Annual Report 2014

SICAS improves patient’s health by advancing

Computer Assisted Surgery

Contents!!Preface! ! ! ! ! ! ! ! 4!

Responsibilities and Actors! ! ! ! ! 6!

Establishment of the SICAS Institute! ! ! ! 8!

Events and Courses!! ! ! ! ! ! 10!

Medical Image Computing Lab! ! ! ! ! 12!

Innovation - Knowledge and Technology Transfer! ! 18!

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The year 2014 pushed the foundation a significant step forward. On the one hand the agreement with the Canton Jura regarding the support by the “Nouvelle Politique Régionale” (NPR) could be signed. On the other hand, this made it possible to become fully operational, and to establish the institute with a medical computing lab and a data center at the Media.Lab in Le Noirmont. Hence, SICAS finally has become a corporation with four highly qualified employees at the Creapole Medtech.Lab in Courroux.!!SHAPE 2014, the international conference on statistical shape modelling undoubtedly represented the highlight of the year. For three days, more than 100 scientists, representing industry and universities, came to Delémont from around the world. They admittedly appreciated the high quality conference and they avowedly enjoyed the steam train excursion and the lovely landscape. Attendees underlined that the special character of the lab, located outside the city, made the place a great venue. Finally, the local economy enjoyed benefits of around 30’000 CHF, directly invested by SHAPE, and we hope that many of the participants returned back home equipped with a Wenger knife and as an ambassador of the Jura.!!In the scope of the Medical Image Computing Lab, two major project activities have marked the year: !First, the SICAS Medical Image Repository has concentrated its resources at the Medtech.Lab in Courroux. On the one hand, a latest technological environment was created and a medical data center was established at the Media.Lab in Le Noirmont, in collaboration with CDROM SA. On the other hand, a software engineer (M.Sc.) and a scientific coordinator (Ph.D) could be hired at the Courroux laboratory. Furthermore, SMIR was recognised by the renown NATURE journal as an official data repository for authors.!!Second, a substantial and encompassing collabo-ration project was launched, spanning from data acquisition, to image processing, operation planning and finally to the surgical intervention. CHF 240’000 have been granted for this by ETH on behalf of the SICAS community. The project is realised in an alliance of the Balgrist University Hospital, ETH Zürich, the Universities of Bern and Basel and

SICAS, which provides the Medical Image Data Repository SMIR as the central hub for the handling and exchange of data and results; in addition, SICAS provides workforce for the project support and we create and represent the legal framework for the project.!!With regard to knowledge and technology transfer, the SICAS network continued!(i) to build on partnerships by involving the industry and hospitals in R&D collaboration projects, such as in a project with University Hospital Geneva, University Hospital Basel (UHBS) and Busch SA, managed by the SICAS office. Rapid prototyped models as a result of the work, were exhibited at the MEDICA 2014 fair in Düsseldorf and became the basis for routine collaboration among Busch SA and UHBS;!(ii) to support or to give courses, such as the course for Paranasal Sinus and Skull Base Surgery (PSSB) in Bern, or a course on the application of 3D-planning software for medical doctors organised and held by the SICAS office in Courroux;!(iii) to organise or to be involved in a leading role in international conferences, such as SHAPE in Delémont or the Bernd Spiessl Symposium in Basel;!(iv) to be a backbone of Swiss Master’s Programs in Biomedical Engineering (BME) and to support the BME career Day, that gave company representatives an excellent opportunity to meet highly qualified and motivated students.!!In 2014’s KTT efforts, a major achievement was the granting of 15 Mio for MIRACLE @ SIP NWCH:!SICAS foundation council member Hans-Florian Zeilhofer and researcher Philippe Cattin received a grant of CHF 15,2 Mio by the Siemens foundation for projects on laser and robotic technology, intra-operative navigation and on the development of custom-made implants. New professorships will be created and the centre is established at the Swiss Innovation Park of Northwest Switzerland (SIP NWCH) in Allschwil BL.!!!!!Prof. Dr. Gabor Székely, ETH Zürich!President of the Foundation Council

Preface!

