fhir and dicom
TRANSCRIPT
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FHIR and DICOM
Brad GenereauxFHIR Developer DaysNovember 20, 2015
@integratorbrad
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Who am I?
Name: Brad Genereaux Company: Agfa HealthCare Background:
10 years in Canadian healthcare IT Putting HL7 and DICOM into all the things
5 years with Agfa HealthCare Imaging integrator, architect, product manager
Co-chair DICOM WG-27 (Web Technologies)
@integratorbrad
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DICOM is Imaging
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Imaging Resources
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THE NEED FOR IMAGING EVERYWHERE
What are we trying to solve:
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Worth 1,000 Words
“While written descriptions of lesions and infectious processes may be detailed, the visual presentation of these conditions is much more accurate and effective for diagnosis and treatment.” Imaging: New Electronic Tool For Clinicians,
2003 (Susan I. Reynolds)
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What do we need to do?
Image-enable everything! Put the images in the EMR / EHR / reports Share them in collaborative workflows Generate quick previews using thumbnails Convey the patient condition in ways text just can’t
do
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If I Can’t Find It, It Does Not Exist If imaging studies are not available, patients will
be re-imaged Increased risk -> radiation Increased cost -> unnecessary exams Increased delay for the patient Increased delay for other patients (or need for additional
perhaps unnecessary capacity)
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WHAT IS DICOM?Digital Imaging and Communications in Medicine
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Basic Imaging Workflow
Modality creates images in DICOM and transmits them to archive
Archive stores the images Radiologist requests images for reading Radiologist creates the report
?
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Active Modalities AR - Autorefraction AU - Audio BDUS - Bone Densitometry
(ultrasound) BI - Biomagnetic imaging BMD - Bone Densitometry (X-Ray) CR - Computed Radiography CT - Computed Tomography DG - Diaphanography DOC - Document DX - Digital Radiography ECG - Electrocardiography EPS - Cardiac Electrophysiology ES - Endoscopy FID - Fiducials GM - General Microscopy HC - Hard Copy HD - Hemodynamic Waveform IO - Intra-Oral Radiography IOL - Intraocular Lens Data IVOCT - Intravascular Optical
Coherence Tomography IVUS - Intravascular Ultrasound
KER - Keratometry KO - Key Object Selection LEN - Lensometry LS - Laser surface scan MG - Mammography MR - Magnetic Resonance NM - Nuclear Medicine OAM - Ophthalmic Axial
Measurements OCT - Optical Coherence Tomography
(non-Ophthalmic) OPM - Ophthalmic Mapping OP - Ophthalmic Photography OPT - Ophthalmic Tomography OPV - Ophthalmic Visual Field OSS - Optical Surface Scan OT - Other PLAN - Plan PR - Presentation State PT - Positron emission tomography
(PET) PX - Panoramic X-Ray REG - Registration
RESP - Respiratory Waveform RF - Radio Fluoroscopy RG - Radiographic imaging
(conventional film/screen) RTDOSE - Radiotherapy Dose RTIMAGE - Radiotherapy Image RTPLAN - Radiotherapy Plan RTRECORD - RT Treatment Record RTSTRUCT - Radiotherapy Structure
Set RWV - Real World Value Map SEG - Segmentation SMR - Stereometric Relationship SM - Slide Microscopy SRF - Subjective Refraction SR - SR Document STAIN - Automated Slide Stainer TG - Thermography US - Ultrasound VA - Visual Acuity XA - X-Ray Angiography XC - External-camera Photography
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Extended imaging workflows
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Foreign studies Regional archives
Non-DICOM modalities
EHR / EMR
Mobile Devices
Sharing Portals
Prior studies
Long-term archives
Other modalities 3D visualization
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Patient ;
1
Study 1
1Study x
Each patient has x studies, which has y series,
Instance 1
Instance z
Series 1
Series y
which has z instances… and could have f frames.
