{"id":4730,"date":"2025-11-12T12:26:21","date_gmt":"2025-11-12T11:26:21","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=4730"},"modified":"2026-01-27T13:19:28","modified_gmt":"2026-01-27T12:19:28","slug":"divide-by-roi","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/","title":{"rendered":"Analyzing and Comparing Regions of Interest \u2013 \u201cDivide by ROIs\u201d Special"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">What makes <a href=\"http:\/\/www.mikaia.ai\">MIKAIA<sup>\u00ae<\/sup><\/a> a powerful tool for image analysis is its ability to compute statistics and make comparisons not only between scans, but also within a scan between different regions of interests (ROIs). One key feature, the \u201cDivide by ROIs\u201d option, available in MIKAIA\u2019s analysis apps, allows users to aggregate statistics and gain a clearer understanding of how cell populations differ across various regions of interest. The concept is very generic, but concrete examples include:<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Count positive cells both inside a metastasis and in the surrounding microenvironment<\/li>\n\n\n\n<li>Calculate immune cell density in the metastasis core, across three bands of inwards and outwards concentric margins, and the remaining area outside of the tumor.<\/li>\n\n\n\n<li>Analyze IHC staining across TMA cores.<\/li>\n<\/ol>\n\n\n\n<p class=\"wp-block-paragraph\">If you\u2019re using MIKAIA<sup>\u00ae <\/sup>for the first time or if you haven\u2019t explored all its features yet, you might find that the Divide by ROIs option requires a little extra guidance. That\u2019s exactly what this <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-university-app-notes\/\">MIKAIA<sup>\u00ae<\/sup> University app note<\/a> aims to do: break down the terminology and guide you through the necessary steps to make comparisons within a slide\u2019s image.<\/p>\n\n\n\n\n\n\n<div id=\"ez-toc-container\" class=\"ez-toc-v2_0_84 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\/divide-by-roi\/#Scan_areas_Analyzing_specimens_individually_on_multi-specimen_slides\" >Scan areas: Analyzing specimens individually on multi-specimen slides<\/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\/divide-by-roi\/#Special_case_TMAs\" >Special case: TMAs<\/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\/divide-by-roi\/#Defining_and_analyzing_regions_of_interest\" >Defining and analyzing regions of interest<\/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\/divide-by-roi\/#Options_for_analyzing_ROIs\" >Options for analyzing ROIs<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-5\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/#Option_1_Analyzing_a_specific_ROI_or_multiple_ROIs\" >Option 1: Analyzing a specific ROI or multiple ROIs<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-6\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/#Option_2_Batch-analyzing_ROIs\" >Option 2: Batch-analyzing ROIs<\/a><\/li><\/ul><\/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\/divide-by-roi\/#Divide_by_ROIs\" >Divide by ROIs<\/a><ul class='ez-toc-list-level-3' ><li class='ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-8\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/#Step_1_Define_ROIs\" >Step 1: Define ROIs<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-9\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/#Step_2_Assign_detected_cells_into_separate_classes\" >Step 2: Assign detected cells into separate classes<\/a><\/li><li class='ez-toc-page-1 ez-toc-heading-level-3'><a class=\"ez-toc-link ez-toc-heading-10\" href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/#Step_3_Results\" >Step 3: Results<\/a><\/li><\/ul><\/li><\/ul><\/nav><\/div>\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Scan_areas_Analyzing_specimens_individually_on_multi-specimen_slides\"><\/span>Scan areas: Analyzing specimens individually on multi-specimen slides<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">When glass slides contain multiple specimens (e.g., to save scanning time or when working with Tissue Microarrays, see below), the scan must first be subdivided into scan areas so you can compute statistics for each specimen individually. You can create scan areas either manually or automatically by using the Tissue Detection App.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">If you choose to draw scan areas manually, start by creating a special class \u201cScan Areas\u201d using the option in the annotation classes side panel\u2019s toolbar menu.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"438\" height=\"433\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image.png\" alt=\"create a special class \u201cScan Areas\u201d in the options menu\" class=\"wp-image-4734\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image.png 438w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-300x297.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-370x366.