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Responsibilities and Actors!!Foundation Council!Prof. Dr. Gabor Székely, ETH Zurich President, and Member of the Board !Prof. Dr.-Ing. Lutz-Peter Nolte, University of Bern Vice President and Member of the Board !Dr. Bernhard Reber, ETH Zurich Member of the Board !Dr. med. Yves Rohner, Hôpital du Jura !Olivier Tschopp, Republique et Canton du Jura, Chef du Service de la formation !Prof. Dr. Dr. h.c. Hans-Florian Zeilhofer University Hospital Basel!!The Head Office!Ruth Steinmann, Managing Director !Dr. med. Jörg Beinemann, Medical Advisor !Dr. Michael Kistler, Project Coordinator !Roman Niklaus, Software Engineer !Patrick Roth, Innovation Consultant!

!SHAPE Group!Dr. Ghazi Bouabene, University of Basel, GRAVIS !Prof. Dr. Philippe Büchler, University of Bern, ISTB !Prof. Dr. Orcun Göksel, ETH Zurich, CVL !Dr. Marcel Lüthi, University of Basel, GRAVIS !Prof. Dr. Mauricio Reyes, University of Bern, ISTB !PD Dr. Guoyan Zheng, University of Bern, ISTB!

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The significant occurrence of the year 2014 was the signing of the NPR agreement with the Canton Jura (RCJU) in the middle of the year.!

This made it possible to definitely install the Medical Image Computing Lab (MIC-Lab) and the SICAS Head Office (HO) at the Creapole Medtech. Lab in Courroux, and in particular to hire qualified personnel and to acquire the computational and educational infrastructure.!

These facilities, together with our manpower, and combined with the latest cloud computing infrastructure established at the Media.Lab in Le Noirmont with CDROM SA, represent an NPO corporation with four employees in the cutting-edge hightech business of the Canton Jura. A corpo-ration, by the way, that is not only linked to the Swiss Innovation Park (SIP NWCH) and a number of start-up companies (some of which meanwhile established on the world market), but that is also a branch of ETH and the universities of Bern and Basel. It is furthermore linked to leading institutions, for example the US National Alliance for Medical Image Computing, and respected persons abroad, who, in the past 15 years, have either been a project partner or who have substantially built their career with us together.!

The MIC-Lab acquires, hosts and processes medical image data and supports the development of tools for the analysis, visualisation and operation planning. The purpose is to provide the infrastructure and environment for the develop-ment of (open-source) technologies, and then supports the training and dissemination to the medical community or to industry. !

The core component of the MIC-Lab is the SICAS Medical Image Repository (SMIR), a highly specialised database including a medical ontology and linked to various computational tools. !

Currently, the MIC-Lab coordinates an encom-passing collaboration project spanning from data acquisition, image processing, operation planning to the surgical intervention. The MIC-Lab partners in this project are Balgrist University Hospital, ETH and the Universities of Bern and Basel; see p. 16.!

In addition, the HO has established a working group in the SICAS focus area of Statistical Shape Modelling (SSM) and the related international SHAPE Symposium. SSM today is an established novel field, to the state-of-the art of which the SICAS collaboration network has vigorously contributed. Together with the HO, the working group was in charge of the organisation of the SHAPE 2014 Symposium. 30’000 CHF were spent to the local economy of the canton Jura by the SHAPE 2014 Symposium. !

Furthermore, the HO created an instructional environment for the knowledge transfer of visualisation techniques to medical doctors and organised two related surgeon courses at the Medtech.Lab in Courroux.!

Finally, the HO realised media contributions, such as in the “Landliebe” magazine, featuring the steam train excursion of the international audience of the SHAPE Symposium. The article dominantly referred to landscape, leisure and tourism in the Jura. !