Image Hierarchy
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Instance UID Height Width Position SOP Class UID
Instance Series UID Modality Description Series Number Body Part
Series Study UID Date of Study Description Refer Physician Accession Availability
Study
Image Metadata
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DICOM Tagging
DICOM’s binary structure for representing meta-data; i.e., (0010,0010) -> Patient name (0008,0090) -> Referring physician name
Tags are defined using a VR (a data type) and an VM (multiplicity factor)
In the XML and JSON representations, it is easier
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Some simple rules
UIDs (i.e., Study, series and SOP instance UIDs) are intended to be globally unique Unlike accession numbers, which have historically
had collision problems You are not supposed to change DICOM
objects themselves; if you do, they must get an updated SOP Instance UID
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Key Objects and Markup
Key Objects Way to represent a set of images besides “all of
the images” For example, “marked for review”, “marked for
quality issues”, “XDS publishable set” GSPS
Markup and annotations on the images Includes factors like window/level Applied on images or image sets
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1. Get DICOM images 2. Get a DICOM viewer 3. Get a DICOM library
Blog post at http://goo.gl/hSNSUt
Hacking DICOM : Primer
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Good place to start :Cancer Imaging Archive https://goo.gl/RY2cFD
1. Get DICOM Images
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Good place to start :MicroDicom http://www.microdicom.com/
2. Get a DICOM Viewer
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Good place to start :DCM4CHE http://goo.gl/4h9ck8
3. Get a DICOM Library
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Imaging used to be hard
Image complication Retrieving images is done via a non-trivial protocol Processing images uses non-trivial file format Displaying images has much to take into consideration Saving images requires in-depth knowledge
Image ecosystem complication Image lifecycle (acquisition, ingestion, storage) challenging Metadata extraction requires parsing of binary data Scaling is a problem that must be addressed Storage and bandwidth/latency challenges are ever-present as
image sizes grow into gigabytes
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DICOMWEB™ MAKES IT LOOK EASY
Imaging Interoperability enters the REST arena :
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Becomes possible to consume content directly by clients (browsers, mobile) No “special tools” required Minimize what is
transferred Allows for rapid
development and consumption of content
Frees content from closed systems and spawns integrations into today’s technologies
Why Web for Imaging?
X
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WADO (Web Access to DICOM Objects) was created in 2003, providing object level access only
MINT (Medical Imaging Network Transport) was created ~2011 (not part of DICOM) out of a recognition of the importance of REST transport, and has since been deprecated for newer, interoperable technologies
DICOMweb™ was thus developed, and resources have been added ever since
History of Medical Imaging on the Web
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What is DICOMweb™?
EMR
PACS VNA XDS Image Processors
Teaching Systems Research Patients Care
Teams
DICOMweb™DICOMweb™DICOMweb™DICOMweb™DICOMweb™
DICOMweb™ DICOMweb™ DICOMweb™ DICOMweb™
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DICOMweb™ Services• QIDO-RS (Query based on ID for DICOM Objects)• DICOM PS3.18 6.7Query• WADO-RS (Web Access of DICOM Objects)• DICOM PS3.18 6.5 Retrieve• STOW-RS (Store over the web)• DICOM PS3.18 6.6Store• UPS-RS (Worklist Service)• DICOM PS3.18 6.9Tasks• Capabilities Service• DICOM PS3.18 6.8Server Info
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Study Date LinkAbdomen CT
Jan. 17, 2014
http://<url>
Chest CR Mar. 23, 2015
http://<url>
Query (QIDO-RS) Example
What studies do you have for John Doe?
GET ht
tp://s
erver.
com/st
udies/
?00100
010=DO
E^JOHN
* There is synergy here with FHIR ImagingStudy
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Retrieve (WADO-RS) Example
Show me images for the Abdomen CT
GET ht
tp://s
erver.
com/st
udies/
1.2.3/
series
/4.5.6
/
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Stored
Store (STOW-RS) Example
POST h
ttp://
server
.com/s
tudies
Store this image
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Tasks (UPS-RS) Example
GET ht
tp://s
erver.
com/wo
rkitem
s/?007
41202=
DRBRAD
What do I need to do today?
Study Date LinkAbdomen CT
Nov. 20, 2015
http://<url>
Abdomen CT
Nov. 20, 2015
http://<url>
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Capabilities Example
OPTION
S http
://ser
ver.co
m/What can you do for me?
