MIKAIA® University App Notes are blog articles, where we describe a particular MIKAIA® app or a medical use case in a step-by-step fashion. Our app notes typically describe what the expected input images look like and what quantitative outputs can be generated. They contain many screenshots and explain the concepts or in some cases even the technical background of the image analysis apps.
We are frequently releasing new app notes.
Gallery
IHC Cell Quantification AI Gallery
This gallery shows results of MIKAIA’s AIs for IHC cell analysis for various IHC markers and organs in both human and mouse tissue.
new: 15.7.2025
Use Case
Overview of mIF cell segmentation, phenotyping and spatial analysis capabilities
Videos of AI Cell Segmentation + Cell Typing + Cell-cell Connections + Cellular Neighborhoods + Density Heatmaps + Grid Analysis + Proximity Analysis + Spatial Clustering
new: 22.5.2025
Use Case
Analyzing MACSima 47-plex mIF with MIKAIA
AI Cell Segmentation + Cell Typing + Cell-cell Connections + Cellular Neighborhoods
Concept
MIKAIA Cellular Neighborhood App
The Cellular Neighborhood does two insightful analyses at once
Use Case
Proximity Analysis
Quantifying Cell Subpopulations in Vicinity of Intratumoral Microdevice (IMD)
Use Case
Programming-free Single Cell Analysis of CODEX TMA with MIKAIA
Poster at Europ. Spatial Bio conference in Dec 2024, Berlin, together with TU Munich
Use Case
Quantify histological growth pattern or spatial heterogeneity with the Grid Analysis App
Result of Grid Analysis App shows histological growth pattern and spatial heterogeneity
Workflow
MIKAIA Plugin API: “Plug in your own AI”
How bioinformaticians plug in their own Python (or other) scripts into the MIKAIA® app center
Use Case
Build H&E Analysis using multiple AIs
Video 1: Quantify cells in colon mucosa
Video 2: Detect tumor infiltratring lymphocytes (TILs)
Use Case
Differential IHC Cell Detection by ROI
Video: Count IHC+ cells and compare inside vs outside metastasis
Concept
WSI and Annotation File Format I/O Support in MIKAIA
MIKAIA® supports various I/O formats, find out which ones
Use Case
Quantifying Perineural Invasion in Duplex IHC
… using the Mask-by-Color App and stain deconvolution
Concept
Annotation Concepts in MIKAIA for Whole-Slide-Images
Learn about MIKAIA® annotation concepts, tools, etc.
Use Case
IHC Profiler – Assessing new IHC assay using multi-organ TMA
Computing intensity and positive area per core
Workflow
Spatial Clustering App
Grouping spatially adjacent cells into clusters and computing histogram of cluster sizes
Use Case
MIKAIA-Analysis of Human Pancreas 4plex Scanned with NanoString GeoMx DSP
Cell segmentation & cell-cell-connections
Use Case
MIKAIA-Analysis of Human Tonsil 15plex Imaged with Akoya PhenoCycler-Fusion
Cell segmentation & cell-cell-connections
Workflow
FL Cell Analysis App
AI segmentation of nuclei or membrane. Phenotype by marker, by co-expression, or by clustering
Workflow
Tile Export App
Exporting tiles, optionally with masks, to train AIs outside of MIKAIA®
available in MIKAIA® lite
Workflow
IHC Cell Detection App
Quantifying IHC+ and IHC- cells in most nuclear, membranous, or cytoplasmic stains. Finding hotspots, cluster, group by ROI.
