Bug 30

Summary:	Bad colorspace if using OpenSlide
Product:	Orthanc	Reporter:	Sébastien Jodogne <s.jodogne>
Component:	Whole-slide imaging	Assignee:	Sébastien Jodogne <s.jodogne>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	---
Version:	unspecified
Hardware:	All
OS:	All
Attachments:	unnamed.jpg

Description Sébastien Jodogne 2020-06-29 15:11:54 CEST

[BitBucket user: Sébastien Jodogne]
[BitBucket date: 2017-01-20.12:12:15]

From abdou.matthew@gmail.com on 2016-01-19:

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

Comment 1 Sébastien Jodogne 2020-06-29 15:18:19 CEST

Created attachment 85 [details]
unnamed.jpg

Comment 2 Sébastien Jodogne 2020-06-29 15:19:29 CEST

[BitBucket user: Sébastien Jodogne]
[BitBucket date: 2017-01-20.12:17:07]

The problem was that the "R" and the "B" color channels were swapped when decoding images using OpenSlide.

This is fixed by the following changelist:
https://hg.orthanc-server.com/orthanc-wsi/changeset/16b8e1cc9bbfeec5c2cd4e601e6259edec5a0d85