In addition, SICAS had a booth at the Hannover Industrial Fair in April 2014 as part of the Swiss Pavillon, that was visited by a Swiss Council of States delegation.!

Rapid prototyping manufactured 3D-surgical guides and models were presented together with Busch SA, Porrentruy, at the World Forum For Medicine, Medica Fair in Düsseldorf in November 2014.!!The Staff!SICAS is proud that it succeeded to hire highly qualified personnel: The managing director, a scientific coordinator, a software engineer and a part-time advisory medical doctor. An external consultant was contracted for innovation issues, in short term related to an upcoming event in spring 2015 at Medtech.Lab,.!

It is planned to add internships for IT engineers to be recruited from the higher professional education sector of the Canton Jura.!!

Establishment of the SICAS Institute!

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Medical Image Computing Lab and the SICAS Head Office

Education Minister Elisabeth Baume-Schneider and SICAS President Gabor Székely at the Shape 2014 Conference Dinner in Le Noirmont.

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Shape 2014 Symposium at Delémont!This first SHAPE symposium was held on June, 11-13, 2014. Given its success beyond all expectations, it marked the highlight of the year and contributed to the international branding of SICAS. 100 persons from 15 countries all over the world have travelled to the Medtech.Lab at Courroux to attend this conference on statistical shape modelling (SSM), which is a novel, however established scientific field, to which the SICAS community has greatly contributed. Participant’s feedback underlined that the combination of high overall quality, high educational value of the keynotes and tutorials, pronounced interest from academia and industry, the single-track format, the great venue at the Medtech.Lab outside the city and leisure time with the steam train in the lovely Jura countryside - all this made the symposium unique in its kind. In brief, the need for this new symposium was confirmed without any doubt.!

Most recent results shaping the future of this exciting research area were intensively discussed within the numerous sessions. Six keynote talks were given by renown experts from research and industry. Ten oral contributions and 37 presentations and posters were accepted und published in the conference proceedings. !

The SHAPE Symposium as a major initiative of SICAS is intended to become an annual pillar of the centre. The Foundation Council highly appreciated the great work of the conference board. It was partially composed of SICAS Head Office staff and mainly of young researches and junior professors who had built their career within the SICAS network. It turned out that this constellation was perfectly suited to make this new congress in a new field attractive for young scientists and international experts.!!BME Day !SICAS supported the BME Day 2014, held on May 16, at the University Hospital Bern. This career day offers companies the opportunity to meet students and Master and PhD graduates from the Biomedical Engineering Master program of the University of !

!Bern. The SICAS community is a strong backbone of the program.!

Steven Balestra received the SICAS Award 2014 for the best Master thesis for his work “Statistical Shape Model-Based Articulated 2D-3D Reconstruction”. The SICAS Award 2014 for the best PhD thesis was given to Alois Pfenniger for his work “Intra-corporeal Energy Harvesting with a Focus on the Human Cardiovascular System”. !!Surgical Skills Training!Piloting 3-D Software Planning courses for medical doctors of University Hospital Basel were organised and held at the Medtech.Lab in Courroux in October and November 2014. The participants appreciated the undisturbed, whole day learning atmosphere far from the hospital. !

The pilot courses offered the opportunity to set up the basic training infrastructure, to establish a provisional learning environment, to develop an appropriate course format and to test this with clinicians from the University Hospital Basel. !

The good experience confirmed the basic concept and the need. The second course had to be given earlier than intended due to doctor’s demand. The piloting course offers good potential to be designed as a module in a Master of Advanced Studies Program for Computer Assisted Surgery as considered for the future with UHBS, provided that additional partners and sponsors can be brought on board, as for example 3D software industry.!!PSSB and OMMIT !The Endoscopic Course for Paranasal Sinus and Skull Base Surgery (PSSB) and the Otological Microsurgery Course with emphasis on Minimally Invasive Techniques (OMMIT) were held in September 2014 at the University Hospital Bern. The well established international annual courses are organised by the SICAS member Marco Caversaccio. The instrumentation with SICAS technology was supported by the ARTORG Center.

