{"id":2128,"date":"2024-05-29T14:10:15","date_gmt":"2024-05-29T12:10:15","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=2128"},"modified":"2026-08-03T09:23:17","modified_gmt":"2026-08-03T07:23:17","slug":"mikaia-io-formats","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-io-formats\/","title":{"rendered":"WSI and Annotation File Format I\/O Support in MIKAIA"},"content":{"rendered":"\n

MIKAIA\u00ae<\/sup> <\/a>supports various I\/O formats, find out which ones.<\/p>\n\n\n\n

Importable whole-slide-image file formats<\/h2>\n\n\n\n
Format \/ Vendor<\/strong><\/th>Comments<\/strong><\/th><\/tr><\/thead>
OME-TIFF<\/strong><\/td>Brightfield and fluorescence.
Z-stacks and timelines supported (mutually-exclusive).
No multi-file support.<\/td><\/tr>
DICOM-WSI<\/strong><\/td>Brightfield only<\/td><\/tr>
Aperio SVS<\/strong><\/td>Brightfield only<\/td><\/tr>
Aperio SCN<\/strong><\/td>Brightfield & Fluorescence<\/td><\/tr>
Hamamatsu NDPI & NDPIS<\/strong><\/td>Brightfield and fluorescence<\/td><\/tr>
3DHISTECH Mirax<\/strong><\/td>Brightfield and fluorescence (3 channels only)<\/td><\/tr>
Roche Ventana TIFF<\/strong><\/td>Brightfield only<\/td><\/tr>
MetaMorph TIFF<\/strong><\/td>Fluorescence only. Z-stacks supported<\/td><\/tr>
Leica SCN<\/strong><\/td>Brightfield and fluorescence<\/td><\/tr>
PreciPoint VMIC<\/strong><\/td>Brightfield only                                                                      <\/td><\/tr>
Olympus VSI<\/strong><\/td>Brightfield and fluorescence<\/td><\/tr>
Zeiss CZI<\/strong><\/td>Brightfield and fluorescence. Z-stacks supported
Support must be unlocked. Get in touch for further details.<\/td><\/tr>
Kfbio<\/strong><\/td>Brightfield only. Use *.svs format<\/td><\/tr>
Perkin Elmer QPI<\/strong><\/td>Brightfield and fluorescence<\/td><\/tr>
NanoString GeoMX TIFF<\/strong><\/td>Image only (not RNAs)<\/td><\/tr>
Quanterix \/ Akoya Biosciences \/ <\/strong>
CODEX<\/strong><\/strong> QPTIFF <\/strong>
(PhenoImager & PhenoCycler)<\/td>		Fluorescence<\/td><\/tr>
Lunaphore COMET Ome-TIFF<\/strong><\/td>Fluorescence<\/td><\/tr>
Milteny MACSima TIFFs<\/strong><\/td>Fluorescence highplex.
Channels are single-tiff. They can be loaded as a
multiplex, by adding a *.multifile.csv file
(refer to MIKAIA user manual)
see also: Analyzing MACSima 47-plex mIF with MIKAIA: <\/a>
AI Cell Segmentation + Cell Typing + <\/a>
Cell-cell Connections + Cellular Neighborhoods<\/a><\/em><\/strong><\/mark><\/td><\/tr>
10x Genomics Xenium<\/strong><\/td>multi-omics stack comprising “morphology” channel
and multiple protein channels.
Cell polygons and RNA spots are natively displayed as
annotations. Genes are mapped to annotation classes.
(since MIKAIA v3.0)
see also: Xenium Analysis with the MIKAIA <\/a>
Cell x Gene App<\/a><\/em><\/strong><\/mark><\/td><\/tr>
Singular Genomics G4x <\/strong><\/td>multi-omics stack comprising H&E channel and
multiple protein channels. Cell polygons and RNA
spots are natively displayed as annotations.
Genes are mapped to annotation classes.
(upcoming in MIKAIA v3.1)<\/td><\/tr>
Keyence TIFF<\/strong><\/td>Brightfield and fluorescence<\/td><\/tr>
Motic TIFF<\/strong><\/td>Brightfield only<\/td><\/tr>
ImageJ TIFF<\/strong><\/td>Brightfield only<\/td><\/tr>
multipe TIFFs<\/strong>
(one per channel)
<\/td>		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.<\/td><\/tr><\/tbody><\/table>
If you are missing a format, let us know. Notably, Philips *.iSyntax, or *.kfbio are currently not supported.<\/figcaption><\/figure>\n\n\n\n

MIKAIA supports most Spatial Proteomics file formats<\/h2>\n\n\n\n

MIKAIA supports most spatial proteomics formats, notably those by Lunaphore Comet, Miltenyi MACSima, Akoya\/Quanterix PhenoCycler or PhenoImager. MIKAIA has no built-in channel maximum, but a higher plexity correlates with higher memory consumption. <\/p>\n\n\n\n

Also, low-plex fluorescence formats<\/strong> such as Olympus VSI, Zeiss CZI, Hamamatsu NDPIS or Aperio SVN are supported. <\/p>\n\n\n\n

CycIF: The MIKAIA Slide Align<\/strong> module can be used to align and stack multiple cycles of low-plex scans into a single high-plex scan: Manual Spatial Proteomics: Fusing Cycles into OME-TIF was Never Easier<\/a><\/p>\n\n\n\n

MIKAIA supports these Spatial Transcriptomics file formats<\/h2>\n\n\n\n

MIKAIA supports natively opening these spatial transcriptomics \/ multi-omics formats:<\/p>\n\n\n\n

Vendor \/ Instrument \/ Format<\/th>Comments<\/th><\/tr><\/thead>
10x Genomics Xenium<\/strong><\/td>multi-omics stack comprising “morphology” channel
and multiple protein channels.
Cell polygons and RNA spots are natively displayed
as annotations. Genes are mapped to annotation classes.
Open by opening the experiment.xenium<\/mark><\/em> file.
support added in MIKAIA 3.0<\/mark>
see also: Xenium Analysis with the MIKAIA <\/a>
Cell x Gene App<\/a><\/em><\/strong><\/td><\/tr>
Resolve Biosciences <\/strong>
(HDF5 format)<\/td>		multi-omics stack comprising DAPI channel
and multiple protein channels.
Cell polygons and RNA spots are natively displayed
as annotations. Genes are mapped to annotation classes.
Open the self-contained *.hdf5<\/mark><\/em> file.
support added in MIKAIA 3.0<\/mark><\/td><\/tr>
Singular Genomics G4x <\/strong><\/td>multi-omics stack comprising H&E channel and
multiple protein channels.
Cell polygons (membrane and nuclei) and RNA
spots are natively displayed as annotations.
Genes are mapped to annotation classes.
Open by opening the run_meta.json<\/mark><\/em> file.
support coming up with MIKAIA 3.1 release<\/mark><\/td><\/tr><\/tbody><\/table><\/figure>\n\n\n\n

For other formats not listed above, MIKAIA may be able to open the image layer.<\/p>\n\n\n\n

Please get in touch with us and let us know which other formats you would like to see added (Merfish, Visium, Visium HD, Cosmx, ..?): mikaia@iis.fraunhofer.de<\/p>\n\n\n\n

Importable “flat” image file formats<\/h2>\n\n\n\n

The following “flat” image formats can be opened:<\/p>\n\n\n\n