Orthanc WSI

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1

Hello all, I very interested in using this software for viewing whole slide images. I would appreciate any assistance in setting up Orthanc for this purpose. I believe my issue is not being able to appropriately configure the json file to add the plug-in for the webviewer, feel free to see the code below. I am assuming the WSI are viewed through the webviewer just the same as the other DICOM files.
I am using Windows (64bit) with the .dll files as plug-ins.

Now I have problem…The following errors occur during the conversion of the .svs file:

W0825 12:27:51.677887 Dicomizer.cpp:870] The input image is: c:\temp\CMU-2.svs
W0825 12:27:51.687900 Dicomizer.cpp:873] File format of the input image: TIFF
E0825 12:27:51.701865 HierarchicalTiff.cpp:206] This is not a tiled TIFF image
W0825 12:27:51.708880 Dicomizer.cpp:903] This is not a standard hierarchical TIFF file
W0825 12:27:51.715896 Dicomizer.cpp:913] Trying to open the input pyramid with OpenSlide
W0825 12:27:51.772884 Dicomizer.cpp:950] Compression of the individual source tiles: Unknown
W0825 12:27:51.793867 Dicomizer.cpp:167] Size of source tiles: 512x512
W0825 12:27:51.799878 Dicomizer.cpp:168] Pixel format: RGB24
W0825 12:27:51.807964 Dicomizer.cpp:169] Smoothing is disabled
W0825 12:27:51.815869 Dicomizer.cpp:180] No repainting of the background
W0825 12:27:51.823870 Dicomizer.cpp:192] Size of target tiles: 512x512
W0825 12:27:51.831870 Dicomizer.cpp:196] Target image compression: Jpeg with quality 90
W0825 12:27:51.840893 Dicomizer.cpp:91] Creating level 0 of size 78000x30462
W0825 12:27:51.848904 Dicomizer.cpp:91] Creating level 1 of size 19500x7615
W0825 12:27:51.854882 Dicomizer.cpp:91] Creating level 2 of size 4875x1903
W0825 12:27:51.861966 Dicomizer.cpp:91] Creating level 3 of size 2437x951
W0825 12:27:51.869887 Dicomizer.cpp:96] Transcoding the source pyramid
W0825 12:27:51.879871 ApplicationToolbox.cpp:107] Running 9815 tasks
W0825 12:27:51.883871 ApplicationToolbox.cpp:108] Using 2 threads for the computation
W0825 12:27:53.158950 ApplicationToolbox.cpp:92] Progress: 1%
W0825 12:27:54.417013 ApplicationToolbox.cpp:92] Progress: 2%
W0825 12:27:55.492056 ApplicationToolbox.cpp:92] Progress: 3%
W0825 12:27:56.644119 ApplicationToolbox.cpp:92] Progress: 4%
W0825 12:27:57.799185 ApplicationToolbox.cpp:92] Progress: 5%
W0825 12:27:59.057258 ApplicationToolbox.cpp:92] Progress: 6%
W0825 12:28:00.420312 ApplicationToolbox.cpp:92] Progress: 7%
W0825 12:28:01.598371 ApplicationToolbox.cpp:92] Progress: 8%
W0825 12:28:02.851509 ApplicationToolbox.cpp:92] Progress: 9%
W0825 12:28:04.011520 ApplicationToolbox.cpp:92] Progress: 10%
W0825 12:28:05.296656 ApplicationToolbox.cpp:92] Progress: 11%
E0825 12:28:06.763659 HttpClient.cpp:65] Error code 7 in libcurl: Couldn’t connect to server
E0825 12:28:06.771665 OrthancException.h:85] Error in the network protocol: libCURL error: Couldn’t connect to server
E0825 12:28:06.783646 BagOfTasksProcessor.cpp:53] Exception while processing a bag of tasks: Error in the network protocol
E0825 12:28:06.895658 ApplicationToolbox.cpp:133] Error has occurred, aborting
W0825 12:28:06.947660 DicomPyramidWriter.cpp:183] Closing the DICOM pyramid (1103 tiles were written)
E0825 12:28:08.167764 HttpClient.cpp:65] Error code 7 in libcurl: Couldn’t connect to server
E0825 12:28:08.174732 OrthancException.h:85] Error in the network protocol: libCURL error: Couldn’t connect to server
E0825 12:28:08.185735 DicomPyramidWriter.cpp:195] Cannot push the pending tiles to the DICOM pyramid while finalizing
W0825 12:28:08.196740 TiledPyramidStatistics.cpp:40] Closing the input image (0 raw accesses to the tiles, 1104 decoded tiles)
E0825 12:28:08.218720 Dicomizer.cpp:962] Terminating on exception: Internal error

