Le logiciel libre au service de l'imagerie médicale par Sébastien Jodogne | Liege Creative, 21.03.14

Vendredi 21 mars

Le logiciel libre au service de l'imagerie médicale

Sébastien JODOGNE, Medical Imaging Engineer, ULg - CHU, Department of Medical Physics

Dans le cadre du festival ImagéSanté

Avec le soutien de :

IntroductionOrthanc

Free and Open-Source Software

Le logiciel libre au service de l’imagerie medicale

Sebastien Jodogne

21 mars 2014

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IntroductionOrthanc


Who Am I?

PhD in Computer Science (ULg, 2006):

Software engineering.Computer vision = machine learning + image processing.High-performance computing.Theoretical computer science.

Professional experience in private companies:

CCTV – Closed circuit television (Euresys, Secosys),Machine vision (Euresys, Jomago),Broadcasting (EVS).

Since 2011: Medical imaging engineer at the CHU of Liege(Department of medical physics).

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1 IntroductionRadiology and RadiotherapyProblems with DICOM in HospitalsThe Need for Another Free Tool

2 OrthancPhilosophyOrthanc in ActionCurrent Usage

3 Free and Open-Source SoftwareDefinitionPractical, Economic Benefits of FOSSSummary




IntroductionOrthanc


Radiology and RadiotherapyProblems with DICOM in HospitalsThe Need for Another Free Tool

Imaging Flows for Radiology

Hospital Information System

Radiology Information System

Picture Archiving &Communication System (PACS)

+

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RIS/PACS Manufacturers

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RIS/PACS Manufacturers

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Radiotherapy

What is Radiotherapy?

“The medical use of ionizing radiation, generally as partof cancer treatment, to control or kill malignant cells.”

CHU of Liege

≈ 2600 new cases per year.

First radiotherapy department in Belgium (6 linacs).

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Radiotherapy Manufacturers

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The Evolution of Radiotherapy

Surgical Strike

Main Problem

How to identify the target? ⇒ Medical Imaging

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The Evolution of Radiotherapy

Surgical Strike

Main Problem

How to identify the target? ⇒ Medical Imaging

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Multimodal Medical Imaging for Radiotherapy

CT + MRI + PET-CT

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Imaging Flows for External Radiotherapy

Simulation CT

MRI

PET-CT Nuclear medicine

Contouring Ballistics

Treatment

CyberKnife

Many imaging flows, everything is done with DICOM!

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Imaging Flows for External Radiotherapy

Simulation CT

MRI

PET-CT Nuclear medicine

Contouring Ballistics

Treatment

CyberKnife

Many imaging flows, everything is done with DICOM! 9 / 43




IntroductionOrthanc



What Is DICOM?

1 File Format:

One image slice + Patient metadata

2 Network Protocol — Early example of Web services:

Send local images,

Search remote images,

Retrieve remote images.

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What Is DICOM?

1 File Format:



Send local images,



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What Is DICOM?

1 File Format:



Send local images,



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What’s the Matter with DICOM?

Part of the Solution

De-facto standard in medical imaging.

Mature (30 years old).

Supported by any medical device.

Part of the Problem

Large and complex (over 4000 pages).

Old format (redundant with XML, JPEG, PNG. . . ),

Custom network protocol (redundant with SOAP, REST. . . ).

Huge number of files (e.g. 3D images split slice-by-slice)⇒ Redundancies between DICOM files.

Not developer-friendly (complex parsing).

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IntroductionOrthanc



What’s the Matter with DICOM?

Part of the Solution

De-facto standard in medical imaging.

Mature (30 years old).

Supported by any medical device.

Part of the Problem

Large and complex (over 4000 pages).

Old format (redundant with XML, JPEG, PNG. . . ),

Custom network protocol (redundant with SOAP, REST. . . ).

Huge number of files (e.g. 3D images split slice-by-slice)⇒ Redundancies between DICOM files.

Not developer-friendly (complex parsing).

