugin can even run in a Docker or on another computer (even Mac or Linux).","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570724503","position":38,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570724503","name":"Can my AI use TensorFlow, PyTorch, or XYZ framework?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Your plugin can use any framework as using the AI model is entirely handled by the plugin and not by MIKAIA\u00ae. This gives the plugin complete freedom in terms of pre- or post-processing the AI input and output.\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570828729","position":39,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570828729","name":"What is difference between MIKAIA\u00ae lite and MIKAIA\u00ae studio?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae lite is free. Most image analysis capabilities are locked in MIKAIA\u00ae lite, though. They are only available in MIKAIA\u00ae studio. Many, but not all apps are included in MIKAIA\u00ae studio \u2013 some require purchasing an optional add-on bundle. Browse the editions <a href=\"https:\/\/www.iis.fraunhofer.de\/en\/ff\/sse\/health\/medical-image-analysis\/mikaia\/mikaia-apps-and-ais.html\">here<\/a><strong>.<\/strong>\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570849804","position":40,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570849804","name":"Can I evaluate the features that are locked in MIKAIA\u00ae lite?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"Yes, get in touch (<a href=\"mailto:mikaia@iis.fraunhofer.de\">mikaia@iis.fraunhofer.de<\/a>) and we are happy to provide voucher codes that let you temporarily use the locked features.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570953643","position":41,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570953643","name":"What is the price of MIKAIA\u00ae studio?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae has a very fair price. We are happy to put you in touch with one of our distributors, who can give information on pricing or issue a quotation.<br\/>The default is a perpetual node-locked license for a one-time up-front free that includes one year of updates &amp; support. We also offer floating or multi-user network licenses.\u00a0","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1751474371673","position":42,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1751474371673","name":"What types of licenses are offered for MIKAIA\u00ae?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"By default, we offer <strong>perpetual licenses<\/strong>, i.e., once activated, features are available forever, without any follow-up costs.<br\/>A license can be <strong>node-locked<\/strong>, which means it is locked to a particular PC, or alternatively, we offer <strong>single-user or multi-user floating licenses<\/strong>. Here, the activation file is imported on a server in your network. MIKAIA\u00ae can then be installed on any computer in your network or on a (VPN-connected) <strong>home office<\/strong> laptop. At startup, MIKAIA\u00ae will automatically detect the license server and, if a user-slot of the single- or multi-user license is currently free, it will start up as MIKAIA\u00ae studio, else as MIKAIA\u00ae lite. The licensing modes are also illustrated in the <a href=\"https:\/\/www.iis.fraunhofer.de\/content\/dam\/iis\/en\/doc\/il\/bmt\/MIKAIA_Brochure.pdf\"><strong>MIKAIA<\/strong><\/a><strong><a href=\"https:\/\/www.iis.fraunhofer.de\/content\/dam\/iis\/en\/doc\/il\/bmt\/MIKAIA_Brochure.pdf\">\u00ae\u00a0product brochure<\/a><\/strong>.","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570983195","position":43,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738570983195","name":"Is MIKAIA\u00ae CE-IVD, CE-IVDR, or FDA cleared?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"No, MIKAIA\u00ae is designed for life science researchers. Most apps are quite generically usable. The <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ai-authoring-app\/\">AI Author<\/a> is a good example: <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/digital-pathology-batch-analysis-with-mikaia\/\">Users can train their own AIs directly in MIKAIA\u00ae<\/a>.<br\/><strong>MIKAIA\u00ae<\/strong>, <strong>incl. all apps, i<\/strong>s <strong>for research use only (RUO).<\/strong>","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738580265149","position":44,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738580265149","name":"Can MIKAIA\u00ae be used in a GLP setting?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae contains a funtionality that helps with documentation and ensures repeatability. When batch-analysing a cohort, the results folder will contain shortcuts to the analyzed slides, the app settings file that contains all parameters that were used in the particular anylsis, a *.micbat file that lists the entire batch job (and can later be executed again), and the CSV file with all quantitative results. This additionally states the software version, computer and user name, and date.<br\/>","inLanguage":"en-US"},"inLanguage":"en-US"},{"@type":"Question","@id":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738580619053","position":45,"url":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-faqs\/#faq-question-1738580619053","name":"Does MIKAIA\u00ae communicate with the cloud?","answerCount":1,"acceptedAnswer":{"@type":"Answer","text":"MIKAIA\u00ae works offline. The only communication is at startup, when by default, MIKAIA\u00ae checks with a Fraunhofer server if a new version is available and, if that is the case, then shows a notification dialog. This check can optionally be disabled and has no further impact of the functionality of MIKAIA\u00ae. ","inLanguage":"en-US"},"inLanguage":"en-US"}]}},"_links":{"self":[{"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/posts\/3139","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/comments?post=3139"}],"version-history":[{"count":26,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/posts\/3139\/revisions"}],"predecessor-version":[{"id":4729,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/posts\/3139\/revisions\/4729"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/media\/4468"}],"wp:attachment":[{"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/media?parent=3139"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/categories?post=3139"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/tags?post=3139"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-json\/wp\/v2\/coauthors?post=3139"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}