{"id":2128,"date":"2024-05-29T14:10:15","date_gmt":"2024-05-29T12:10:15","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=2128"},"modified":"2025-10-14T11:12:12","modified_gmt":"2025-10-14T09:12:12","slug":"mikaia-io-formats","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/","title":{"rendered":"WSI and Annotation File Format I\/O Support in MIKAIA"},"content":{"rendered":"\n<p><a href=\"https:\/\/www.iis.fraunhofer.de\/en\/ff\/sse\/health\/medical-image-analysis\/mikaia.html\">MIKAIA<sup>\u00ae<\/sup> <\/a>supports various I\/O formats, find out which ones.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Importable whole-slide-image file formats<\/h2>\n\n\n\n<figure class=\"wp-block-table has-small-font-size\"><table><thead><tr><th><strong>Format \/ Vendor<\/strong><\/th><th><strong>Comments<\/strong><\/th><\/tr><\/thead><tbody><tr><td><strong>OME-TIFF<\/strong><\/td><td>Brightfield and fluorescence. <br>Z-stacks and timelines supported (mutually-exclusive). <br>No multi-file support.<\/td><\/tr><tr><td><strong>DICOM-WSI<\/strong><\/td><td>Brightfield only<\/td><\/tr><tr><td><strong>Aperio SVS<\/strong><\/td><td>Brightfield only<\/td><\/tr><tr><td><strong>Hamamatsu NDPI &amp; NDPIS<\/strong><\/td><td>Brightfield and fluorescence<\/td><\/tr><tr><td><strong>3DHISTECH Mirax<\/strong><\/td><td>Brightfield and fluorescence (3 channels only)<\/td><\/tr><tr><td><strong>Roche Ventana TIFF<\/strong><\/td><td>Brightfield only<\/td><\/tr><tr><td><strong>MetaMorph TIFF<\/strong><\/td><td>Fluorescence only. Z-stacks supported<\/td><\/tr><tr><td><strong>Leica SCN<\/strong><\/td><td>Brightfield and fluorescence<\/td><\/tr><tr><td><strong>PreciPoint VMIC<\/strong><\/td><td>Brightfield only&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<\/td><\/tr><tr><td><strong>Olympus VSI<\/strong><\/td><td>Brightfield and fluorescence<\/td><\/tr><tr><td><strong>Zeiss CZI<\/strong><\/td><td>Brightfield and fluorescence. Z-stacks supported<br>Support must be unlocked. Get in touch for further details.<\/td><\/tr><tr><td><strong>Kfbio<\/strong><\/td><td>Brightfield only. Use *.svs format<\/td><\/tr><tr><td><strong>Perkin Elmer QPI<\/strong><\/td><td>Brightfield and fluorescence<\/td><\/tr><tr><td><strong>NanoString GeoMX TIFF<\/strong><\/td><td>Image only (not RNAs)<\/td><\/tr><tr><td><strong>Akoya Biosciences QPTIFF<\/strong><\/td><td>Fluorescence<\/td><\/tr><tr><td><strong>Lunaphore Ome-TIFF<\/strong><\/td><td>Fluorescence<\/td><\/tr><tr><td><strong>MACSima TIFFs <\/strong><\/td><td>Fluorescence<\/td><\/tr><tr><td><strong>Keyence TIFF<\/strong><\/td><td>Brightfield and fluorescence<\/td><\/tr><tr><td><strong>Motic TIFF<\/strong><\/td><td>Brightfield only<\/td><\/tr><tr><td><strong>ImageJ TIFF<\/strong><\/td><td>Brightfield only<\/td><\/tr><tr><td><strong>multipe TIFFs<\/strong> (one per channel)<br><\/td><td>multiple TIFFs (one per channel) can be combined into a multiplex<br>fluorescence scan by placing a CSV file next to it with the <br>*.multifile.csv extension. Details explained in the user manual.<\/td><\/tr><\/tbody><\/table><figcaption class=\"wp-element-caption\">If you are missing a format, let us know. Notably, Philips *.iSyntax, or *.kfbio are currently not supported.<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Importable &#8220;flat&#8221; image file formats<\/h2>\n\n\n\n<p>The following &#8220;flat&#8221; image formats can be opened:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>JPG \/ JPEG<\/li>\n\n\n\n<li>PNG<\/li>\n\n\n\n<li>BMP<\/li>\n\n\n\n<li>TIF \/ TIFF<\/li>\n<\/ul>\n\n\n\n<p>These images can be interpreted as<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>RGB bright-field image or<\/li>\n\n\n\n<li>3-channel fluorescence image.<\/li>\n<\/ol>\n\n\n\n<p>When opening an image, MIKAIA<sup>\u00ae<\/sup> will prompt you how to interpret the image and also ask for the resolution in \u00b5m\/px.<\/p>\n\n\n\n<p>When opening a flat image for the first time, the prompt pops up. You can optionally choose to save the settings, either for this image only or for all images contained in the same folder. The settings will then be saved into a small text file in that folder.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" width=\"550\" height=\"275\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-2.png\" alt=\"\" class=\"wp-image-2129\" style=\"width:314px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-2.png 550w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-2-300x150.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-2-370x185.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-2-270x135.png 270w\" sizes=\"(max-width: 550px) 100vw, 550px\" \/><\/figure>\n\n\n\n<p>These format settings can be changed later at any time, either<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>by clicking Main Menu | Slide | Format Settings \u2026 or<\/li>\n\n\n\n<li>by using the context menu of an item in the work space (in album view mode).<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Exportable image file formats<\/h2>\n\n\n\n<p>MIKAIA<sup>\u00ae<\/sup> can convert brightfield images or scans into these formats:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Brightfield only\n<ul class=\"wp-block-list\">\n<li>Leica SVS<\/li>\n\n\n\n<li>OME-TIFF<\/li>\n\n\n\n<li>DeepZooom (+ single-file html document with openseadragon WSI viewer)<\/li>\n\n\n\n<li>flat image formats (*.jpg, *.png, *.bmp).<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Brightfield and Fluorescence\n<ul class=\"wp-block-list\">\n<li>OME-TIFF<\/li>\n\n\n\n<li>flat image formats (*.jpg, *.png, *.bmp).