Events and Courses!

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The MIC-Lab acquires, hosts and processes medical image data and supports the development of tools for the analysis, visualisation and operation planning. The purpose is to provide the infrastructure and environment for the development of (open-source) technologies and their application. The institute supports the dissemination to the medical community or to industry, including training of qualified personnel, clinicians or engineers.!

The MIC-Lab is therefore a competence center composed of two parts:!

- A network part (A) involved on the one hand, in cutting edge development of segmentation algorithms and modelling, and on the other hand, in clinical application and instrumentation development.!

- An in-house (institute) part (B), providing infrastructure (computing center, SMIR database) and specialised workforce for maintenance and project support. Furthermore, it provides the necessary interaction platform for the statistical shape modelling community. This inter-dependence is emphasised by the facts, that on one side, the SMIR database links and integrates SSM models, on the other side, the Balgrist Pipeline Project (see p. 16) demonstrates that in an impact and application related perspective, both parts (data + modelling) need to be managed and sold in a package, which includes service support. Possibly, this may become the basis of a future business model.!

The core component of the MIC-Lab is the!

SICAS Medical Image Repository (SMIR)!The SMIR is a specialised database including an anatomy ontology and linked to various computational tools, such as for statistical shape modelling or image segmentation. !

The basic objective of the SMIR is to provide a database system and image content for use by researchers, clinicians and industrials. It provides tools for storing and sharing large amounts of images and related information such as scientific models, biomechanical properties or clinical information. SICAS staff runs the hardware infra-structure in Le Noirmont/JU at the Media.Lab.,

provides programming assistance and offers services to the users and customers.!

Initiated as “Virtual Skeleton Database” (VSD) by various groups in the scope of the ETH-lead NCCR, it has evolved in a first phase as a distributed system, primarily satisfying the needs and interests of the respective locations and teams. Phasing it out from the terminated NCCR, SICAS on the one hand strives to continuously integrate SMIR in focal project contexts and broader user communities (SSM, SHAPE, EU CHIC, …); on the other hand, we concentrated and consolidated the infrastructure and the support team.!

To this end, in 2014!

(a) A SICAS staff team for maintenance work was set up.!

(b) Up-to-date and dedicated hardware facilities have been established at the Le Noirmont data centre.!

(c) An encompassing collaboration key project funded with CHF 240’000 by ETH on behalf of the SICAS network, was launched, focusing the complete SSM application pipeline (see p. 16).!!

Official Data Repository of NATURE!

The recognition of SMIR by the renown NATURE journal as an official data repository for authors of journal articles marked an important step of the international visibility and credibility of the project and of the SICAS Foundation.!

In 2014, the software was systematically integrated and the SMIR now runs in a fully virtual and redundant mode of operation.!

67 full body post-mortem datasets were uploaded in the course of the year, and 800 MR sets were hosted for the BRATS 2014 challenge. In addition, 60 segmented liver datasets for the SHAPE 2014 challenge were made available. By the end of 2014 a total of around 30'000 segmented datasets were integrated in the database.!

10'000 visits, 45'000 page views and about 800 downloads were monitored during the year, representing around 500 users from 30 research units.!!

Medical Image Computing Lab!

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EU-CHIC !This European Union's Seventh Framework project focuses on the development of clinically driven, multi-scale cancer models. By the project participation of SICAS researcher Philippe Büchler from ISTB Bern, the database is used as the clinical data repository of the project in order to store images, genetic data and information related to clinical research. In 2014, a private CHIC cloud was realised, and the core with a Single-Sign-On authentication procedure was extended to interact with a Trusted-Third-Party security institution. !

