{"id":4868,"date":"2026-01-14T09:41:52","date_gmt":"2026-01-14T08:41:52","guid":{"rendered":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/?p=4868"},"modified":"2026-05-08T11:46:12","modified_gmt":"2026-05-08T09:46:12","slug":"mikaia-slide-alignment","status":"publish","type":"post","link":"https:\/\/websites.fraunhofer.de\/smart-sensing-insights\/mikaia-slide-alignment\/","title":{"rendered":"MIKAIA’s Slide Alignment: An Overview"},"content":{"rendered":"\n

With the MIKAIA\u00ae<\/sup> 3 release (April 2026), MIKAIA\u00ae<\/sup> received a new multi-omics slide alignment module, “MIKAIA\u00ae<\/sup> Slide Align<\/strong>“. Based on a 3-phase registration process, the last one being a non-rigid deformation for highest alignment accuracy, the module lets you generate new aligned slides in SVS or OME-TIFF format. Additionally, multiple layers are tied together via a companion text file (*.multifile.csv), which can be directly opened to view the multi-layered images in MIKAIA’s multi-omic viewer.
The MIKAIA\u00ae<\/sup> Slide Align module is powered by the HistokatFusion technology<\/a> by Fraunhofer MEVIS.<\/p>\n\n\n\n

Three use cases: Serial sections, CycIF, and multi-omics<\/h2>\n\n\n\n

The slide alignment module will support three main use cases:<\/p>\n\n\n

\n
\"Visualization<\/figure>\n<\/div>\n\n\n

1. Alignment of H&E and IHC serial sections<\/strong> (brightfield)<\/h2>\n\n\n\n
\"\"<\/figure>
\n

In a typical scenario, you will align H&E stains with one or multiple IHC stains. For each scan, an alignment version is generated, alongside a companion file that links them together.

This stack can be opened in MIKAIA\u00ae<\/sup>, allowing you to toggle between the aligned brightfield layers.
You can use the various MIKAIA\u00ae<\/sup> analysis apps by selecting the specific layers for analysis. For instance, use the Universal IHC Cell AI<\/a> to quantify immune cells in the IHC layers, and then evaluate their colocalization with the Grid Analysis App<\/a><\/strong>. Or you can mask the DAB+ areas with the Mask by Color App<\/a><\/strong> and use these masks as training annotations for the AI Author<\/strong><\/a> to train an H&E AI.<\/p>\n<\/div><\/div>\n\n\n\n

\n

This is an example of nine serial sections (H&E plus 9x IHC) aligned and displayed side-by-side in MIKAIA\u00ae<\/sup>. The viewers can by navigated synchronously, with the mouse pointer mirrored from the focused viewer to the other views.<\/em><\/p>\n<\/div>

\"\"<\/figure><\/div>\n\n\n\n

2. Alignment of Cyclic Immunofluorescence<\/strong> (CycIF): Create high-plex OME-TIF<\/h2>\n\n\n\n
\"\"<\/figure>
\n

In a typical scenario, you have manually stained, scanned, bleached, restained, and rescanned a tissue section using your low-plex fluorescence scanner (e.g., from Zeiss or Olympus). Let’s say you now have five cycles with four channels each: Each cycle contains a DAPI channel along with the same set of three additional fluorophores targeting different antibodies. Your goal is to align and merge these 5 4-plexes into a single high-plex OME-TIFF (e.g., DAPI + 5×3 markers = 16 plex, if you choose to discard all but one DAPI channel). Throughout this process, you can even change the channel names, colors, and order as needed.<\/p>\n<\/div><\/div>\n\n\n\n

\n

This screenshot shows the wizard page, where all detected markers from three cyclic 4-plexes are listed and can be customized. You can modify the marker names and colors, deselect channels to discard them, and rearrange the output order .<\/em><\/p>\n<\/div>

\"\"<\/figure><\/div>\n\n\n\n

3. Alignment of multi-omics scans (e.g., Xenium with H&E, or MALDI with H&E)<\/h2>\n\n\n\n
\"\"<\/figure>
\n

Multi-omics spatial biology promises to revolutionize discovery. A key challenge at the outset of each bioinformatic analysis is merging the various omics together to facilitate joint analysis. MIKAIA’s slide alignment module supports the alignment multi-omics scans.<\/p>\n\n\n\n

Spatial transcriptomics<\/strong>: Align a Xenium Morphology<\/strong> OME-TIFF scan with an H&E brightfield scan (any scanner format) and view them togehter in the MIKAIA\u00ae<\/sup> multi-omics viewer. You can then perform H&E-guided spatial transcriptomics analysis by using the AI Author to analyze the H&E morphology (e.g., finding tumors) and compare the transcriptome across different H&E-derived annotations or regions of interests.<\/p>\n\n\n\n

Mass spectrometry imaging<\/strong> (MSI): Align a low-res\/high-plex DESI or MALDI<\/strong> OME-TIFF image with an H&E scan. You can subsequently conduct H&E-guided MSI analysis using the AI Author to analyze the H&E morphology (e.g., locating tumor) and then investigate the lipidome or metabolome across different H&E-derived annotations, regions of interests, or cells.<\/p>\n<\/div><\/div>\n\n\n\n

MIKAIA\u00ae<\/sup> Slide Align<\/strong> is powered by award-winning science: HistokatFusion by Fraunhofer MEVIS<\/h2>\n\n\n\n
\n
\n

Top precision<\/h4>\n\n\n\n