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IntroductionOrthanc



Real-World Software Problems in Hospitals (1/4)

Data from a single patient:

No uniform convention to organize this data.

How to exchange this data between computers?

How to easily access the embedded medical information?

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Wish #1

Transparent, automated indexing of DICOM files.

Work on low-end desktop computer.

Create ZIP files of a patient.

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Radiotherapy systems

Another hospital

No DVD reader?!

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Radiotherapy systems

Another hospital

No DVD reader?!

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Wish #2

Read CD/DVD with DICOM images with any computer.

Upload the images to various DICOM stores.

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Nuclear medicine

Radiotherapy

CT + PET + Contours

Removed each day!

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Nuclear medicine

Radiotherapy

CT + PET + Contours

Removed each day!

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Nuclear medicine

Radiotherapy

CT + PET + Contours

Removed each day!

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Wish #3

Deploy decentralized, task-centric DICOM buffers.

Browse their content from anywhere in the hospital to:1 Quickly re-transmit images.2 Connect to viewers or specialized analysis tools.

Nuclear Medicine

DICOM Buffer

Radiotherapy

(1) Re-transmit

(2) View/analyze

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CBCT

DICOM

Study server

SFTP

Script

Automated anonymization/forwarding for public clinical studies?

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Wish #4

React to the incoming of DICOM images.

Drive low-level DICOM tasks (e.g. anonymization) byhigh-level requirements.

Focus on network administrators (scripting).

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Summary: The Medical Context

1 Explosion of the number and volume of medical images.

2 Data management and exchange of images are problematic.3 Many manufacturers are involved:

Proprietary, costly, closed software.Limited interoperability.

4 Imaging workflow is to be automated (cf. anonymization).

5 Low-end, locked computers.

Summary: The Software Expectations

Need for automated image indexing.

Need for intuitive, ubiquitous interface (Web browsers).

Need for DICOM scripting.

Need for free, open product (customizable).

Need for lightweight software (1 installation for 1 flow).

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Summary: The Medical Context

1 Explosion of the number and volume of medical images.

2 Data management and exchange of images are problematic.3 Many manufacturers are involved:

Proprietary, costly, closed software.Limited interoperability.

4 Imaging workflow is to be automated (cf. anonymization).

5 Low-end, locked computers.

Summary: The Software Expectations

Need for automated image indexing.

Need for intuitive, ubiquitous interface (Web browsers).

Need for DICOM scripting.

Need for free, open product (customizable).

Need for lightweight software (1 installation for 1 flow).20 / 43

IntroductionOrthanc



Main Free Software for DICOM

DICOM Toolkits

DCMTK (format, protocol),

GDCM (format, client-only).

Limitations

Close-to-metal: sysadmins?

No indexing.

No Web interface.

PACS Engines

Dcm4che,

ClearCanvas,

ConQuest.

Limitations

Heavyweight, complex.

Not for low-end computers.

Still need a DICOM parser.

Conclusion

Hospitals need another free tool!

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DICOM Toolkits



Limitations


No indexing.

No Web interface.

PACS Engines

Dcm4che,

ClearCanvas,

ConQuest.

Limitations




Conclusion


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IntroductionOrthanc




DICOM Toolkits



Limitations


No indexing.

No Web interface.

PACS Engines

Dcm4che,

ClearCanvas,

ConQuest.

Limitations




Conclusion


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IntroductionOrthanc


PhilosophyOrthanc in ActionCurrent Usage

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Philosophy

1 Compromise between a DICOM toolkit and a PACS.

2 Lightweight DICOM store (runs on low-end computers).

3 Cross-platform (Windows, Linux, Mac OS).

4 Immediate to deploy (standalone, no external database).

5 Simple Web interface to explore the content of the store⇒ Connect from anywhere in the hospital.

6 DICOM to modern formats and protocols (PNG, JSON, HTTP).

7 Open-source and developed inside the CHU of Liege.

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Web Interface in Action

Features

“Patient → Study →Series → Instance”transparent indexing.

Preview 2D images.

Inspect DICOM tags.