In addition, “ricordo” (www.ricordo.eu), a multi-scale ontological framework, was prepared for integration in the CHIC core and will be available overall SMIR.!!BRATS 2014!The 2014 edition of the NCI-MICCAI Grand Challenge in Image Segmentation was hosted by SMIR. This segmentation challenge mainly includes training and testing in order to enable researchers to compare their algorithms on the basis of a data reference. During the training phase, scientists have access to both, the multi-modal MR images and to the ground truth segmentations. During the challenge phase, only the image data is available to the participants. 130 users had registered to the BRATS challenge, 14 finally submitted 6'200 segmentation results to SMIR which is considered as a good result. The evaluation tool remains available for continued benchmark of algorithms.!

!SHAPE 2014 challenge !Similar to the BRATS and MICCAI, a challenge for statistical shape models, hosted by SMIR, was organised under the lead of Guoyan Zheng from the ISTB, University of Bern, as part of the SHAPE 2014 symposium at the Medtech.Lab in Courroux. Participants downloaded training datasets and submitted their result to the repository where they were evaluated. !!!!

Statismo!This program library, hosted by the Graphics and Vision Research Group GRAVIS from the University of Basel is a software framework for statistical shape model building. It was initially created and then further used and extended by the SICAS SSM & SMIR community. In 2014 version 0.10.1 was released. The file format was updated, and easy installation on Mac/OSX and Ubuntu Linux was enabled. The framework code is hosted on GitHub and is open source.!

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This encompassing collaboration project, entitled “From Images To Statistical Shape Models: A Complete Pipeline” spans from data acquisition, to image processing, operation planning and finally the surgical intervention. CHF 240’000 have been granted by the ETH on behalf of the SICAS community. The project is realised in an alliance of Balgrist University Hospital, ETH Zürich, the Universities of Bern and Basel and SICAS.!

SICAS provides the Medical Image Data Repository SMIR as the central hub for the handling and exchange of data and (intermediate) results and it provides workforce for the project support. In addition SICAS will create the legal framework for the project with regard to access handling and user group management on the SICAS platform. This includes IPR, patient data privacy, contracting with industrial partners and potential ROI. SICAS on the one hand contracts data providers, and on the other hand commits users and researchers.!

In 2014 the proposal was elaborated and reviewed. In addition, ethical approval was granted, and approval was received by the ETH vice-president. A first provisional privacy contract was established among partners and preliminary work started for the upload of image data to the SMIR.!

Overall, the project aims at valorising several years of collaborative research in the SICAS/NCCR network by bringing together methodology and clinical data to compute statistical shape models. In the context of the SMIR development, algorithms and infrastructure have been designed and implemented which allow to store and exchange medical images, segment anatomical structures, and compute SSMs. This project integrates these individual tools in a complete pipeline to compute several SSMs from images obtained from clinical and academic partners. The resulting SSMs will then be evaluated for their use in clinical practice through operation planning and the intervention.!

In order to allow for processing diverse image sources, the pipelines are modular such that individual parts can easily be adapted to a specific anatomy or modality. This is supported by using the SICAS Medical Image Repository (SMIR) as the backbone of the project, where image data and results can be stored and pushed along the pipeline.

A key aspect of this central data storage is the clarification of access and usage rights of patient images, resulting segmentations and models.!

Furthermore, this project computes statistical models for a number of anatomical test cases of scientific and clinical value. Therefore, a focus of the project is to deliver SSMs for:!

1) the radius and ulna bone from forearm CT scans, with the goal to deploy them in clinical practice at Balgrist University Hospital;!

2) the pelvic bone from hip CT scans, in order to quantitatively validate the results of our pipeline with available ground truth from one of the participating scientific partners.!

3) In order to maximise synergy and provide additional data for the SMIR, additional models will be generated for abdominal muscles from multimodal MR, and for leg bones from full body CT scans.!!

