[Girder-users] Slicer interfacing with Girder

[Brian E Chapman]

Hi Brian,

I think I’m mostly interested in things from the Girder side as what I would like to do is be able to directly access images stored in Girder via a Jupyter notebook or Slicer (for two examples). Also more general than DICOM as we would tend to have as many jpeg, nifti, nrrd, or meta images as DICOM. This is something I struggled with in Midas and wrote some work-arounds for to get SimpleITK to read files from Midas (creating soft links with the correct file extension to the stored resource in Midas).

 I should delve into your dermatology code more as I imagine what you are doing in that is close to what I envision doing with volumetric medical images.

Brian

From: Brian Helba <brian.helba at kitware.com<mailto:brian.helba at kitware.com>>
Date: Friday, September 11, 2015 at 4:19 PM
To: Patrick Reynolds <patrick.reynolds at kitware.com<mailto:patrick.reynolds at kitware.com>>
Cc: "girder-users at public.kitware.com<mailto:girder-users at public.kitware.com>" <girder-users at public.kitware.com<mailto:girder-users at public.kitware.com>>, Brian Chapman <brian.chapman at utah.edu<mailto:brian.chapman at utah.edu>>, Jean-Christophe Fillion-Robin <jchris.fillionr at kitware.com<mailto:jchris.fillionr at kitware.com>>, "pieper at isomics.com<mailto:pieper at isomics.com>" <pieper at isomics.com<mailto:pieper at isomics.com>>
Subject: Re: [Girder-users] Slicer interfacing with Girder


What a timely question!

Today, at the DICOMweb 2025 hack session, JC and I worked on adding support for RESTful DICOM protocols (WADO first) into Girder.

Steve Pieper, who was with us, worked on (and got a working demo for) adding similar support into Slicer.

A goal that we discussed is to allow data exchange via this mechanism.  If you're more interested in the Girder side, talk to me, JC, and Zack Mullen (but feel free to CC the list too). If you're more interested in the Slicer side, talk to JC and Steve.

Hi Brian,

This is certainly something we'd like to do. I believe we'll be doing some of this work sometime in the next few months, but JC (in copy) can probably better comment on that (he's our Slicer guy).

Thanks,
Patrick Reynolds
Technical Leader
Kitware, Inc.
919 869 8848<tel:919%20869%208848>

On Fri, Sep 11, 2015 at 4:52 PM, Brian E Chapman <Brian.Chapman at utah.edu<mailto:Brian.Chapman at utah.edu>> wrote:
Hi Everyone,

I was wondering whether a Slicer extension for Girder (similar to ThingiverseBrowser or XNATSlicer) exists or is being developed to allow Slicer to interact directly with resources in Girder.

Brian
—
Brian E. Chapman, Ph.D.
Associate Professor
Department of Radiology
University of Utah


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