Send to remotemodalities.

Download ZIP files.

Anonymize.

Demo

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http://192.168.215.82:8042/

IntroductionOrthanc




Features


Preview 2D images.

Inspect DICOM tags.


Download ZIP files.

Anonymize.

Demo

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http://192.168.215.82:8042/

IntroductionOrthanc




Features


Preview 2D images.

Inspect DICOM tags.


Download ZIP files.

Anonymize.

Demo

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http://192.168.215.82:8042/

IntroductionOrthanc




Features


Preview 2D images.

Inspect DICOM tags.


Download ZIP files.

Anonymize.

Demo

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http://192.168.215.82:8042/

IntroductionOrthanc



Scripting Orthanc

Orthanc features a powerful scripting language (REST API).

Software administrators can automate imaging flows:1 Watch the arrival of new DICOM images,2 Check the value of some DICOM tags,3 React accordingly (forward, anonymize. . . ).

Orthanc can be embedded into third-party systems for theorganization of medical images (replacement to storescp).

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Python Sample — Autorouting to the PACS

current = 0while True:

# Wait for new events in Orthanc (event polling loop)r = DoGet(’http://localhost:8042/changes’, { ’since’ : current })

# React when a new instance is receivedfor change in r[’Changes’]:

if change[’ChangeType’] == ’NewInstance’:

# Send the new instance to the PACSinstanceId = str(change[’ID’])DoPost(’http://localhost:8042/modalities/pacs/store’, instanceId)

# Remove the instance from OrthancDoDelete(’http://localhost:8042/instances/%s’ % instanceId)

current = r[’Last’]time.sleep(1)

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IntroductionOrthanc



Current Applications of Orthanc

DICOM buffer for transmission errors:

Nuclear Medicine dept. → Radiotherapy dept.,Treatment Planning System → Treatment machines,

Autorouting and filtering to third-party DICOM servers.

Anonymization platform for clinical research with firms.

Collect in-room images for radiotherapy research.

Automated quality control of PET-CT scanners.

Automated quantification of focal fibrosis on cardiac MRI.

Import of CD/DVD from other hospitals (for modalities notintegrated with the PACS).

Mini-PACS on desktop computers⇒ medical and image processing research.

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Orthanc is not a PACS, but a Complement to a PACS

Missing Features

Interfacing with RIS and HIS, worklists.

Tools for radiologists (viewer, reporting).

Long-term, legal archiving.

Scalability.

Distinctive Features

Lightweight (many instances in an hospital).

Easy configuration.

Scriptable.

Open-source for better compatibility between vendors.

Bridge from DICOM to Web 2.0 (JSON/REST/AJAX).

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Worldwide Usage

17,000 visits to the Web site (≈ 36% of new visitors).

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2014-03-13

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Downloads

3,900 downloads (≈ 12 per day) as of 2014-03-13.

Part of Linux (Debian Med and Fedora Medical).

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IntroductionOrthanc


DefinitionPractical, Economic Benefits of FOSSSummary

What is Free and Open-Source Software (FOSS)?

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Proprietary Software

Most often paying.

Black box: What is it made of?

Duplication, modification and/or usage is limited.32 / 43

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Free Software

1 Freedom to use the source code.

2 Freedom to inspect the source code.

3 Freedom to modify the source code.

4 Freedom to distribute the sources or binaries (possibly paying).

⊂ “Open-source software”: freedom to use and inspect.

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Free Software






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Free Software






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Free Software






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Free Software






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Free Software





⊂ “Open-source software”: freedom to use and inspect.33 / 43

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What is the Advantage of Free Software?

“I’m often asked todescribe the ’advantages’ offree software. But the word’advantages’ is too weak whenit comes to freedom.”

[Richard Stallman,for the 30th birthday of GNU project]

⇓

Philosophical point of view:“Librisme” (FR).

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What is the Advantage of Free Software?

“I’m often asked todescribe the ’advantages’ offree software. But the word’advantages’ is too weak whenit comes to freedom.”