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-270x267.png 270w\" sizes=\"auto, (max-width: 438px) 100vw, 438px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">Then, draw a rectangle for each scan area, ensuring that the areas do not overlap. For each rectangle, enter a text label that will be used as the scan area name. If you don\u2019t provide a label, the scan areas will be automatically assigned names like &#8216;Scan Area 1,&#8217; &#8216;Scan Area 2,&#8217; and so forth.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"945\" height=\"448\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1.png\" alt=\"Illustration of two scan areas\" class=\"wp-image-4735\" style=\"width:588px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1.png 945w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-300x142.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-768x364.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-370x175.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-270x128.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-570x270.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1-740x351.png 740w\" sizes=\"auto, (max-width: 945px) 100vw, 945px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">Once scan areas are created, all image analysis apps that support the \u201cDivide by ROIs\u201d functionality in their configuration panel will be able to collect separate statistics per scan area, provided the \u201cDivide by Scan Areas\u201d option is enabled (see below).<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Special_case_TMAs\"><\/span>Special case: TMAs<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">In the case of Tissue Microarrays (TMAs), each TMA core constitutes a scan area. The Tissue Detection App can be configured to automatically create one scan area per TMA Core (see figure below). This way, downstream analysis apps such as the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ihc-cell-detection-app\/\">IHC Cell Detection App<\/a>, the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">FL Cell Analysis App<\/a>, or the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/ihc-profiler-in-mikaia\/\">Annotation Metrics App<\/a> will automatically compute statistics separately per TMA core.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Please refer to the <a href=\"https:\/\/www.iis.fraunhofer.de\/en\/ff\/sse\/health\/medical-image-analysis\/mikaia\/manual.html\">MIKAIA<sup>\u00ae<\/sup> manual<\/a> to learn more about TMA de-arraying options.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"945\" height=\"724\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2.png\" alt=\"illustration of TMA cores\" class=\"wp-image-4747\" style=\"width:548px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2.png 945w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-300x230.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-768x588.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-370x283.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-270x207.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-570x437.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-740x567.png 740w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-2-80x60.png 80w\" sizes=\"auto, (max-width: 945px) 100vw, 945px\" \/><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Defining_and_analyzing_regions_of_interest\"><\/span>Defining and analyzing regions of interest<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">When preparing slides for analysis, you might not only want to subdivide them into scan areas, but define additional regions of interest (ROIs), e.g., to distinguish a metastasis and the surrounding microenvironment.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"945\" height=\"438\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3.png\" alt=\"Illustration of ROI concept\" class=\"wp-image-4748\" style=\"width:579px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3.png 945w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-300x139.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-768x356.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-370x171.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-270x125.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-570x264.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-3-740x343.png 740w\" sizes=\"auto, (max-width: 945px) 100vw, 945px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">In MIKAIA<sup>\u00ae<\/sup>, you can define ROIs manually (e.g., by arbitrarily drawing&nbsp;a freeform annotation) or automatically by using one of the tissue analysis apps (<a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-ai-authoring-app\/\">AI Author<\/a>, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-multiple-he-ais\/\">H&amp;E Crypt AI App<\/a>, or Mask-by-Color App.)&nbsp; The ROIs you or the app define serve as the basis for subsequent cell-analysis.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Ultimately, you can define as many ROIs as necessary and aggregate your analyses using the \u201cDivide by ROIs\u201d analysis option (<a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=4730#1_Define_ROIs\">see below<\/a>).