SM modality OHIF viewer plugin

[Robertus IO]

Hello:

I am trying to view SM images from pathology samples. 

The images were uploaded without problems on the XNAT server, but they do not show on the OHIF viewer plugin. 

When they were tested on the native OHIF viewer (https://v3-demo.ohif.org/local) they were showed properly. 

From the logs, the image is expected to have a dicom tag: ImageOrientationPatient but the modality of the image is SM. The SM modality does not contain this tag. 

The SM image has the ImageOrientationSlide tag . 

Where is the problem? Is it supported on the OHIF viewer plugin?

Here are the ohifviewer.log lines:

2022-10-10 10:21:29,408 [reactorDispatcher-11] INFO  icr.etherj.AbstractPathScan - Scanning 12 files from /data/xnat/archive/Test11/arc001/2000000/SCANS...

2022-10-10 10:21:29,410 [reactorDispatcher-11] WARN  icr.etherj.AbstractPathScan - Exception in client PathScanContext

java.lang.IllegalArgumentException: ImageOrientationPatient missing or invalid - Frame: 1

      at icr.etherj.dicom.impl.MultiframeSopInstance.getImageOrientationPatient(MultiframeSopInstance.java:589)

      at icr.etherj.dicom.impl.MultiframeSopInstance.<init>(MultiframeSopInstance.java:108)

      at icr.etherj.dicom.impl.MultiframeSopInstance.<init>(MultiframeSopInstance.java:87)

      at icr.etherj.dicom.impl.DefaultDicomToolkit.createSopInstance(DefaultDicomToolkit.java:214)

      at icr.etherj.dicom.DicomReceiver.notifyItemFound(DicomReceiver.java:135)

      at icr.etherj.dicom.DicomReceiver.notifyItemFound(DicomReceiver.java:53)

      at icr.etherj.AbstractPathScan$ContextTreeWalker.onFile(AbstractPathScan.java:296)

      at icr.etherj.AbstractPathScan.walkTree(AbstractPathScan.java:220)

      at icr.etherj.AbstractPathScan.scan(AbstractPathScan.java:163)

      at icr.etherj.AbstractPathScan.scan(AbstractPathScan.java:103)

      at org.nrg.xnatx.ohifviewer.inputcreator.CreateOhifViewerMetadata.scanPath(CreateOhifViewerMetadata.java:106)

      at org.nrg.xnatx.ohifviewer.inputcreator.CreateOhifViewerMetadata.jsonify(CreateOhifViewerMetadata.java:86)

      at org.nrg.xnatx.ohifviewer.inputcreator.ConfigServiceJsonCreator.create(ConfigServiceJsonCreator.java:109)

      at org.nrg.xnatx.ohifviewer.inputcreator.JsonMetadataHandler.createAndStoreJsonConfig(JsonMetadataHandler.java:122)

      at org.nrg.xnatx.ohifviewer.event.listeners.OhifViewerEventListener.generateJson(OhifViewerEventListener.java:209)

      at org.nrg.xnatx.ohifviewer.event.listeners.OhifViewerEventListener.checkAnonAndGenerateJson(OhifViewerEventListener.java:202)

      at org.nrg.xnatx.ohifviewer.event.listeners.OhifViewerEventListener.handleEvent(OhifViewerEventListener.java:161)

      at org.nrg.xnatx.ohifviewer.event.listeners.OhifViewerEventListener.accept(OhifViewerEventListener.java:99)

      at org.nrg.xnatx.ohifviewer.event.listeners.OhifViewerEventListener.accept(OhifViewerEventListener.java:68)

      at reactor.bus.EventBus$3.accept(EventBus.java:317)

      at reactor.bus.EventBus$3.accept(EventBus.java:310)

      at reactor.bus.routing.ConsumerFilteringRouter.route(ConsumerFilteringRouter.java:72)

      at reactor.bus.EventBus.accept(EventBus.java:591)

      at reactor.bus.EventBus.accept(EventBus.java:63)

      at reactor.core.dispatch.AbstractLifecycleDispatcher.route(AbstractLifecycleDispatcher.java:160)

      at reactor.core.dispatch.MultiThreadDispatcher$MultiThreadTask.run(MultiThreadDispatcher.java:74)

      at reactor.core.dispatch.WorkQueueDispatcher$3.onEvent(WorkQueueDispatcher.java:115)

      at reactor.core.dispatch.WorkQueueDispatcher$3.onEvent(WorkQueueDispatcher.java:112)

      at reactor.jarjar.com.lmax.disruptor.WorkProcessor.run(WorkProcessor.java:138)

      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

      at java.lang.Thread.run(Thread.java:750)

[Simon Doran]

Hi ,

  This is the expected behaviour for the moment and XNAT's integration does not yet support microscopy viewing.

