MIKAIA® University

the central MIKAIA® learning portal
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(note: in February 2024 MICAIA was renamed to MIKAIA®)

MIKAIA® University is the central MIKAIA® learning portal. Here you can find various App Notes and Video Tutorials that describe typical MIKAIA® workflows either from a technical or medical perspective. As we are continuously adding more content, please check back frequently or subscribe to the MIKAIA® newsletter, where we announce newly released app notes.

Table of Contents

Apps & AIs

MIKAIA® 2.0 includes 16 Apps.
The AI Author App and Plug-in your own AI App can be used to develop additional user-specific apps.

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More details, incl. a description of each app is available here.

Concepts

Just like Stuttgart Public Library, MIKAIA University is a hub for learning.

1. Annotation Concepts in MIKAIA®

2. Image and Annotation File Format Support

App Notes

1. IHC Cell Detection App – Immune cell infiltration in Tumor Microenvironment

2. Tile Export App – Create your own AI Training Dataset

3. AI Authoring App – Train your own AI Interactively. Only very few annotations required

4. FL Cell Analysis App – Cell segmentation and Marker Co-expression Analysis in mIF High-plexes

5. Analysis of Human Tonsil 15plex Imaged with Akoya PhenoCycler Fusion

6. Analysis of Human Pancreas 4plex scanned with NanoString GeoMx DSP

7. Spatial Clustering App – Cell Clustering Profile for IHC Assays

8. Annotation Metrics App / IHC Profiler – Assessing new IHC Assay using Multi-organ TMA

9. FISH HER2/neu App – Nuclei and FISH Spots Detection

10. Quantifying Perineural Invasion in Duplex-IHC

11. Differential IHC Cell Detection by ROI ^{(new: July 17th 2024)}

12. Build H&E Analysis Using multiple AIs ^{(new: July 17th 2024)}

13. Plug-in your Own AI: MIKAIA® Plugin API ^{(new: July 26th 2024)}

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.

User Manual

A detailed 90+ pages user manual is included in the free MIKAIA® installer (download here) and available from within MIKAIA® by clicking “User Manual” in the main “Help” menu.

MIKAIA® Configurations

Don’t worry about selecting which apps you want to purchase. You do not need to select each individual app. Currently, three feature sets are available:

MIKAIA® lite (free)
MIKAIA® studio
MIKAIA® studio + AI App Bundle

If you’d like to try out the MIKAIA® apps on a temporary basis or request a quote, please feel free to email us at mikaia@iis.fraunhofer.de.

Licensing Options

By default, we offer perpetual licenses, i.e., once activated, features are available forever, without any follow-up costs.

A license can be node-locked, which means it is locked to a particular PC, or alternatively, we offer single-user or multi-user floating licenses. Here, the activation file is imported on a server in your network. MIKAIA® can then be installed on any computer in your network or on a (VPN-connected) home office laptop. At startup, MIKAIA® will automatically detect the license server and, if a user-slot of the single- or multi-user license is currently free, it will start up as MIKAIA® studio, else as MIKAIA® lite. The licensing modes are also illustrated in the MIKAIA® product brochure.

Working collaboratively

Even though MIKAIA® is not a web-based software, it still can be used collaboratively: The free MIKAIA® lite edition can be used to create annotations manually, but it can also view annotations generated by an analysis conducted with MIKAIA® studio. In other words, user A can run an analysis with MIKAIA® studio on computer A, and later users B-Z can view the results on their own computers using the free MIKAIA® lite edition. MIKAIA® stores annotations decentrally in a small *.ano file next to the whole-slide-image file:

This is handy, because it enables users to move the slide (incl. *.ano file) into another folder and the connection between slide and annotation will not get broken. Users can also keep multiple versions of annotations, simply by creating copies of the *.ano file, or create backups of annotation files, for instance after they have created manual annotations.

It is also possible to create shortcuts to the slides and then put an *.ano file next to the shortcut. When opening the shortcut, MIKAIA® will open the annotations located next to the shortcut instead of the annotation file located next to the original slide. This way, multiple annotation sets can be maintained, without having to duplicate the (large) WSIs. MIKAIA® has built-in dialogs that can be used to batch-create shortcuts or retarget existing shortcuts (in case the original WSIs have been relocated).

Required Hardware and OS

Currently, MIKAIA® is available for Microsoft Windows, not for Linux or Mac OS.

We offer both an installer and a portable version. The installer is an *.exe file and it requires admin rights for installation. The portable version is a ZIP file that must be manually extracted and then MIKAIA.exe can be started from there. This process does not require admin rights.

AI-enabled image analysis apps run faster, when a NVIDIA CUDA-enabled GPU is available. We recommend a GeForce card with tensor cores, e.g. GeForce RTX 40xx. When no such GPU is available, the apps will still work and use the CPU instead.

MIKAIA® has good touch-support. Here, it is used on a touch-enabled screen

Both 2K and 4K displays are supported. MIKAIA® has also good touch-support. For creating accurate annotations, we recommend using a tablet with a stylus pen (we use WACOM tablets). At exhibitions, we sometimes show MIKAIA® on a touch-enabled digital whiteboard (we use a Samsung Flip 2).

Due to the large size of whole-slide-images, it is recommended to have 16 GB RAM or more.