SMART SENSING insights

WSI and Annotation file format I/O support in MIKAIA®

Importable whole-slide-image file formats

Format / VendorComments
OME-TIFFBrightfield and fluorescence.
Z-stacks and timelines supported (mutually-exclusive).
No multi-file support.
DICOM-WSIBrightfield only
Aperio SVSBrightfield only
Hamamatsu NDPI & NDPISBrightfield and fluorescence
3DHISTECH MiraxBrightfield and fluorescence (3 channels only)
Roche Ventana TIFFBrightfield only
MetaMorph TIFFFluorescence only. Z-stacks supported
Leica SCNBrightfield only
PreciPoint VMICBrightfield only                                                                      
Olympus VSIBrightfield and fluorescence
Zeiss CZIBrightfield and fluorescence. Z-stacks supported
Support must be unlocked. Get in touch for further details.
Perkin Elmer QPIBrightfield and fluorescence
NanoString GeoMX TIFFImage only (not RNAs)
Akoya Biosciences QPTIFFFluorescence
Lunaphore Ome-TIFFFluorescence
Keyence TIFFBrightfield and fluorescence
Motic TIFFBrightfield only
ImageJ TIFFBrightfield only
If you are missing a format, let us know. Notably, Philips *.iSyntax or *.kfbio are currently not supported.

Importable “flat” image file formats

The following “flat” image formats can be opened:

  • JPG / JPEG
  • PNG
  • BMP
  • TIF / TIFF

These images can be interpreted as

  1. a RGB bright-field image or
  2. a 3-channel fluorescence image

When opening an image, MIKAIA will prompt you how to interpret the image and also ask for the resolution in µm/px.

When opening a flat image for the first time, the prompt pops up. You can optionally choose to save the settings, either for this image only or for all images contained in the same folder. The settings will then be saved into a small text file in that folder.

These format settings can be changed later at any time, either

  • By clicking Main Menu | Slide | Format Settings … or
  • By using the context menu of an item in the work space (in album view mode)

Exportable image file formats

MIKAIA can convert brightfield images or scans into these formats:

  • Leica SVS
  • DeepZooom (+ single-file html document with openseadragon WSI viewer)
  • flat image formats (jpg, png, bmp)

For all formats, it is possible to crop & export, e.g.exporting only a ROI or the current field-of view (FoV). Additionally, the export can have a lower resolution (µm/px).

When exporting into a flat format (jpg, png, bmp), the overlays can optionally be burnt in.

Importable annotation file formats

MIKAIA can import the following annotation formats

  • *.geojson (can be imported by QuPath)
  • *.xml (Leica) (can be imported by Leica ImageScope)
  • *.ano (MIKAIA’s proprietary format. Actually XML in uncompressed zip)
  • *.csv

Exportable annotation file formats

MIKAIA can export annotations into the following annotation formats

  • *.geojson (can be exported by QuPath)
  • *.xml as created by Leica ImageScope
  • *.dat file from a 3DHISTECH mrxs scan
  • *.ano (MIKAIA’s proprietary format. Actually XML in uncompressed zip)

The free Annotation Image Export App included in MIKAIA lite can also generate grey-level annotation masks as they are required for training of segmentation AIs.

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Questions, remarks, feature
requests, project inquiries, …
email us: mikaia@iis.fraunhofer.de

Dr. Volker Bruns
Group Manager
Medical Image Analysis (MIA)
Digital Health and Analytics | Fraunhofer IIS

Get started now

Download MIKAIA for free from www.mikaia.ai

Don’t miss any news

Sign up now for the MIKAIA newsletter

Get in touch with us

Questions, remarks, feature
requests, project inquiries, …
email us: mikaia@iis.fraunhofer.de

Dr. Volker Bruns
Group Manager
Medical Image Analysis (MIA)
Digital Health and Analytics | Fraunhofer IIS