Invalid tiff file

[Amit-Tomar]

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.

This is what the console log on server says :

(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

Any suggestions on what could be wrong here ? Any other suggested tool which could be used for compatible file conversion related to minerva ?

[Amit-Tomar]

I tried some sample files from https://docs.openmicroscopy.org/ome-model/6.0.0/ome-tiff/data.html, thinking that there might be an issue in my conversion process. But these files give similar error.

[dgault]

Further reports of a similar issue have been reported on image.sc thread https://forum.image.sc/t/converting-scn-files-to-16-bit-unsigned-8-bit-integers-ome-tiff-files-for-usage-in-minerva-browser/51857

It looks like it may be due to support only being available for a limited number of pixel types, would it be possible to add support for the full range of possible pixel types?

[YubinXie]

I have the same issue here too.

[Starahoush]

Same issue here