Cannot get the pyramid structure of series

Google Groups archive
1

Hi Team

I am not able to view the DICOM images in Orthanc Viewer. I get the error ‘Cannot get the pyramid structure of series’. I installed the Orthanc Server in my system, and upload, and try to view the images.

Of course, i am sure, the problem is with our newly created images from our Microscope.

Is there a way we can find, or are there any logs which DICOM tags are actually creating the problem ?

Thank you,
Anil TA

2

Hi Anil,

Here’s a reference to the same kind of discussion: https://groups.google.com/g/orthanc-users/c/S1v39Uv_iBA/m/Y35n-0jKDwAJ

HTH,

Alain.

3

Hello,

You don’t provide enough information for use to be able to help you.

Please share a sample (low-resolution) image from your microscope, and provide the command-line you use to DICOM-ize it. Also, carefully describe your environment so that people can have a minimal working example to help you:
https://book.orthanc-server.com/users/support.html#discussing-a-minimal-working-example

Regards,
Sébastien-

4

Hi Team,

https://www.dropbox.com/s/7murqsrarn72pv7/Images.zip?dl=0

I have uploaded one of the sample files in the above link. I am able to upload the images in the Whole Slide Imaging Viewer.
Only the first level is shown. But Zoom In/Zoom Out is not working. to traverse the different levels We have four levels with 308, 24, 2 and 1 frames/images (pyramid).
Any help will be really appreciated. Thanks in advance.

Regards,
Anil TA

5

Hello,

After in-depth investigation, it appears that your modality is swapping the tag Column Position In Total Image Pixel Matrix Attribute (0048,021E) with the tag Row Position In Total Image Pixel Matrix Attribute (0048,021F). This inverse the x/y position of your tiles.

Here is a patch to make your files work with the mainline of the WSI plugin:

diff -r a6e4834ac141 Framework/Inputs/DicomPyramidInstance.cpp
--- a/Framework/Inputs/DicomPyramidInstance.cpp Mon Jul 10 16:22:14 2023 +0200
+++ b/Framework/Inputs/DicomPyramidInstance.cpp Mon Jul 10 16:23:24 2023 +0200
@@ -228,7 +228,7 @@
         }
         else
         {
-          frames_.push_back(std::make_pair(x / tileWidth_, y / tileHeight_));
+          frames_.push_back(std::make_pair(y / tileHeight_, x / tileWidth_));
         }
       }
     }

Obviously, I cannot include such a patch in the Orthanc project, as this is an issue that should be solved by the manufacturer of your modality.

Consequently, I would highly advise you to get in touch with the technical support team of MetaSystems Neon.

Kind Regards,
Sébastien-