• QIDO-RS (Query based on ID for DICOM Objects)• DICOM PS3.18 6.7Query• WADO-RS (Web Access of DICOM Objects)• DICOM PS3.18 6.5 Retrieve• STOW-RS (Store over the web)• DICOM PS3.18 6.6Store• UPS-RS (Worklist Service)• DICOM PS3.18 6.9Tasks• Capabilities Service• DICOM PS3.18 6.8Server Info
* There is synergy here with FHIR’s Conformance
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<DicomAttribute Tag="00080020" VR="DT" Keyword="StudyDate"> <Value number="1">20130409</value></DicomAttribute><DicomAttribute Tag="00080061" VR="CS" Keyword="ModalitiesInStudy"> <Value number="1">CT</value></DicomAttribute><DicomAttribute Tag="00100010" VR="PN" Keyword="PatientName"> <PersonName number="1"> <SingleByte> <FamilyName>Doe</FamilyName> <GivenName>John</GivenName> </PersonName></DicomAttribute><DicomAttribute Tag="0020000D" VR="UI" Keyword="StudyInstanceUID"> <Value number="1"> 1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873 </Value></DicomAttribute>
Data Structures
XML
"00080020": { "vr": "DT", "Value": ["20130409"]},"00080061": { "vr": "CS", "Value": ["CT"]}, "00100010": { "vr": "PN", "Value": [ { "Alphabetic": { "Family": ["Doe"], "Given": ["John"] } }]},"0020000D": { "vr": "UI", "Value": [
"1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873"
]}
JSON
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DICOMweb™ CheatsheetVerb Path Type DescriptionPOST {s}/studies Store PS3.18 6.6
.1Store instances
GET {s}/studies?... Query PS3.18 6.7.1
Query for matching studies
GET {s}/studies/{studyUID} Retrieve PS3.18 6.5.1
Retrieve entire study
POST {s}/studies/{studyUID} Store PS3.18 6.6.1
Store instances
GET {s}/studies/{studyUID}/metadata Retrieve PS3.18 6.5.6
Retrieve metadata
GET {s}/studies/{studyUID}/series?... Query PS3.18 6.7.1
Query for matching series in a study
GET {s}/studies/{studyUID}/series/ {seriesUID}
Retrieve PS3.18 6.5.2
Retrieve entire series
GET {s}/studies/{studyUID}/series/ {seriesUID}/metadata
Retrieve PS3.18 6.5.6
Retrieve series metadata
GET {s}/studies/{studyUID}/series/ {seriesUID}/instances?...
Query PS3.18 6.7.1
Query for matching instances in a series
GET {s}/studies/{studyUID}/series/ {seriesUID}/instances/ {instanceUID}
Retrieve PS3.18 6.5.3
Retrieve instance
GET {s}/studies/{studyUID}/series/ {seriesUID}/instances/ {instanceUID}/metadata
Retrieve PS3.18 6.5.6
Retrieve instance metadata
GET {s}/studies/{studyUID}/series/ {seriesUID}/instances/ {instanceUID}/frames/{frames}
Retrieve PS3.18 6.5.4
Retrieve frames in an instance
GET /{bulkdataReference} Retrieve PS3.18 6.5.5
Retrieve bulk data
Verb Path Type DescriptionPOST {s}/workitems
{?AffectedSOPInstanceUID}PS3.18 6.9.1 CreateUPS
POST {s}/workitems/{UPSInstanceUID} {?transaction}
PS3.18 6.9.2 UpdateUPS
GET {s}/workitems{?query*} PS3.18 6.9.3 SearchForUPS
GET {s}/workitems/{UPSInstanceUID} PS3.18 6.9.4 RetrieveUPS
PUT {s}/workitems/{UPSInstanceUID}/state
PS3.18 6.9.5 ChangeUPSState
POST {s}/workitems/{UPSInstanceUID}/ cancelrequest
PS3.18 6.9.6 RequestUPS Cancellation
POST {s}/workitems/{UPSInstanceUID}/ subscribers/{AETitle}{?deletionlock}
PS3.18 6.9.7 CreateSubscription
POST {s}/workitems/1.2.840.10008.5.1.4.34.5/
PS3.18 6.9.8 SuspendGlobal Subscription
DELETE {s}/workitems/{UPSInstanceUID}/ subscribers/{AETitle}
PS3.18 6.9.9 DeleteSubscription
GET {s}/subscribers/{AETitle} PS3.18 6.9.10 OpenEventChannel
N/A N/A PS3.18 6.9.11 SendEventReport
Available at:http://dicomweb.org/DICOMweb-Cheatsheet.pdf
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DICOM Main Site http://dicom.nema.org
DICOMweb™ Reference PS3.18 http://goo.gl/bIFHV3 http://dicomweb.org
Get involved with DICOM Link to join mailing list off main DICOM website
Where do I find more information?
