Ventana slides

[enmunari]

Hi there, i am new to QuPath and i am trying to move the first steps... however, i am facing some problems in viewing slides scanned with ventana in bif format! Anyone could please help me out? Thanks!!

[Pete]

Can you describe what happens when you try it?

And are you able to open other images, such as the suggested examples on the wiki under 'First steps'?  And are you trying this on Windows/Linux/Mac?

QuPath users OpenSlide, and OpenSlide should have at least some support for .bif images.  I've tried it with some of the OpenSlide sample data and it works for me.

However, it doesn't work for me immediately if I have the Bio-Formats extension installed - because Bio-Formats tries to open the image first instead of OpenSlide, and only actually opens a very low resolution version rather than the whole thing.

If this is what you are seeing, you should probably disable Bio-Formats specifically for images with '.bif' extensions; you can do this by typing .bif into the preference setting for 'Never use Bio-Formats for specified image extensions' as described at the bottom of this page: https://github.com/qupath/qupath-bioformats-extension

[enmunari]

Dear Pete,

first of all thank you for your quick response!

I did as you suggested, and now i can see the whole thing; however, the image is quite messed up, as you can see in the snaphot attached... probably Qu Path struggles a bit with .bif!

Thanks!

[Pete]

This isn't really a QuPath problem - QuPath doesn't handle whole slide image formats itself, but instead depends on OpenSlide or Bio-Formats (or potentially some other library, if there was one and could be added as a QuPath extension).

As far as I recall, Bio-Formats doesn't handle .bif at all - so it's down to OpenSlide.

There's a known issue with OpenSlide and some Ventana images connected to the tile alignment, which sounds like what you're seeing: https://github.com/openslide/openslide/issues/132

Unless this issue can be resolved in OpenSlide (which looks like a challenging problem, based on the description in the link) then it won't be possible to view the images properly in QuPath.

Do you have any option to export the images in any format other than .bif?

[enmunari]

I see...the scanner would allow to export slides in .tif as well, so do you think it may work this way?

Thank you Pete!

[Pete]

I really don't know - TIFFs can be very variable, sometimes compatible, sometimes not.

If you could try it with one or two images, I'd be interested to know whether it works!

[enmunari]

I just scanned a slide using .tif and it seems to be working.

Thanks!