  We have an experimental alpha build for XNAT, but we are waiting for the finalisation of a large piece of work to provide DICOMweb compatibility within XNAT. The native OHIF viewer's implementation of microscopy viewing relies on accessing images via DICOMweb.

  This is a priority, though, and we will be returning to this very soon after the XNAT workshop in November.

  Best wishes,

Simon

[Robertus IO]

Hello!

Thank you for your response.

• It would be very useful for us to upload the images to XNAT. 
• Would it be possible to config the app or to modify the images so they could be uploaded?
• Is there a possibility to modify the Dicom tags in order to upload the images and view them on OHIF-Viewer?                                         

Regards.

[David Clunie]

When you get XNAT DICOMweb service going, the MGH SLIM viewer was written to address the limitations of OHIF (since the latter does not support a "virtual microscopy" viewing paradigm with pan and zoom of the pyramidal tiled representation used in DICOM WSI).

See http://github.com/herrmannlab/slim.

David

[Robertus IO]

Hello again:

Back in this thread was told there would be the possibility of having Microscopy modalities supported into XNAT. 

For the Anatomical Pathology discipline, this is a very useful tool to have. 

Would it be possible to know if is there any estimated date for such avaliability? 

Regards.

[Rick Herrick]

My understanding is that the OHIF viewer doesn't support microscopy data without full DICOMweb support and we are still working on building DICOMweb in XNAT.

Rick Herrick

Senior Software Developer

rickh...@flywheel.io

------ Original Message ------

From "Robertus IO" <iorob...@gmail.com>

To "xnat_discussion" <xnat_di...@googlegroups.com>

Date 12/13/2022 7:17:59 AM

Subject [XNAT Discussion] Re: SM modality OHIF viewer plugin

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[Simon Doran]

Hi All,

  Just to let you guys know that this work is still ongoing. We have an alpha version running but there are still some performance issues with the DICOMweb support that we hope to fix in the first quarter of 2023. Unfortunately, I can't be any more specific about release dates.

  Best wishes,

Simon

[Robertus IO]

Thank you very much for the estimated release.

[Robertus IO]

Hello again:

Is there any news about the SM modality support or the new version of XNAT?

Thank you in advance.

[Rick Herrick]

It’s not really support for the SM modality that’s the issue atm (XNAT already supports SM as a session data type) but full support for DICOMweb operations, which isn’t on the roadmap for the upcoming 1.8.8 release.

Rick Herrick

Senior Software Developer

rickh...@flywheel.io

------ Original Message ------

From "Robertus IO" <iorob...@gmail.com>

To "xnat_discussion" <xnat_di...@googlegroups.com>

Date 3/21/2023 8:27:05 AM

Subject Re: [XNAT Discussion] Re: SM modality OHIF viewer plugin

To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/108bf998-63d0-434d-af76-98baaa46a316n%40googlegroups.com.

[Robertus IO]

Thank you for your response. Finally we got it solved by other means.

[Robertus IO]

Hello!

BTW, would you have any estimation for the implementation of the DICOMweb? 

Thank you!

[Akshaykumar Kamble]

Hi Robertus

How did you solve this issue?

We are also looking for microscopy images to be shown in the OHIF viewer, right now we are converting them to PNG and then to dicom again but that way it is loosing lot of resolution. Useful for teaching but not for diagnostic purposes.

Thanks for help.

[Simon Doran]

Hi Akshaykumar and Robertus,

  Viewing microscopy images is on our roadmap and scheduled to be released as version 3.7 of the XNAT-OHIF viewer plugin with an anticipated release date of early August 2023.

  Best wishes,

Simon

[Robertus IO]

Hello Sir,

We solved it opening the images outside of XNAT with a native viewer.

It would be really nice to have SM images supported by the OHIF plugin.

Regards.

[Julián Perez]

Hi,

I have the same question. Would it be possible to have the OHIF plugin supporting the SM images? Could you please provide an update on estimate date of completation? 

Thanks! 

Cheers, Julián

[Simon Doran]

Hi Julián,

  We apologise that the new version of the viewer plugin supporting SM is not yet out. We encountered some technical difficulties during the implementation, which have delayed the release date. However, we are working hard to get this ready and will certainly announce the new version widely as soon as it is ready.

  Best wishes,

Simon  

[David Clunie]

Hi Simon

Are these issues with the DICOMweb server implementation or the viewer plugin itself?

I ask, because it would be interesting to test the Slim WSI SM viewer (which is now
maintained by IDC [1]) with XNAT once DICOMweb support is ready. We know it currently
works with GCP and dcm4chee-5.

