Orthanc WSI image quality issue

[Drexler Chao]

Dear Sir,

We try to compare Orthanc WSI viewer and 3DHISTECH SlideViewer that support WSI DICOM.
1. The Orthanc version is docker jodogne/orthanc-plugins:latest
2. We download WSI DICOM from Orthanc and upload to the SlideViewer.
3. Use the /wsi/tiles/{id}/{z}/{x}/{y} URI to retrieve the individual tiles images.
4. (0002,0010)TransferSyntaxUID is 1.2.840.10008.1.2.4.50


Enclosed you could find the zip file for the test result.
The SlideViewer showed the contour was more clearly then retrieving the titles from the Orthanc via URI.

1. The retrieved tiled from /wsi/tiles/{id}/{z}/{x}/{y} URI is compressed or not?
2. How to make retrieved tiled quality better?
3. How to get the uncompressed or JPEG2k lossless via URI?
4. We are not sure the course of quality issue, any suggestion?

You will find the file: blob_https... to the browser and show the image.
Any advice will be sincerely appreciated.
Thank you.

[Drexler Chao]

Dear Sir,

According to Orthanc Book(Whole-slide microscopic imaging) as following link,

https://book.orthanc-server.com/plugins/wsi.html#decoding-the-individual-tiles

How to set up configuration file that Orthanc WSI plugin will re-encode the tile to PNG or JPEG2k?

If we modify DICOM tag (0002,0010)TransferSyntaxUID to 1.2.840.10008.1.2 or 1.2.840.10008.1.2.4.90 is correct solution?

I’d appreciate some help.

Best regards.

Drexler Chao

Drexler Chao 在 2023年3月24日 星期五晚上11:00:00 [UTC+8] 的信中寫道：

[Stephen Douglas Scotti]

1.2.840.10008.1.2.4.50

JPEG Baseline (Process 1):

Default Transfer Syntax for Lossy JPEG 8-bit Image Compression

I suspect that what you retrieved from Orthanc was compressed, although I don't know how it was stored originally in the first place on Orthanc.

The Orthanc config has numerous options for controlling comperssion encoding, etc.

https://hg.orthanc-server.com/orthanc/file/Orthanc-1.11.3/OrthancServer/Resources/Configuration.json

e.g.

  // Whether Orthanc transcodes DICOM files to an uncompressed
  // transfer syntax over the DICOM protocol, if the remote modality
  // does not support compressed transfer syntaxes (new in Orthanc 1.7.0).

  "TranscodeDicomProtocol" : true,

   "IngestTranscoding" : "1.2.840.10008.1.2",

If you decode the BLOB header (online) it shows:

bits_per_sample

8

category

image

color_components

3

encoding_process

Baseline DCT, Huffman coding

file_name

wsi_image.jpg

file_size

1445 kB

file_type

JPEG

file_type_extension

jpg

image_height

2353

image_size

2561x2353

image_width

2561

jfif_version

1.01

megapixels

6

mime_type

image/jpeg

resolution_unit

inches

x_resolution

96

y_cb_cr_sub_sampling

YCbCr4:2:0 (2 2)

y_resolution

96

Stephen D. Scotti, M.D.

[Drexler Chao]

Dear Sir,

We retrieved tiled from /wsi/tiles/{id}/{z}/{x}/{y} URI is JPEG image that might affect WSI image quality.

Is there any configuration we can set up and retrieve uncompressed or JPEG2k lossless WSI image?

And is there any API or URI we can use?

What do you think if we modify metadata 0002,0010 (TransferSyntaxUID) to 1.2.840.10008.1.2 or 1.2.840.10008.1.2.4.90 ?

Would you mind sharing suggestion or reference?

Any help would be sincerely appreciated.

Thank you very much.

Stephen Douglas Scotti 在 2023年3月27日 星期一凌晨12:30:55 [UTC+8] 的信中寫道：

[Alain Mazy]

Hi Drexler,

If you receive a file with Lossy Transfer Syntax eg 1.2.840.10008.1.2.4.50, it means that your device has sent it in this format and Orthanc won't be able to improve the image quality.  The transfer syntax must be configured to lossless on the device itself before sending the image to Orthanc.

On Orthanc side, you can however check that you have not set IngestTranscoding to "1.2.840.10008.1.2.4.50"

  // If this option is set, Orthanc will transparently transcode any
  // incoming DICOM instance to the given transfer syntax before
  // storing it into its database. Beware that this might result in
  // high CPU usage (if transcoding to some compressed transfer
  // syntax), or in higher disk consumption (if transcoding to an
  // uncompressed syntax). Also, beware that transcoding to a transfer
  // syntax with lossy compression (notably JPEG) will change the
  // "SOPInstanceUID" DICOM tag, and thus the Orthanc identifier at
  // the instance level, which might break external workflow.
  /**
     "IngestTranscoding" : "1.2.840.10008.1.2",
  **/

Hope this helps,

Alain

--
You received this message because you are subscribed to the Google Groups "Orthanc Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to orthanc-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/orthanc-users/5c68a474-8e14-4b86-bef6-5286cd488492n%40googlegroups.com.