Volker BrunsMIKAIA® supports various I/O formats, find out which ones.
Importable whole-slide-image file formats
| Format / Vendor | Comments |
|---|---|
| OME-TIFF | Brightfield and fluorescence. Z-stacks and timelines supported (mutually-exclusive). No multi-file support. |
| DICOM-WSI | Brightfield only |
| Aperio SVS | Brightfield only |
| Hamamatsu NDPI & NDPIS | Brightfield and fluorescence |
| 3DHISTECH Mirax | Brightfield and fluorescence (3 channels only) |
| Roche Ventana TIFF | Brightfield only |
| MetaMorph TIFF | Fluorescence only. Z-stacks supported |
| Leica SCN | Brightfield and fluorescence |
| PreciPoint VMIC | Brightfield only |
| Olympus VSI | Brightfield and fluorescence |
| Zeiss CZI | Brightfield and fluorescence. Z-stacks supported Support must be unlocked. Get in touch for further details. |
| Kfbio | Brightfield only. Use *.svs format |
| Perkin Elmer QPI | Brightfield and fluorescence |
| NanoString GeoMX TIFF | Image only (not RNAs) |
| Akoya Biosciences QPTIFF | Fluorescence |
| Lunaphore Ome-TIFF | Fluorescence |
| MACSima TIFFs | Fluorescence |
| Keyence TIFF | Brightfield and fluorescence |
| Motic TIFF | Brightfield only |
| ImageJ TIFF | Brightfield only |
| multipe TIFFs (one per channel) | multiple TIFFs (one per channel) can be combined into a multiplex fluorescence scan by placing a CSV file next to it with the *.multifile.csv extension. Details explained in the user manual. |
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
- RGB bright-field image or
- 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:
- Brightfield only
- Leica SVS
- OME-TIFF
- DeepZooom (+ single-file html document with openseadragon WSI viewer)
- flat image formats (*.jpg, *.png, *.bmp).
- Brightfield and Fluorescence
- OME-TIFF
- 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)
- *.dat file from a 3DHISTECH mrxs scan
- *.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
- *.csv. (one row per annotation, with some attributes and micron-coordinates as text)
- *.tif mask (e.g. for importing into MACS® iQ View)
- *.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.
For more information about I/O formats and MIKAIA®, feel free to reach out to us. Please also check out our app notes in the MIKAIA® University.
Image copyright: Fraunhofer IIS
Grit Nickel
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