WSI Photometric interpretation YBR_FULL_422 to RBG?

[abdou....@gmail.com]

After converting whole slide image files with the DICOMizer command line tool, the slide viewed in Orthanc's WSI web viewer (and those seen on the WSI demo site) are a deep purple instead of the usual H&E colors (pink/red & purple/blue). See attached photo (left side is normal H&E color of original WSI file, right side shows DICOMizer converted slide color interpretation).

This color interpretation is not accurate.

I believe this is due to the (PhotometricInterpretation) set as YBR_FULL_422 instead of RBG. I have tried using multiple (including RGB) icc color profiles with the DICOMizer, however all converted slides have the same deep purple result.

Is there a way to change the default DICOMizer conversion to use an RGB color interpretation/representation? How can I achieve accuracte color representation with the DICOMizer command line tool? Otherwise all DICOMizer converted slides will not be usable from a pathologist's standpoint. Thank you!

Matthew

[Sébastien Jodogne]

Dear Matthew,

You're obviously right!

This problem results from an inversion between the "red" and "blue" color channels if decoding images using OpenSlide. I have introduced an issue on our bug tracker to keep track of it:

https://bitbucket.org/sjodogne/orthanc/issues/30/bad-colorspace-if-using-openslide

The fix was almost trivial:

https://bitbucket.org/sjodogne/orthanc-wsi/commits/16b8e1cc9bbfeec5c2cd4e601e6259edec5a0d85

It will however take some time before the next release, and before the images of the demo server are updated. The Docker image is currently being rebuilt in order to include the fix.

Regards,

Sébastien-

[Sébastien Jodogne]

The sample images have just been updated:

http://wsi.orthanc-server.com/demo/

Please could you confirm they are now usable from a pathologist's standpoint?

Thanks!

Sébastien-

[abdou....@gmail.com]

Yes! These are representative of their native H&E representations and will be usable for pathologists to now view the native color interpretation. Thank you so much for updating the demo. I will be awaiting the next release.

[Sébastien Jodogne]

Hello Matthew,

FYI, the 0.4 release of the whole-slide imaging framework is now available, with associated 32bit Windows binaries:

http://www.orthanc-server.com/browse.php?path=/whole-slide-imaging

HTH,

Sébastien-