[Richard Stallman,for the 30th birthday of GNU project]

⇓

Philosophical point of view:“Librisme” (FR).

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A Pragmatic Perspective to FOSS

Technology: Backbone applications (e.g. Orthanc).Feedback/contributions from a large community.Independent code review (e.g. Karen Sandler).

Ethics: Collaborative sharing of tools and knowledge.Avoid piracy (e.g. in education).

Society: ↘ “Fracture numerique” (e.g. XP end-of-life).Developing countries.

Economics: Building boxes to boost private companies.Generate local activities of services.

Sustainability: Software can be maintained after bankruptcy.Code can be adapted for new uses (fork).

Strategy: Security and technological independence (Snowden). 37 / 43

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Economics of FOSS (1/3)

World

79% of smartphones use Linux (Android).

96% of supercomputers use Linux (weather, finance. . . ).

Worldwide infrastructure of Google, Facebook, Twitter. . .

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IntroductionOrthanc




France (Conseil National du Logiciel Libre, 2012)

Market size: 2,5 billions of euros.

300 companies.

30000 employees.

30% of annual growth.

5/6 software developers use or have used FOSS.

Thanks FOSS, creating a proprietary software costs 10 timesless than in 2002 ⇒ boost of competitiveness.

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Wallonia and Brussels

150 towns use FOSS for their Web site and theiradministration (through IMIO).

OpenERP S.A. is the “promising company” of 2013 (≈ 100employees).

Robert Viseur (CETIC) maintains a list of companies active inopen-source.

FOSDEM annual conference (ULB).

CIRB promotes FOSS for Brussels region.

Many (all?) software companies internally use FOSS.

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The Special Case of Medical Software

Improve interoperability between vendors (backbone).

Open an ecosystem that is trusted by the major players, byuncoupling proprietary systems (cf. David vs. Goliath).

Enhance the technological independence of hospitals.

Code review to improve the security and quality of healthcare.

Allow the patient to deal with her personal data at home.

Improve healthcare in developing countries.

Reference implementation for standard formats and protocols.Give a consistent interpretation of badly specified file formats,such as DICOM-RT (radiotherapy and nuclear medicine).

FOSS as building blocks of commercial software for medicalimaging: DCMTK, GDCM, ITK/VTK, Python. . .

Examples of complete medical applications: GNUmed, GNUHealth (Jamaica), OsiriX, 3DSlicer. . .

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Orthanc was Nominated at Zenobe Award 2013

FOSS Acknowledged as a Vector of Social Innovation

Innovative product.

Social need: Healthcare and biomedical research.

Not enough satisfied by the market.

Open, collaborative and sustainable approach to software.42 / 43




IntroductionOrthanc



Summary

http://www.orthanc-server.com/

Open-source, Web-based DICOM store.

Lightweight, scriptable, versatile.

Comes from real-world, clinical needs.

Availability: Linux, Windows, Mac OS.

FOSS can help the medical sectorfor better interoperability and healthcare quality.

Publications: ISBI 2013, ESTRO 2013, 2 @ BHPA 2013.43 / 43

http://www.orthanc-server.com/

Appendix

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Code Statistics

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[Ohloh]

Software Architecture

Major Components

DCMTK (for DICOM format and protocol).

Mongoose (for embedded HTTP server).

jQuery Mobile (for the Web interface).

Boost, JsonCpp and libpng.

Orthanc Server (C++)

DCMTK(DICOM protocol)

SQLite (indexing)

DICOM C-StoreDICOM C-FindDICOM C-Move

REST services

Orthanc Explorer(Javascript/HTML5)

Web browsers

zLib (compression)

Filesystem

Mongoose (HTTP server)

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Focus on Code Quality in Orthanc

Daily challenged with large volumes of real-world images.

Continuous Integration Server.

Unit testing.

Integration tests through REST API.

Valgrind.

Trello for project management (roadmap).

FAQ, issue tracking and discussion group available.

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Compatibility between FOSS Licenses

Orthanc is GPLv3.

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