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Available open-source server libraries dcm4chee Orthanc
Available open-source client libraries Cornerstone
Great resource: https://github.com/chafey/dicomWeb
Some DICOMweb™ Tools
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dcm4cheehttps://github.com/mohannadhussain/dcm4chee4-quick-start-vagrant
Orthanchttps://github.com/chafey/orthanc-vagrant
DICOMweb™ Vagrants
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FHIR AND IMAGINGOnwards to Imaging and FHIR
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ImagingStudy
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Study Date LinkAbdomen CT
Jan. 17, 2014
http://<url>
Chest CR Mar. 23, 2015
http://<url>
ImagingStudy Example
What studies do you have for John Doe?
GET ht
tp://s
erver.
com/fh
ir/
Imagin
gStudy
?subje
ct.nam
e=Doe%
2CJohn
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ImagingObjectSelection
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Hacking with FHIR+DICOMweb You can stage a FHIR server and a
DICOMweb server, and synchronize data We can hook you up with that!
SIIM (Society for Imaging Informatics in Medicine) has graciously offered access to their Hackathon infrastructure and unified datasets for FHIR Developer Days participants
Access will be good for 3 months
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Supporting Healthcare Through Innovation, Creativity, and Discovery The Society for Imaging Informatics in Medicine (SIIM) is the leading healthcare professional organization representing the interests and goals of those who work with and whose work is affected by the rapidly changing world of imaging technologies and information management. SIIM seeks to spearhead research, education, and discovery of innovative solutions to advance imaging informatics, enable the best use of images throughout the healthcare enterprise, and improve the delivery and quality of patient care. SIIM facilitates this mission through activities such as: SIIM 2016 Annual Meeting | June 29 - July 1, 2016 | Portland, OR | SIIM2016.org 2016 SIIM Hackathon hosted at SIIM 2016 - aimed at supporting workflow and process
improvement across healthcare to provide a set of cloud-based APIs to highlight the next generation of health IT standards.
Innovation Challenge Prize hosted at SIIM 2016 - $10,000 to encourage, recognize and reward innovation that will lead enterprise imaging change.
Publication of the Journal of Digital Imaging. Educational Webinar Series, eCommunity, Online Learning Materials and More! SIIM.org
Imaging REST Resources and data provided by SIIM Hackathon
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Getting Access to SIIM Servers and Datasets If you are not a SIIM member:
Open your web browser to http://siim.org/ In the top-right, click “Join SIIM eCommunity”. On the registration page, select registration type as “Contact”, and
click Continue. Note: There is no cost to register as a Contact.
Complete the form, and accept the agreement. Notify me (Brad) of your username so I can grant you
access Click “My Profile” -> Groups -> Innovation: Hackathon
@integratorbrad
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IHE RADIOLOGY, DICOM AND FHIR
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Web-based Image Capture Uses DICOMweb’s
Store (STOW-RS) methods to enable acquisition of images using web services
WIC Profile
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IID Profile
Invoke Image Display Connects user to a zero-footprint web viewer in a
standardized way to visualize an imaging study Aside from grabbing thumbnails using WADO-RS, this
is a great method for embedding a viewer with an EMR as a viewer should handle advanced functionalities (like applying GSPS and appropriate contrasting)
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MHD-I Profile
Mobile access to Health Documents for Imaging RESTful access to XDS-I imaging repositories Updated to use FHIR’s ImagingObjectSelection
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Activity being investigated by the HL7 II Group RadReport.org defines ubiquitous international
radiology report templates Using an IHE profile called MRRT – Management of Radiology
Report Templates Standardized reports, with ontological references, can be
generated out of these templates Some of these attributes can be bubbled up to the
DiagnosticReport level, and exposed via a FHIR profile
MRRT, RadReport, and FHIR Profiles
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PUTTING IT ALL TOGETHER
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Image-Enabling Reports
FHIR® DICOMweb™
EMR Image Cache
Discover radiology reports as
CDA
Retrieve associated key images
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Enabling Richer Worklists
FHIR® DICOMweb™
HIS Image Cache
Enrich with patient
metadata
Retrieve work list for
modality
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THANK YOU!Any questions?
@integratorbrad