I am trying to run minerva-author on a H&E dataset of file type .scn . Since, minerva supports OME-TIFF/SVS formats, I opened the .scn file in QuPath (https://qupath.github.io/) and exported it out as OME-TIFF format. However, I get error on using this TIFF file.
(author) vscode ➜ /workspaces/minerva-browser/minerva-author (master ✗) $ python src/app.py Closing tiff file Closing mask files Closing import pool Closing tiff file Closing mask files Closing import pool Opening file: /workspaces/minerva-browser/sample003/Untitled.ome.tif OME 6 'Array' object has no attribute 'values' Opening file: /workspaces/minerva-browser/sample003/Untitled.ome.tif
I tried doing this conversion using lib-vips, but got same error. I then tried some sample OME TIFF files from OME-TIFF sample data — OME Data Model and File Formats 6.0.0 documentation, but they give same error.
Minerva documentation says : " All OME-TIFF channels must be 16-bit integers, as output by the mcmicro pipeline, or unsigned 8-bit integers."
Is there a way I could generate the OME-TIFF files in this expected format ?