Dicomizer - wrong Pixel Spacing (0028,0030)?

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1

Hi,

Maybe I’m doing something wrong, but I’m converting an Aperio SVS file to dicom using the OrthancWSIDicomizer.exe tool (with openslide windows build 20160717). Everything works fine, other than the PixelSpacing tag (0028,0030) is assigned a value of 0.000723658828\0.000750300125. The original svs file has a mpp of 0.2473um making it a factor of 2.93 out given conversion to mm from um.

I’m a bit confused. Is this a bug? Openslide reports it correctly. I thought it might be something to do with the corresponding svs tif-tag being in inches (tif allows both Inches and mm I think), but that’s the wrong factor out.

Additionally, I can’t see if the objective (x40 in this case) is transferred over to a tag?

Thanks

Derek Magee

2

Hello,

Please could you share a sample Aperio SVS file so that we can investigate your question?
https://book.orthanc-server.com/users/support.html#discussing-a-minimal-working-example

Regards,
Sébastien-

3

I have sent a link in a private message.

Derek

4

I confirm the good reception of the sample image: Thanks!

I’ll have a look at it in the following weeks.

Regards,
Sébastien-

5

To add. I got the google wsi-dicom converter ( GitHub - GoogleCloudPlatform/wsi-to-dicom-converter: Conversion tool/library for converting whole slide images to DICOM ) working now and that sems to have pixel spacing correct at 0.000248\0.000248.

Derek

6

Hi,

Not sure how you are getting on with this, but other images I’ve acquired from scanners seem to have this field (0028,0030) correct .

In my original question I asked about lens objective (e.g. 20X, 40X) apparently this is tag 0x0048,0x0112. Dicomiser does not create this tag (it is available in openslide).

Additionally, no label (or othr auxillary image) seems to be generated - at least as far as I can tell as the image type tag (0x0008,0x0008). Looking at images from scanners (Leica/Philips/Hammamatsu) this field is usually one of:

ORIGINAL\PRIMARY\VOLUME\NONE - Full resolution image (or DERIVED\PRIMARY\VOLUME\NONE in a Hammamatsu image I have)
DERIVED\PRIMARY\LOCALIZER\RESAMPLED - Localizer image
DERIVED\PRIMARY\VOLUME\RESAMPLED - Downsampled level image
ORIGINAL\PRIMARY\LABEL\NONE - Label image
ORIGINAL\PRIMARY\OVERVIEW\NONE - Overview image

Auxilliary images, such as the label image, are also available from Openslide.

Yours

Derek

7

Hello,

Your problem is simply that OrthancWSIDicomizer in releases <= 1.1 of the WSI plugin, does not support the automated extraction of the imaged volume from openslide.mpp-x and openslide.mpp-y properties.

In releases <= 1.1 of the WSI plugin, you have to explicitly provide these dimensions as follows:

$ ./OrthancWSIDicomizer --openslide=libopenslide.so 171802.svs --imaged-height=4.944022 --imaged-width=5.126034

In forthcoming release 2.0 of the WSI plugin, this automated detection will be implemented thanks to the following changeset: orthanc-wsi: 77afef2cf64b

So, in the near future, the OrthancWSIDicomizer will no longer necessitate explicit calls to --imaged-height and --imaged-width, and will automatically detect the proper pixel spacing (at least if this information is provided by OpenSlide).

Kind Regards,
Sébastien-