SICAS/ETH Key Project for the Application Pipeline of Statistical Shape Models

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NZZ am Sonntag, 10.5.2015

Knowledge Transfer!The SICAS network continued to build on partnerships by involving the industry and hospitals in R&D collaboration projects. Examples, often in the scope of CTI projects, are wide spread in the M.Sc., Ph.D. and PostDoc programs. A special type of a transfer alliance is the above mentioned pipeline project with Balgrist Hospital.!

We are still a backbone of Swiss Master’s Programs in Biomedical Engineering. The BME career Day gave company representatives an excellent opportunity to meet highly qualified and motivated students.!

We continued to be involved in a leading role in international conferences and courses such as the Bernd Spiessl Symposium for Innovative and Visionary Technologies in CMF surgery, on June, 19 - 21, 2014 at the University Hospital Basel, organised and chaired by the SICAS Foundation Council member Hans-Florian Zeilhofer. A workshop session on SICAS navigation technology was supported by our staff member Jörg Beinemann. !

Another example is the 3rd annual meeting of the European Computer-Assisted Liver Surgery Society (ECALSS) in Seoul in March 2014. ECALSS was founded in Bern, 2012 under the lead of the Image Guided Therapy (IGT) group of ARTORG Center, Bern, directed by SICAS researcher Stefan Weber and supported by the SICAS start-up CAScination AG.!!Technology Transfer and Innovation!The SICAS network, including its significant number of start-up companies, continues to be a source to the industry for highly qualified experts and for sophisticated solutions. We are also involved in a leading role for CAS related matter of the Swiss Innovation Park of Northwest Switzerland (SIP NWCH).!!15 Mio for MIRACLE @ SIP NWCH!In 2014, SICAS foundation council member Hans-Florian Zeilhofer and SICAS researcher Philippe Cattin received a grant of CHF 15,2 Mio from the Siemens foundation. The focus is on laser and

robotic technology, intra-operative navigation and on the development of custom-made implants. Two additional professorships for "medical robotics and mechatronics" and "medical laser physics and optics" are to be created.!

The centre is established at the Swiss Innovation Park of Northwest Switzerland (SIP NWCH) in Allschwil BL. !Collaboration with Busch SA, Porrentruy!A feasibility study on accuracy requirements for rapid prototyped models for surgical planning was conducted. SICAS staff Jörg Beinemann co-ordinated the project and realised part of the work with partners from University Hospital Geneva, University Hospital Basel (UHBS) and Busch SA. !

As a follow up, the collaboration of UHBS with Busch SA continued on a day to day routine basis. Some of the models were exhibited at the MEDICA 2014 fair in Düsseldorf in November.!!Hannover Industrial Fair!In April 2014, at the Hannover industrial fair, SICAS staff presented surgical planning software for knee replacement and the application platform for statistical shape modelling. A Swiss Council of States delegation with president Hannes Germann visited the SICAS booth.!!Advancement of Start-up Companies!The Austrian manufacturer of cochlear implants, MED-EL, together with SICAS start-up CAScination AG, have initiated the joint commercialisation process for the robot-assisted system for implantation of cochlear implants. The method has been developed during eight years by SICAS researchers Marco Caversaccio and Stefan Weber, University Hospital and ARTORG Center, Bern.!

CAScination AG announced FDA 510(k) clearance of its surgical navigation system for open liver surgery. The CAS-ONE LIVER device guides surgical instruments for effective tumor removal while sparing healthy parts. It is in use in several European cancer centres.!

Innovation - Knowledge and Technology Transfer!

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Coypright Elsbeth Heinzelmann

SICAS at Hannover Industrial Fair 2014.

Models of Busch SA for University Hospital Basel

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!!!!SICAS, Swiss Institute for!

Computer Assisted Surgery!

Place des Sciences 1!

CH-2822 Courroux!!+41 32 422 58 20!

contact@si-cas.com!

www.si-cas.com!

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SICAS, Swiss Institute for Computer Assisted Surgery Place des Sciences 1 CH-2822 Courroux!

+41 32 422 58 20 contact@si-cas.com www.si-cas.com!!