Error for WSI in Orthanc Explorer 2

General
1

Hey everyone,

Even though my error message was already discussed, I did not find the correct solution there.
Unfortunately, Orthanc Explorer 2 is not able to visualize WSIs from the DICOM files in the database returning the error: Error - Cannot get the pyramid structure of series: c87da3aa-a1bf12dd-db95800b-b854f91f-27e48356.

Starting from scratch: After starting an Orthanc server with my configuration.json with enabled WSI and Explore2 plugin, I am able to access http://localhost:8042/app/explorer.html as well as http://localhost:8042/ui/app/index.html#/
In the config file, I further added this to enable explorer 2:

  "OrthancExplorer2": {
    "Enable": true,
    "IsDefaultOrthancUI": true
  },

Both UIs show the same list of cases which I imported using the shipped OrthancWSIDicomizer:

OrthancWSIDicomizer --openslide /usr/lib/x86_64-linux-gnu/libopenslide.so.0 H.18.655.svs --dataset dataset.json

I also included several other WSI formats (ndpi, mrxs). All of them can be visualized, zoomed etc. in the shipped WSI viewer, but not in Explorer 2.
dciodvfy results in the following result:

Warning - Value dubious for this VR - (0x0010,0x0010) PN Patient's Name  PN [1] = <SOME PATIENT> - Retired Person Name form
VLWholeSlideMicroscopyImage
Error - Missing attribute Type 1 Required Element=<WholeSlideMicroscopyImageFrameTypeSequence> Module=<WholeSlideMicroscopyImageFrameTypeMacro>
Warning - CodingSchemeDesignator is deprecated - attribute <CodingSchemeDesignator> = <SRT>

As a new user, I am not allowed to upload files such as my config or data to test. If necessary, I try to share them via cloud.

I am looking forward for your assistance.

Best,
Christoph

2

Hi @ChrisB

Just to make things clear, can you confirm you are using this button to open the WSI button in OE2 ?

image
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If yes, the output should be the same, no matter if you open it from the legacy UI or from OE2.

If not, please share a sample file via a cloud share.

Best,

Alain

3

Thanks for the hint and the screenshot.
Here, I recognized that my view is different. This button you highlighted is not even available for me. I clicked on the eye icon as the leftmost button of each patient.

grafik
grafik1920×527 87.7 KB

I created a folder with the original .ndpi file and one of the corresponding DICOM files:

To create the DICOM files, I used OrthancWSIDicomizer and the sample metainfo json file. In addition, I added the --folder flag to export the DICOM files instead of storing them in the Orthanc database.

BTW: Visualizing the exact same study / WSI with the “old” explorer (/app/explorer) works well with the build-in whole slide image viewer (smooth, zoom etc).

4

The WSI viewer is available at the series level, not the study level → you have to click on the SM line.

5

Thanks for the answer … I just recognized it myself. However, I still get the same error message when clicking on it instead of the eye button in the upper left.

It still did not work, but trying to download the slide via python library dicomweb_client and dicomslide had a more detailed logging:
“Skip image because it does not have a Frame of Reference UID attribute”

Therefore, I added the following line to dataset.json to be included in the DICOM metadata:
“FrameOfReferenceUID” : “789”

Now, everything works fine!

According to the DICOM tag documentation, it replaces some old location tag. Maybe my .ndpi file is “too” old …

6

Hello,

I have just tried to download your NDPI file, but the link has expired. Feel free to share it again if you need further support.

Regards,
Sébastien-

7

Hey Sebastien,

thanks for trying to download the NDPI.
I was able to solve the problem so you do not need to further investigate it.

The Orthanc Explorer 2 is working smoothly for me. Currently, I have implemented an additional script storing an annotation region as DICOM SR which is added to Orthanc Explorer 2 and shown in Slim Viewer.

Best,
Christoph