MIKAIA® studio v3.1 includes native support for viewing and analyzing multi-omics datasets created with Singular Genomics’ G4X™ instrument. G4X features 500plex transcriptomics, 18plex proteomics and same-slide...
Tag - MIKAIA® App Note
MIKAIA University App Notes are blog articles that provide a detailed, step-by-step demonstration of specific MIKAIA® apps or medical use cases. They illustrate how MIKAIA® can be used to make discoveries or automate quantitative analysis in Digital Pathology & Spatial Biology.
Volker Bruns
Cell Typing and Neighborhood Analysis of mIF 20plex Tonsil Tissue Using MGI VisiOmics and MIKAIA studio
The collaboration aims to show how researchers can use VisiOmics image data within MIKAIA® workflows for cell segmentation, phenotyping, and spatial analysis. This work supports greater flexibility in downstream...
Xenium Analysis with the MIKAIA Cell x Gene App
The MIKAIA® Cell x Gene App can be used to analyze FISH (or similar, e.g., RNAscope), CISH, or spatial transcriptomics scans, including Xenium by 10x Genomics. For Xenium data in particular, this app is the right...
CISH App Explained
Chromogenic in situ hybridization (CISH) is used to detect specific DNA or RNA sequences in tissue samples. It uses enzyme-based staining rather than fluorescence (FISH), allowing for high-resolution imaging...
Train your own AI with the Segmentation AI Author: Ovarian Cancer Example
This MIKAIA® University app note demonstrates how to quickly and interactively train your own AI using just a few training annotations, all in a matter of minutes. In the app center, select the Segmentation AI Author...
Michaela Benz
Segmentation AI Author Example: Train H&E Vulvar Cancer AI Based on Aligned IHC Serial Sections
This MIKAIA® University app note illustrates how to interactively train a new H&E segmentation AI with serial sections, without having to annotate tumor regions. Instead, an IHC epithelial marker (pan-cytokeratin...
MIKAIA’s Slide Alignment: An Overview
With the MIKAIA® 3 release (April 2026), MIKAIA® received a new multi-omics slide alignment module, “MIKAIA® Slide Align“. Based on a 3-phase registration process, the last one being a non-rigid deformation...
Manual Spatial Proteomics: Fusing Cycles into OME-TIF was Never Easier
Spatial Proteomics was named the Nature Method of the Year 2024. One predominant method is Cyclic Immunofluorescence (CycIF). Here, a tissue sample is stained and scanned during a first cycle. Next, the stain is...
Analyzing and Comparing Regions of Interest – “Divide by ROIs” Special
The “Divide by ROIs” feature in MIKAIA’s analysis apps enables users to compile statistics and enhance their understanding of variations in cell populations. This functionality allows for comparisons between user...
Grit Nickel
MIKAIA’s Universal IHC Cell AI App explained
The Universal IHC Cell AI App features a universal subcellular IHC cell AI that is compatible with a wide range of markers, tissues, and cell types. Our 23-minute video tutorial guides MIKAIA® step by step through the...
