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...
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
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 upcoming MIKAIA® 3 release (scheduled for Q1 2026), MIKAIA® will receive a new multi-omics slide alignment module, “MIKAIA® Slide Align“. Based on a 3-phase registration process, the last one being...
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
IHC Cell Detection App explained
The IHC Cell Detection 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 app...
MIKAIA mIF Cell Segmentation AI Gallery
This gallery highlights MIKAIA's mIF Cell Segmentation in the FL Cell Analysis App, featuring various examples and an overview of the AI's three segmentation modes and various cell typing options.
MIKAIA First Steps
New to MIKAIA®? This blog post is here to help you get started on your first steps.
