ImagingDataCommons / slim

Interoperable web-based slide microscopy viewer and annotation tool
https://imagingdatacommons.github.io/slim/
Apache License 2.0
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How to get Slim DICOM SR document ? #33

Closed DrexlerChao closed 3 years ago

DrexlerChao commented 3 years ago

Dear Sir, After draw and save ROI, the Slim store them as DICOM comprehensive 3D SR documents. We use 3D Slicer DICOMweb browser to connect slim http://localhost:8008/dicomweb, the list of cases as follow, Screenshot from 2021-07-19 09-26-52 We try to retrieve studies, but the 3D Slicer response the error as follow, Screenshot from 2021-07-21 11-42-23 Here is 3D Slicer debug message, Screenshot from 2021-07-21 14-47-22

Where is the location that slim saved the DICOM files and SR documents ? How to read/write the SR document when AI training / inference ? Could you recommend some tools to us to use DICOM SR document ?

Any help or suggestion will be sincerely appreciate. Thanks a lot.

DrexlerChao commented 3 years ago

Dear Sir, We use Postman API tool to GET slim study, series and instance list via http://localhost:8008/dicomweb/studies http://localhost:8008/dicomweb/series http://localhost:8008/dicomweb/instance Screenshot from 2021-07-21 13-06-44

We are not sure the dicomweb API whether enable to GET the DICOM SR document ?

hackermd commented 3 years ago

The Retrieve Transaction of the DICOMweb Studies Service is specified in part 18 section 10.4 of the DICOM standard.

Retrieving the whole study is generally not a good idea in digital pathology, given the size of the data sets. I would recommend first searching for instances with query string Modality=SR and then retrieving the instances individually. You may want to take a look at DICOMweb Python client (DICOMwebClient.search_for_instances and DICOMwebClient.retrieve_instance)

hackermd commented 3 years ago

I am closing this issue since it's a general question about the DICOMweb standard rather than the Slim application.

DrexlerChao commented 3 years ago

@hackermd Dear Sir, Thanks for your useful suggestions.