You might also want to try Google's open source DICOMweb WSI viewer [3] though that
hasn't been updated in a while and may be GCP-specific to deploy but could be adapted.

IDC has lots of DICOM WSI for you to test with [4], including some particularly large ones
that you might want to stress your server with in cases it freaks out on > 2GB images
(some of these are > 20GB J2K reversibly compressed and when decompressed are over
40GB) [5].

David

1. https://github.com/ImagingDataCommons/idc-slim
2. https://www.nature.com/articles/s41467-023-37224-2
3. https://github.com/GoogleCloudPlatform/dicomweb-wsi-viewer
4. https://portal.imaging.datacommons.cancer.gov/explore/filters/?Modality=SM
5. https://portal.imaging.datacommons.cancer.gov/explore/filters/?collection_id=rms_mutation_prediction

> <https://flywheel.io>

>
>
> ------ Original Message ------
> From "Robertus IO" <iorob...@gmail.com>
> To "xnat_discussion" <xnat_di...@googlegroups.com>
> Date 3/21/2023 8:27:05 AM
> Subject Re: [XNAT Discussion] Re: SM modality OHIF viewer plugin
>
>> Hello again:
>>
>> Is there any news about the SM modality support or the new version of XNAT?
>>
>> Thank you in advance.
>>
>> El miércoles, 14 de diciembre de 2022 a las 11:40:24 UTC+1, Robertus IO escribió:
>>
>> Thank you very much for the estimated release.
>>
>>
>> El miércoles, 14 de diciembre de 2022 a las 10:07:36 UTC+1, Simon Doran escribió:
>>
>> Hi All,
>>
>>   Just to let you guys know that this work is still ongoing. We have an alpha version running but there are still some performance issues with the DICOMweb support that we hope to fix in the first quarter of 2023. Unfortunately, I can't be any more specific about release dates.
>>
>>   Best wishes,
>>
>> Simon
>>
>> On Tuesday, December 13, 2022 at 5:15:06 PM UTC Rick Herrick wrote:
>>
>> My understanding is that the OHIF viewer doesn't support microscopy data without full DICOMweb support and we are still working on building DICOMweb in XNAT.
>>
>> Rick Herrick
>> Senior Software Developer
>> rickh...@flywheel.io

>> <https://flywheel.io>

>>
>>
>> ------ Original Message ------
>> From "Robertus IO" <iorob...@gmail.com>
>> To "xnat_discussion" <xnat_di...@googlegroups.com>
>> Date 12/13/2022 7:17:59 AM
>> Subject [XNAT Discussion] Re: SM modality OHIF viewer plugin
>>
>>> Hello again:
>>>
>>> Back in this thread was told there would be the possibility of having Microscopy modalities supported into XNAT.
>>> For the Anatomical Pathology discipline, this is a very useful tool to have.
>>> Would it be possible to know if is there any estimated date for such avaliability?
>>>
>>> Regards.
>>>
>>> El viernes, 14 de octubre de 2022 a las 15:39:52 UTC+2, dcl...@dclunie.com escribió:
>>>
>>> When you get XNAT DICOMweb service going, the MGH SLIM viewer was written to address the limitations of OHIF (since the latter does not support a "virtual microscopy" viewing paradigm with pan and zoom of the pyramidal tiled representation used in DICOM WSI).
>>>

>>> See http://github.com/herrmannlab/slim <http://github.com/herrmannlab/slim>.
>>>
>>> David

[Simon Doran]

Hi David,

  Thanks very much for your interest in the XNAT-OHIF implementation of digital pathology viewing. We know that it is very important to the community and have been focusing a lot of attention on it at ICR and NCITA.

  I didn't want to go into lots of technical detail in the previous brief update, but, broadly, the delays have come about because we are trying to optimise the implementation of the DICOMweb server implementation. We had a proof-of-concept plugin available as early as the start of 2022, but have been discussing with Steve Moore and the Flywheel folks a number of different strategies for implementing DICOMweb at the XNAT backend. Some of the issues arise from the well-documented differences [1] between the DICOM and XNAT information models, which mean that a completely generalised DICOMweb implementation for XNAT is hard to achieve. Further work has been involved in optimising the image retrieval from the backend to make the viewing experience as smooth as possible.

  You will be pleased to know that when we release the plugin, our aim will be to provide an integrated version of the SLIM viewer. Thanks for pointing us in the direction of the large SM files on IDC. Our initial testing programme is set to include the DICOM WG-26 multi-vendor connectathon dataset, already loaded onto our dev XNAT platform, but the linked resources that you suggest above should make a very good addition.

[1] https://www.mdpi.com/2379-139X/8/1/40

  Best wishes,

Simon