QuPath 0.2.0 not able to open ome.tiff

bio-formats
ome-tiff
qupath

#1

Hi all,

I just downloaded the new version of Qupath to give it a try but I can’t even open an ome.tiff file that 0.1.3 with BioFormats could open.

Is there anything special to know with the new install and BF ? (Sorry I can’t be more precise, all I get is I can't open the image )


#2

Nothing to install. Can you share the image?

If not, more information would be helpful, e.g.

  • can you open other OME-TIFFs?
  • can you open other images with Bio-Formats at all?
  • can you open the OME-TIFF in Fiji?
  • what are the dimensions of the image?

#3

Hi @petebankhead,

Thanks for the (super) fast answer !

  • I can open other OME-TIFFS
  • I can as well
  • Yes, and I could open it in the previous QuPath version…
  • 7506*7506

You should be able to download the file here.

Thanks for the help ! :slight_smile:


#4

Hmmm, it opens for me in v0.2.0-m1 on Windows… not terribly fast (as it’s not a pyramid) nor with fantastic auto contrast settings, but I can’t see any problem.


#5

Might be an available memory issue if it is not pyramidal? Note that you will want to manually (well, through the Help menu) reset the amount of RAM available to QuPath in the new version.


#6

The file 2019_02_19__7760_s1.ome.tiff contains a nonsense 5th IFD with only one tag. BigTIFF readers might fail when trying to use that IFD.


#7

It works with 0.1.3 that’s what I don’t get…

@Research_Associate Done but didn’t fix anything… :confused:

@petebankhead Still not working on multiple windows and I don’t really get why :confused: but I’ll keep on investigating.


#8

Ok new input : It seems to be a problem with network drives. When the file is on a network drive it doesn’t open, while copying it locally works somehow.

I don’t know what’s the real cause of the problem, but at least I have a way to get past it. :slight_smile:


#9

Ah, I have a similar problem with my desktop and other user folders which are “networked” by locstion name, even when offline. Did not think about that in this case.


#10

Do you have any suggestions for how I could test this… ideally on my laptop while travelling?

Also, could you please open a failing image in an older version of QuPath (where it works) and run the following script, and let me know what it prints? Thanks.

println new File(getCurrentImageData().getServer().getPath()).toURI()

#11

Sent via DM to avoid too much private information.


#12

Is this behaving any better with v0.2.0-m2?


#13

Yes, sorry about that ! The files open just like they did with 0.1.2 now, so all fixed ! :slight_smile:


#14

Excellent. The problem appears to have been the attempt to construct a File from a uri for an image on a network drive. Fixed here.