Life Science Spatial Biology

Analyzing Singular Genomics G4X™ Multi-Omics Datasets with MIKAIA

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 morphology via fluorescent...

Volker Bruns

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Life Science Spatial Biology

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 analysis, helping laboratories...

Volker Bruns

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Life Science MIKAIA University Spatial Biology

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 choice, supporting three types of...

Volker Bruns

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Category - Spatial Biology

Browse through our Spatial Biology article collection around spatial proteomics and spatial transcriptomics, with a focus on data science.

MIKAIA screenshot of a 47-plex spatial proteomics scan created with a MACSima instrument

Life Science MIKAIA University Spatial Biology

Analyzing MACSima 47-plex mIF with MIKAIA: AI Cell Segmentation + Cell Typing + Cell-cell Connections + Cellular Neighborhoods

This MIKAIA® app note demonstrates how to analyze a 47-plex spatial proteomics scan created with MACSima ™ (by Miltenyi Biotec), utilizing sequential immunofluorescence for the analysis: Instrument: MACSima™ by Miltenyi...

Volker Bruns

April 25, 2025

Screenshot of the Cellular Neighborhood App

Digital Pathology Life Science MIKAIA University Spatial Biology

MIKAIA Cellular Neighborhood App Explained

The MIKAIA® Cellular Neighborhood App can yield statistics about the cellular microenvironment, i.e., identify cell niches or cellular communities. This presents a type of spatial analysis of cell populations detected...

Michaela Benz

March 10, 2025

Life Science Spatial Biology

Programming-free Single Cell Analysis of CODEX TMA with MIKAIA

CODEX, now called PhenoCycler, by Akoya Biosciences, along with other sequential immunofluorescence technologies (e.g., Lunaphore (Comet), Miltenyi Biotech (MACSima), Leica Microsystems (Cell DIVE), or other vendors)...

Volker Bruns

December 18, 2024

Digital Pathology MIKAIA University Spatial Biology

MIKAIA University

MIKAIA® University is the central MIKAIA® learning portal.
You will find various app notes and video tutorials that outline typical MIKAIA® workflows.

Volker Bruns

December 17, 2024

Digital Pathology Life Science Spatial Biology

2 Articles in Trillium Pathology 2024

We have contributed two article’s to this year’s Trillium Pathology issue. Here are the abstracts, with links to the full articles: V. Bruns, Programming-free Image-Analysis Workflows for IHC, IF and Spatial...

Volker Bruns

July 30, 2024

DNA string visualizing our Medical Buzzwords glossary

Digital Health Digital Pathology Spatial Biology

Glossary of Medical Buzzwords

In the fast-paced world of healthcare, staying informed about the latest medical buzzwords and trends is essential to understanding where the future of medicine is heading. From computer-aided diagnosis and personalized...

Julia Fröhlich

July 15, 2024

Spatial Biology

List of Commercial Spatial Biology Instruments, Assays & Softwares

Spatial Biology is a big hype right now and a rapidly growing discipline, especially spatial proteomics and spatial transcriptomics. It is the intersection of anatomical pathology where the morphology of tissue is...

Volker Bruns

July 9, 2024

Digital Pathology Life Science MIKAIA University Spatial Biology

WSI and Annotation File Format I/O Support in MIKAIA

MIKAIA® supports various I/O formats, find out which ones. Importable whole-slide-image file formats Format / VendorCommentsOME-TIFFBrightfield and fluorescence. Z-stacks and timelines supported (mutually-exclusive). No...

Volker Bruns

May 29, 2024

Digital Pathology MIKAIA University Spatial Biology

MIKAIA Spatial Clustering App

Tumor cells dynamically interact with their microenvironment to stimulate cancer development, progression, and metastasis. To understand the biology of the tumor-immune interactions, it is essential to identify tumoral...

Nathalie Falk

October 9, 2023

Digital Pathology MIKAIA University Spatial Biology

MIKAIA-Analysis of Human Pancreas 4plex Scanned with NanoString GeoMx DSP

In this MIKAIA® University application note, we guide you through the analysis of a common use case, coexpression of marker combinations in islets of Langerhans and surrounding tissue in a pancreas 4plex imaged with...

Nathalie Falk

August 3, 2023

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