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\n\n\n<p>For all formats, it is possible to crop &amp; export, e.g., exporting only a ROI or the current field-of view (FoV). Additionally, the export can have a lower resolution (\u00b5m\/px).<\/p>\n\n\n\n<p>When exporting into a flat format (*.jpg, *.png, *.bmp), the overlays can optionally be burnt in.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img decoding=\"async\" width=\"602\" height=\"653\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3.png\" alt=\"\" class=\"wp-image-2130\" style=\"width:344px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3.png 602w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3-277x300.png 277w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3-370x401.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3-270x293.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/image-3-570x618.png 570w\" sizes=\"(max-width: 602px) 100vw, 602px\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Importable annotation file formats<\/h2>\n\n\n\n<p>MIKAIA<sup>\u00ae<\/sup> can import the following annotation formats:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>*.geojson (can be imported by QuPath)<\/li>\n\n\n\n<li>*.xml (Leica) (can be imported by Leica ImageScope)<\/li>\n\n\n\n<li>*.dat file from a 3DHISTECH mrxs scan<\/li>\n\n\n\n<li>*.ano (MIKAIA<sup>\u00ae<\/sup>&#8216;s proprietary format; actually XML in uncompressed zip)<\/li>\n\n\n\n<li>*.csv.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Exportable annotation file formats<\/h2>\n\n\n\n<p>MIKAIA<sup>\u00ae<\/sup> can export annotations into the following annotation formats:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>*.geojson (can be exported by QuPath)<\/li>\n\n\n\n<li>*.xml as created by Leica ImageScope<\/li>\n\n\n\n<li>*.csv. (one row per annotation, with some attributes and micron-coordinates as text)<\/li>\n\n\n\n<li>*.tif mask (e.g. for importing into MACS\u00ae iQ View)<\/li>\n\n\n\n<li>*.ano (MIKAIA<sup>\u00ae<\/sup>&#8216;s proprietary format; actually XML in uncompressed zip).<\/li>\n<\/ul>\n\n\n\n<p>The free Annotation Image Export App included in MIKAIA<sup>\u00ae<\/sup> lite can also generate grey-level annotation masks as they are required for training of segmentation AIs.<\/p>\n\n\n\n<p>For more information about I\/O formats and MIKAIA<sup>\u00ae<\/sup>, feel free to reach out to us. Please also check out our app notes in the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-university\/\">MIKAIA<sup><sup>\u00ae<\/sup><\/sup> University<\/a>.<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<p>Image copyright: Fraunhofer IIS<\/p>\n","protected":false},"excerpt":{"rendered":"<p>MIKAIA\u00ae supports various I\/O formats, find out which ones. Importable whole-slide-image file formats Format \/ Vendor Comments OME-TIFF Brightfield and fluorescence. Z-stacks and timelines supported (mutually-exclusive). No multi-file support. DICOM-WSI Brightfield only Aperio SVS Brightfield only Hamamatsu NDPI &amp; NDPIS Brightfield and fluorescence 3DHISTECH Mirax Brightfield and fluorescence (3 channels only) Roche Ventana TIFF Brightfield [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":2134,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,35,28,24],"tags":[110,7,29],"coauthors":[56],"class_list":["post-2128","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-digital-pathology","category-life-science","category-mikaia-university","category-spatial-biology","tag-concept","tag-mikaia","tag-mikaia-app-note"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>WSI and Annotation File Format I\/O Support in MIKAIA - SMART SENSING insights<\/title>\n<meta name=\"description\" content=\"MIKAIA supports various WSI and annotation file formats I\/O, such as SVS, MRXS, OME-TIF, DICOM, QPTIFF, NDPI, and many more.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"WSI and Annotation File Format I\/O Support in MIKAIA - SMART SENSING insights\" \/>\n<meta property=\"og:description\" content=\"MIKAIA supports various WSI and annotation file formats I\/O, such as SVS, MRXS, OME-TIF, DICOM, QPTIFF, NDPI, and many more.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/\" \/>\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=\"2024-05-29T12:10:15+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-10-14T09:12:12+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2024\/05\/MIKAIA-File-Formats-1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"2549\" \/>\n\t<meta property=\"og:image:height\" content=\"1079\" \/>\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=\"4 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-io-formats\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\"},\"author\":{\"name\":\"Volker Bruns\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#\\\/schema\\\/person\\\/fd37d35c4d3576840cf0bc3f74eafb98\"},\"headline\":\"WSI and Annotation File Format I\\\/O Support in MIKAIA\",\"datePublished\":\"2024-05-29T12:10:15+00:00\",\"dateModified\":\"2025-10-14T09:12:12+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\"},\"wordCount\":652,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#organization\"},\"image\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/wp-content\\\/uploads\\\/2024\\\/05\\\/MIKAIA-File-Formats-1.jpg\",\"keywords\":[\"Concept\",\"MIKAIA\u00ae\",\"MIKAIA\u00ae App Note\"],\"articleSection\":[\"Digital Pathology\",\"Life Science\",\"MIKAIA University\",\"Spatial Biology\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\",\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/mikaia-io-formats\\\/\",\"name\":\"WSI and Annotation File Format I\\\/O Support in MIKAIA - 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