<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">As outlined in our <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/annotation-concepts-in-mikaia\/#Before_analysis_Tissue_detection_division_into_Scan_Areas_and_ROIs\">Annotation Concepts for Whole-Slide-Images<\/a>&nbsp;, MIKAIA<sup>\u00ae<\/sup> models a hierarchy for each ROI class. If you have a slide with two specimens (i.e., two scan areas), the analysis app will group detected cells by both scan area and ROI.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"945\" height=\"567\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4.png\" alt=\"illustration of ROI hierarchy\" class=\"wp-image-4749\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4.png 945w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-300x180.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-768x461.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-370x222.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-270x162.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-570x342.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-4-740x444.png 740w\" sizes=\"auto, (max-width: 945px) 100vw, 945px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">The class \u201cScan Area 1 | Metastasis\u201d, for example, will include only the cells located within the boundaries of that specific annotation.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Options_for_analyzing_ROIs\"><\/span>Options for analyzing ROIs<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Option_1_Analyzing_a_specific_ROI_or_multiple_ROIs\"><\/span><strong>Option 1: Analyzing a specific ROI or multiple ROIs<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">In the analysis configuration panel, you can select the mode \u201cRoI\u201d to analyze a specific region of interest. Alternatively, by selecting multiple annotations, you can analyze several ROIs in a single run.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"260\" height=\"38\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-1.jpg\" alt=\"\" class=\"wp-image-4752\"\/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Option_2_Batch-analyzing_ROIs\"><\/span><strong>Option 2: Batch-analyzing ROIs<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">If you have two or more slides selected in the \u201cSlides\u201d pane, you can choose to analyze the selected slides entirely or by ROI. Make sure to check the selected mode: It should say \u201cRoI: entire slides\u201d right next to the \u201cBatch\u201d button or show the class name of the selected ROI.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"382\" height=\"36\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image.jpg\" alt=\"\" class=\"wp-image-4751\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image.jpg 382w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-300x28.jpg 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-370x35.jpg 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-270x25.jpg 270w\" sizes=\"auto, (max-width: 382px) 100vw, 382px\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"488\" height=\"37\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5.png\" alt=\"\" class=\"wp-image-4750\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5.png 488w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5-300x23.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5-370x28.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5-270x20.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-5-470x37.png 470w\" sizes=\"auto, (max-width: 488px) 100vw, 488px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">In the \u201cGeneral Settings\u201d pane, you can specify which existing annotations (i.e., ROI classes) the app will analyze.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1017\" height=\"577\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10.png\" alt=\"\u201cGeneral Settings\u201d pane\" class=\"wp-image-4761\" style=\"width:418px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10.png 1017w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-300x170.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-768x436.png 768w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-370x210.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-270x153.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-570x323.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-10-740x420.png 740w\" sizes=\"auto, (max-width: 1017px) 100vw, 1017px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">For more complex analyses, the \u201c<strong>Divide by ROIs<\/strong>\u201d option will streamline your workflow, allowing you to compile analyses and compare ROIs across a slide.<a id=\"_msocom_1\"><\/a><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Divide_by_ROIs\"><\/span>Divide by ROIs<span class=\"ez-toc-section-end\"><\/span><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">In downstream analysis apps, the \u201cDivide by ROIs\u201d functionality helps you analyze detected cells by sorting them based on their location in relation to specific regions of interest marked on the slide. (Note that that defining scan areas is not a prerequisite for using the Divide by ROIs feature.)