OrthancWSIDicomizer generates pink background

I have some Leica svs images that I am trans/recoding to DICOM using OrthancWSIDicomizer. After generating the files, I am able to open them with MyOrthanc localhost.

However, when I open it with the Whole-Slide Image Viewer I got a different code color image, like:pink_bck.png

Also, if I transcode the image and use “Preview this series” the tiles showed are in the correct color format. Not in the case of the reencoding.

Additionally, I found that the Target Photometric Interpretation varies between the two (RGB and YBR_FULL_422). However, both start with:

W1120 09:33:01.350248 Dicomizer.cpp:906] File format of the input image: TIFF
W1120 09:33:01.352881 Dicomizer.cpp:983] Compression of the individual source tiles: JPEG
W1120 09:33:02.132530 Dicomizer.cpp:170] Size of source tiles: 256x256
W1120 09:33:02.133034 Dicomizer.cpp:171] Pixel format: RGB24
W1120 09:33:02.133374 Dicomizer.cpp:172] Source photometric interpretation: RGB W1120 09:33:02.133684 Dicomizer.cpp:173] Source compression: JPEG
W1120 09:33:02.133988 Dicomizer.cpp:174] Smoothing is enabled
W1120 09:33:02.134284 Dicomizer.cpp:185] No repainting of the background
W1120 09:33:02.134517 Dicomizer.cpp:236] Size of target tiles: 256x256

Finally, I found this post that I think it could be related.

Thanks

Also, kind of related previous post: https://groups.google.com/g/orthanc-users/c/hy8duew3tw0/m/ReHKRd8bCgAJ

Hello,

Please provide sample DICOM images and a minimal working example if you expect support from this forum:
https://book.orthanc-server.com/users/support.html#discussing-a-minimal-working-example

Sébastien-

Apologies for the improper post.
Trying to fix it:

Context and full textual description of your issue
When transforming Leica svs files into DICOM using OrthancWSIDicomizer I got images with an incorrect color palette
The observed vs. expected results
When images are opened with Orthanc localhost I see pink background and greenish cells (like in the image from the first post). I expect to got images with white background and H&E staining
Full configuration files
Here
Full logs as produced by Orthanc in verbose mode.
In this case OrthancWSIDicomizer logs
Sample DICOM files
Low level DICOM image generated
A sequence of command lines that lead to your problem
To generate the DICOM files, I did: ./OrthancWSIDicomizer /mnt/isilon/SIMDCAT_APAT/LEICA/SVS/image1.svs --folder=/mnt/isilon/SIMDCAT_APAT/LEICA/ --max-size=0
To initialize Orthanc I just run Orthanc and go to http://localhost:8042. Then, I uploaded the .dcm files and open them with Whole-Slide Image Viewer (all with GUI)
If applicable, a screenshot is worth a thousand words.
Go to first post’s screenshot Thanks

Hello,

I have well received your DICOM file, but we need the source SVS image too.

Regards,
Sébastien-

Here it is

Thanks,
J

I confirm the reception of the sample files.

I’ll have a look, presumably in the course of January 2021.

Hello,

Your issue should be solved by the following changeset that is pending in the mainline of the WSI repository:
https://hg.orthanc-server.com/orthanc-wsi/rev/c5a8b46c4cba

It will soon be part of release 0.8 of the whole-slide imaging framework.

HTH,
Sébastien-