RE: Can't import entire pyramidal WSI file in OMERO

We’re fairly new to OMERO so this may be something simple we’re missing. We’re importing files with the insight client, then trying to view in the web client. The project folder shows a series of files for macro, label and then ones with appended numbers like [0], #4, #5, #6. The metadata seems correct with diminishing pixel dimensions for each and the one with full dimensions 54k x 91k displays properly, but the ones with hashtag appear with a gray thumbnail labeled ‘no image’ and don’t load in the viewer ?

Filesize is 1.4GB.

We tested with a smaller pyramidal tif file, non-medical image, which loaded fine with all the layers present and viewable.

Thanks for help !
Baxter
RoseAid LLC

Hi Baxter,

Welcome to image.sc! Can I suggest we turn this into a public forum post so that the rest of the community can benefit from it?

All the best,
~Josh

Hi Josh, absolutely ! Being new to the site I wasn’t exactly sure how to do the post so I guess it ended up as a private message ?

thanks
Baxter

No worries at all. I’ll migrate. ~J

There we go. Tags #omero and #wsi added as well.

Is your file accessible anywhere?

Right now it’s on our dev omero.server instance, odev.roseaid.com. I’m reaching out to our Admin guy to see what the options are …

B

We can give you access to our dev server to see directly what’s going on with the files, Admin would like first to do a NDA, is that possible ?

We’re not able to provide direct support on your server or sign an NDA-- that’s not really in the ethos of an open source project. For commercial support of OMERO, contact info@glencoesoftware.com.

We are definitely happy to have discussions here, exchange snippets of log files etc., and will definitely do everything in our power to get you up and running.

Cheers,

Jason

1 Like

Hi Jason, absolutely understood, thanks . btw, Josh had asked about the files we’ve been working with and I realized that the image: 77919.svs is a WSI from the OME website sample images :

https://downloads.openmicroscopy.org/images/SVS/

Don’t know if that clue helps, we’re having that same problem with all the pyramids, the macro image looks good, label etc. , just not getting the intermediate planes.

You mentioned logging which I don’t think we’ve looked into, will do so now.

Hi Baxter,
I just imported the two svs files and couldn’t see any issues. You mentioned that some of the images get a # appended to the name. So you’re cleary seeing something different to me. Which version of the OMERO.server are you running? Could you send us the log file (Blitz.log) after you imported the image?
Kind Regards,
Dominik

Hi Dominik, omero-server-Blitz-0-exception.txt (137.9 KB)

Here’s the blitz log file with logged exceptions from trying to load that WSI file: slide2_20201218_092817-1-1_scan.tif

Thanks @BaxterGarcia,

the logs are very useful and you are absolutely correct they point to some reading issue while accessing the file slide2_20201218_092817-1-1_scan.tif. Could you tell us a bit more about where this file comes from and/or how it was generated?
In order to help you further, we will probably need to see the content of this file. Would that be a possibility?

Best,
Sebastien

Hi Sebastien, thanks for your response and review of the error logs. let me look into (a) whether the slide file is anonymized and (b) what’s the best mechanism to access it, maybe Dropbox or Google Drive.

I’ll get back to you soon.

Best
Baxter

1 Like