Opening qptiff file in CellProfiler

Hi,
I am trying to open qptiff files acquired through Akoya’s Vectra system using Cellprofiler. My understanding is that Cellprofiler uses bioformats package which list qptiff files as compatible but I am not able to open them. Please advise. Thanks!

Hi @chang06,

Yes CellProfiler uses bioformats package. But sharing the screenshot of your error message or your sample image will facilitate us to help you better!!

Regards,
Lakshmi
www.wakoautomation.com


Hi Lakshmi,
Thanks for your response. Attached is a screenshot of the error message. Sample image is really big since it is a 7-plex image of a tonsil.

Hi @chang06,

Thanks. I tried a qptiff file from my side as well. It looks there is a issue in the CellProfiler in supporting the format. I have raised it as a issue in the Github, the team would work on it to resolve the issue.
In the meanwhile, a small work around that may help is open the image in the Fiji/ImageJ using “Bioformats importer” plugin and save it as a tiff file [Actually it worked for me]. Try using this tiff file in CellProfiler.

Hope this helps.
@bcimini
Regards,
Lakshmi
www.wakoautomation.com

Thanks Lakshmi, I will give it a try!
Andres