I appreciate any help with getting me off the ground, I essentially just want to import/upload the WSI files to the Orthanc server and view them through the webviewer, nothing fancy.

Thank you!

-Oleg

2

Hello,

The following excerpt from your log indicates that the WSI DICOM-izer cannot connect to Orthanc:

E0825 12:28:06.763659 HttpClient.cpp:65] Error code 7 in libcurl: Couldn’t connect to server
E0825 12:28:06.771665 OrthancException.h:85] Error in the network protocol: libCURL error: Couldn’t connect to server
E0825 12:28:06.783646 BagOfTasksProcessor.cpp:53] Exception while processing a bag of tasks: Error in the network protocol

By default, the command “OrthancWSIDicomizer” will send the DICOM files it generates to an instance of Orthanc that is running on the localhost. Check out the “–orthanc” option in the manual:
https://dokk.org/manpages/OrthancWSIDicomizer.1

If you don’t want to run Orthanc, you can write the output DICOM files to a folder on the hard disk by using the option “–folder”.

HTH,
Sébastien-

3

Thank you for reply.
Now i get next messages with using --orthanc or --folder option:

E0825 13:25:08.516224 OpenSlideLibrary.cpp:218] OpenSlide has not been initialized, use the “–openslide” command-line option
E0825 13:25:08.526223 Dicomizer.cpp:921] This file is not supported by OpenSlide
E0825 13:25:08.530219 Dicomizer.cpp:962] Terminating on exception: Bad file format

It’s mean my .svs file is not supported by OpenSlide? or maybe i wrong use command:

  1. c:\Temp\openslide\bin>OrthancWSIDicomizer.exe --orthanc http://localhost:80 c:\temp\CMU-2.svs
  2. c:\Temp\openslide\bin>OrthancWSIDicomizer.exe --folder c:\temp c:\temp\CMU-2.svs

-Oleg

4

Please check out the Orthanc Book:
https://book.orthanc-server.com/plugins/wsi.html#proprietary-file-formats

=> You must provide the path to the “libopenslide-0.dll” shared library, that is installed by default by the Windows installers into the following folder:
C:\Program Files[…]\Orthanc[…]\Tools\

5

Sorry, fixed the command, now such an error.

c:\Temp\openslide\bin>OrthancWSIDicomizer.exe --folder=libopenslide-0.dll c:\temp\CMU-2.svs
W0825 14:44:09.902542 ApplicationToolbox.cpp:248] Orthanc WSI version: 0.6
W0825 14:44:09.907547 HttpClient.cpp:739] No certificates are provided to validate peers, set “HttpsCACertificates” if you need to do HTTPS requests
W0825 14:44:09.915543 Dicomizer.cpp:870] The input image is: c:\temp\CMU-2.svs
W0825 14:44:09.920542 Dicomizer.cpp:873] File format of the input image: TIFF
E0825 14:44:09.929545 HierarchicalTiff.cpp:206] This is not a tiled TIFF image
W0825 14:44:09.933613 Dicomizer.cpp:903] This is not a standard hierarchical TIFF file
W0825 14:44:09.938550 Dicomizer.cpp:913] Trying to open the input pyramid with OpenSlide
E0825 14:44:09.944545 OpenSlideLibrary.cpp:218] OpenSlide has not been initialized, use the “–openslide” command-line option
E0825 14:44:09.954559 Dicomizer.cpp:921] This file is not supported by OpenSlide
E0825 14:44:09.958544 Dicomizer.cpp:962] Terminating on exception: Bad file format

6

As written in the Orthanc Book, you must provide the full path to the “libopenslide-0.dll”, or copy all the DLL next to the OrthancWSIDicomizer.exe executable

HTH