Problems with Ventana bif images

I am trying to open a subset of images. When I tried to open them with OpenSlide builder I got the following error:

WARN: Unable to open file:/mnt/V_anato/nouAPERIO/DRA%20COMERMA/SISH%20proves%20escaner/19B027849%20HER2.bif with OpenSlide: Bad direction attribute "LEFT"
WARN: Unable to open UriImageSupport (class qupath.lib.images.servers.openslide.OpenslideServerBuilder) support=2.5, builders=1
WARN: Unable to open UriImageSupport (class qupath.imagej.images.servers.ImageJServerBuilder) support=1.0, builders=1
WARN: Unable to open file:/mnt/V_anato/nouAPERIO/DRA%20COMERMA/SISH%20proves%20escaner/19B027849%20HER2.bif with OpenSlide: Bad direction attribute "LEFT"
WARN: Exception adding Image null
ERROR: Import images: Failed to load one image.

The curious part is when I tried to open it using Bio-Formats builder. The image doesn’t appear anywhere but I do not found any error.
I recall a previous issue about this LEFT attibute format in Bio-Formats but I am not able to find it. In any case, any idea how to solve the issue?
Thanks

I’ve seen a similar error, and don’t have any solution – neither Bio-Formats nor OpenSlide could open the troublesome image. The only way to handle it was to export as TIFF from the acquisition software (I don’t know what exactly that involves - I was just given the files).

I’ve added the Bio-Formats tag to this post, since it’s not something that can be solved in QuPath.

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I found this brach of openslide that seems to solve the issue: https://github.com/openslide/openslide/pull/246

However, it seems that they didn’t commit it to master. Is there any way to edit the code directly in QuPath?

You could try building OpenSlide with the changes, and then replacing the relative native libraries inside QuPath; there shouldn’t be any need to change the QuPath code itself.

As far as I am aware, OpenSlide is no longer actively maintained. I am therefore not very optimistic that a new release with the fix will become available.

Bio-Formats, on the other hand, is very actively maintained.

For cross-referencing purposes, the discussion about supporting Ventana BIF’s LEFT overlap in Bio-Formats has started in https://github.com/ome/bioformats/issues/3570.

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It seems that I found a way to open this images by updating Bio-formats VentanaReader file.

I would like to try it directly in QuPath. How should I change the qupath-extension-bioformats-0.2.0.jar file (is that one, right?) in QuPath 0.2.0 in order to add this new functionality?

@Joan_Gibert_Fernande if you can build Bio-Formats with the change, you can use that – no need to change anything in QuPath, just replace the corresponding Bio-Formats jar in your QuPath installation. If the jar has the same name it should just work.

Otherwise I don’t have any easy way to do this, I suspect it might take quite a bit of hacking around with the code and classpaths.

I am using QuPath on linux and, as far as I can see in the lib folder, there is only no bioformats.jar file rather than the one I just commented before.

Is there any distribution, Windows, Mac, that use bioformats.jar as it is?

Some older v0.2.0 milestones do – I forget when precisely this stopped, but it relates to this discussion

If you have a bioformats.jar that should work, you can try dragging it on top of QuPath and thereby adding it to your extensions directory. You will then likely need to remove any relevant jars from your QuPath installation to avoid conflicts (e.g. anything with ome and formats in the name).

It’s an inelegant approach, which may or may not work… but perhaps worth a try.

Your comment lead me to the correct file. I leave here the way I found to make it work in case someone would like to reproduce it:

  1. Find formats-gpl-6.5.0.jar file inside QuPath /lib/app folder.
  2. Open the attached file (this is the bio-formats last release with the code change) and find the compiled VentanaReader*.class files inside it
  3. Copy this files to the formats-gpl-6.5.0.jar inside /loci/formats/in. Replace the existing ones inside the folder.
  4. Run QuPath

bio-formats-tools-6.5.1-SNAPSHOT.jar (54.0 KB)

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