<\/p>\n\n\n\n<figure class=\"wp-block-table\"><table class=\"has-fixed-layout\"><tbody><tr><td><strong>Analysis Apps featuring the \u201cDivide by ROIs\u201d functionality<\/strong><\/td><\/tr><tr><td>IHC Cell Detection App<\/td><\/tr><tr><td>FL Cell Analysis App<\/td><\/tr><tr><td><a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-multiple-he-ais\/\">H&amp;E Cell AI App<\/a><\/td><\/tr><tr><td>Mask-by-Color App<\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">Downstream analysis apps, such as the <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-fl-colocalization-app\/\">Cell-Cell-Connections App<\/a>, <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/proximity-analysis-imd\/#proximity-analysis-app\">Proximity Analysis App<\/a>, and <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-cellular-neighborhood-app\/\">Cellular Neighborhood App<\/a>, will recognize that cell types are separated by ROIs and maintain this information when analyzing spatial relationships between objects detected by the above-mentioned apps.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">With the \u201cDivide by ROIs\u201d feature, you can easily compare different tissue areas,&nbsp;which streamlines your analysis process. So, how does the \u201cDivide by ROI\u201d fit into your analysis workflow?<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Step_1_Define_ROIs\"><\/span>Step 1: Define ROIs<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">Define ROIs either by manually drawing annotations or by creating them automatically using an app, such as the AI Author App or Mask-by-Color App. These tools can generate masks that serve as ROIs for subsequent cell analyses.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"767\" height=\"638\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7.png\" alt=\"Divide by ROIs section in the Configuration menu\" class=\"wp-image-4755\" style=\"width:445px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7.png 767w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7-300x250.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7-370x308.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7-270x225.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7-570x474.png 570w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-7-740x616.png 740w\" sizes=\"auto, (max-width: 767px) 100vw, 767px\" \/><\/figure>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Specify what existing annotation classes shall be interpreted as ROIs. Select these in the <strong>\u201cDivide by ROIs\u201d section<\/strong> in the app\u2019s configuration panel (see screenshot above).<\/li>\n\n\n\n<li><strong>Choose annotation classes<\/strong>: Here, you can select your predefined annotation classes (e.g., \u201cMetastasis\u201d, \u201cMicroenvironment\u201d) or click the box to \u201cToggle All.\u201d Make sure, though, that the selected ROIs do not overlap!<\/li>\n\n\n\n<li><strong>ROIs \u201cOther\u201d<\/strong>: Once at least one ROI is selected, the ROI \u201cOther\u201d (or \u201cno RoI\u201d or \u201crest\u201d, depending on the app) will be added automatically (see screenshot below). This means, for example, that when you\u2019re assessing areas solely around a metastasis and not using more fine-grained annotations, you do not need to explicitly include \u201cnon-tumor\u201d annotations and the like.&nbsp;<\/li>\n\n\n\n<li><strong>Enable \u201cDivide by Scan Areas\u201d:<\/strong> By default, the \u201cDivide by Scan Areas\u201d option is enabled allowing the app to collect statistics separately for each scan area.<\/li>\n\n\n\n<li><strong>ROIs intersecting tissue area<\/strong>: Note that if any of the selected ROIs extend beyond the detected or manually created tissue area, only the intersection between the ROI and the designated <a href=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/annotation-concepts-in-mikaia\/#Special_Classes_%E2%80%9CIgnore%E2%80%9D_%E2%80%9CTissue%E2%80%9D_%E2%80%9CScan_Areas%E2%80%9D\">&#8220;Tissue&#8221; class<\/a>&nbsp;will be included in the analysis.<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"459\" height=\"298\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-8.png\" alt=\"\" class=\"wp-image-4756\" style=\"width:306px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-8.png 459w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-8-300x195.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-8-370x240.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-8-270x175.png 270w\" sizes=\"auto, (max-width: 459px) 100vw, 459px\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Step_2_Assign_detected_cells_into_separate_classes\"><\/span>Step 2: <strong>Assign detected cells into separate classes<\/strong><span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">The app will now assign detected cells into separate classes (by location) and evaluate the statistics individually for each area. In doing so, the app will not create a single class \u201cpositive\u201d, for example, but a number of classes denoted as \u201c&lt;ROI name&gt;: positive\u201d, depending on the number of ROIs you selected earlier.