Uploading .qptiff format images

[i...@st-andrews.ac.uk]

Dear experts,

I am a new user of QuPath. First of all, thank you so much for this wonderful software.

I have installed the 'bioformats_package' and 'qupath-extension-bioformats' but it didn't make the .qptiff image open.

The images I have is multiplexed immunofluorescence images scanned with Perkin Elmer Vectra Polaris scanner.

The image format I have is .qptiff and its size is 2.2GB.

Would it be possible to upload it in QuPath to analyse?

Thanks for your help.

In Hwa

[Pete]

Hi, are you able to open the .qptiff with Fiji (http://fiji.sc)?

If so, then that would confirm that the problem is on the QuPath side and not on the Bio-Formats side.  There are a few aspects of the QuPath Bio-Formats extension that I want to fix this week, but I don't know if they will address the problem you're seeing.  There was recently an issue 3-channel 8-bit fluorescence images where downgrading to use the v0.0.5 extension meant the image could be opened, although these weren't .qptiff (see here).  However i your images fit this description it may be worth a try...

The small number of .qptiff example images I have all work for me in QuPath using Bio-Formats.  If you are able to share your .qptiff image then I can investigate further here and try to figure out what is different, and incorporate a fix in the next release of the extension.  If you don't want to post a link publicly, it's possible to send private messages here.

[i...@st-andrews.ac.uk]

Hi, Pete,

Thanks for your prompt reply.

I have tried to open it in Fiji and it opens with single channel even though I chose the option for composite.

I would like to share this image with you but the attaching file has been failed here.

If you can tell me how I can send you this image it would be amazing.

Thanks a lot,

In Hwa