<\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"597\" height=\"259\" src=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9.png\" alt=\"\" class=\"wp-image-4758\" style=\"width:415px;height:auto\" srcset=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9.png 597w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9-300x130.png 300w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9-370x161.png 370w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9-270x117.png 270w, https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/image-9-570x247.png 570w\" sizes=\"auto, (max-width: 597px) 100vw, 597px\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\"><span class=\"ez-toc-section\" id=\"Step_3_Results\"><\/span>Step 3: Results<span class=\"ez-toc-section-end\"><\/span><\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">The app displays results in both bar diagrams and tables, showing absolute and relative values. You can copy the table by right-clicking and selecting &#8220;Copy to Clipboard,&#8221; or alternatively, you can export all metrics to a CSV file for downstream analysis using Excel, R, or other tools. The CSV file contains one row per class, along with separate rows for each individual annotation instance within these classes.<\/p>\n\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity\"\/>\n\n\n\n<p class=\"wp-block-paragraph\">Copyright images:&nbsp;<strong>\u00a9<\/strong>Fraunhofer IIS<a id=\"_msocom_1\"><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The \u201cDivide by ROIs\u201d feature in MIKAIA\u2019s analysis apps enables users to compile statistics and enhance their understanding of variations in cell populations. This functionality allows for comparisons between user-defined regions as well as across different scan regions, supporting a thorough examination of spatial relationships within a single image. This app note offers guidance on using the Divide by ROIs feature, clarifying terminology and detailing the essential steps for effective image comparison.<\/p>\n","protected":false},"author":9,"featured_media":4763,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3,28],"tags":[87,7,29,111],"coauthors":[51],"class_list":["post-4730","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-digital-pathology","category-mikaia-university","tag-ihc","tag-mikaia","tag-mikaia-app-note","tag-workflow"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Analyzing and Comparing Regions of Interest \u2013 \u201cDivide by ROIs\u201d Special - SMART SENSING insights<\/title>\n<meta name=\"description\" content=\"MIKAIA\u2019s &quot;Divide by ROIs&quot; feature helps users compile statistics and understand cell population variations. This app note introduces key terms and steps.\" \/>\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\/divide-by-roi\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Analyzing and Comparing Regions of Interest \u2013 \u201cDivide by ROIs\u201d Special - SMART SENSING insights\" \/>\n<meta property=\"og:description\" content=\"MIKAIA\u2019s &quot;Divide by ROIs&quot; feature helps users compile statistics and understand cell population variations. This app note introduces key terms and steps.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/divide-by-roi\/\" \/>\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=\"2025-11-12T11:26:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-01-27T12:19:28+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/wp-content\/uploads\/2025\/11\/Bild7.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1920\" \/>\n\t<meta property=\"og:image:height\" content=\"1040\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"Grit Nickel\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Grit Nickel\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"9 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\\\/divide-by-roi\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/\"},\"author\":{\"name\":\"Grit Nickel\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#\\\/schema\\\/person\\\/fc55925f8da111629c277bcedf848c5e\"},\"headline\":\"Analyzing and Comparing Regions of Interest \u2013 \u201cDivide by ROIs\u201d Special\",\"datePublished\":\"2025-11-12T11:26:21+00:00\",\"dateModified\":\"2026-01-27T12:19:28+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/\"},\"wordCount\":1282,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#organization\"},\"image\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/wp-content\\\/uploads\\\/2025\\\/11\\\/Bild7.png\",\"keywords\":[\"IHC\",\"MIKAIA\u00ae\",\"MIKAIA\u00ae App Note\",\"Workflow\"],\"articleSection\":[\"Digital Pathology\",\"MIKAIA University\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/\",\"url\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/\",\"name\":\"Analyzing and Comparing Regions of Interest \u2013 \u201cDivide by ROIs\u201d Special - SMART SENSING insights\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/divide-by-roi\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/websites.fraunhofer.de\\\/smart-sensing-insights\\\/wp-content\\\/uploads\\\/2025\\\/11\\\/Bild7.png\",\"datePublished\":\"2025-11-12T11:26:21+00:00\",\"dateModified\":\"2026-01-27T12:19:28+00:00\",\"description\":\"MIKAIA\u2019s \\\"Divide by ROIs\\\" feature helps users compile statistics and understand cell population variations. 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