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Annual Report 2013""

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SICAS improves patient‘s health

by advancing Computer Assisted Surgery

preface!

The Foundation „Swiss Institute for Computer Assisted Surgery“ (SICAS) was created in September 2011 in Delémont, Canton Jura, Switzerland. I t was supported by ETH Zürich and the Universities of Bern and Basel. First plans grew in 2009 from discussions launched by the management of the National Center of Competence in Research (NCCR) on Computer Aided and Image Guided Medical Interventions (Co-Me): How could the Co-Me collaboration network - the backbone of

this successful 120 million francs research initiative - after 12 years be transformed into a sustained existence when the NCCR would close its doors in June 2013?"

In 2010, with substantial help of Creapole SA and FITEC (Fondation d‘imipulsion technologique et économiqe), chaired by Wolf Zinkl and Gabriel Prêtre respectively, the process to set up the successor organisation to Co-Me, was launched with the support of the government of the canton Jura, lead by Elisabeth Baume-Schneider, Minister of education, culture and sports and Michel Probst, Minister of economic affairs."

The overall aim of the foundation was"

- to continue developing the field of computer-aided surgery;"- to continue using and nurturing the cooperation and innovation network."And a specific goal was to integrate the Jura area as a place of science with its relevant regional actors from education to hospitals and industrial innovation. "

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In a first period (2012-13), when the smooth phasing out of the NCCR was still administered by the Co-Me Project Office (PO), SICAS was run in parallel and also managed by the PO. With regard to the foundation, the management concentrated on the one hand on a second round of financing, on the other hand on a series of scientific and hands-on events with a focus on practical application in the operating room and with a focus on Co-Me start-up companies. Several of these manifestations have been organized together with Creapole SA for a target audience of the Canton Jura."

In June 2013 the NCCR ended with a strong track record (see for example http://issuu.com/ruthsteinmann/docs/nccr_co-me) and SICAS became self-sufficient, hiring its own manager in autumn of the same year and focusing on shape modeling as a first important field of activity. Shape modeling was one of the scientific foci of the Co-Me network, resulting in major contributions to the international state-of-the-art. SICAS has taken over the coordination and support of the related continuing efforts of numerous Swiss research groups, in order to finally establish a national network center for statistical shape modeling in the Canton Jura. As part of this, computing infrastructure was planned to be installed and related personnel to be hired to run a medical image computing center at the Creapole Media Lab in Le Noirmont, that will serve as an open lab for the scientific community worldwide."

The annual report provides evidence of this exciting phase of transition and change for a promising new beginning."

Prof. Gabor Székely " "President of the Foundation Council"

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look back to the beginning!

As the present account is the first report since the creation, we throw a glance at some early milestone events of the SICAS history. The launch of the foundation was announced on the occasion of an opening ceremony of the Innovation Parc at Delémonton on September 14th, 2011. The announcement went along with a press conference by the government followed by a surprising response in radio and print media of french speaking Switzerland. The foundation has been created only a few days before, on September 11th, 2011, by the four founding members Prof. Dr. Gabor Székely (President), Prof. Dr. Lutz Nolte (Vice President), Dr. Bernhard Reber (Director) and Prof. Dr. med. Dr. med. dent. Dr. h.c. Hans-Florian Zeilhofer."

MEDTECH DAY IN DELÉMONT"The first „Medtech Process Day“, an event platform provided by the innovation promotion agency Creapole SA, took place on October 20th. The related scientific

program, including a booth exhibition of own hands-on research results (demonstrators) and start-up companies was organised and carried by SICAS/Co-Me. More than 100 scientists and engineers from all over Switzerland attended the day."

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POLITICS MEETS SICAS AT THE MEDTECH.LAB"

On December 8th, 2011, SICAS provided a half day program for Ministers of the Cantons Basel and Jura at the Medtech.Lab, seat of the SICAS Foundation. The event included a survey talk on the SICAS portfolio by the Director Bernhard Reber and demonstrations by the start-up company VIRTAMED AG and the Institute for Surgical Technology and Biomechanics (ISTB) of the University of Bern.""

MEETING OF THE SCIENTIFIC ADVISORY BOARD AT THE MEDTECH.LAB"SICAS held the second day of the annual meeting of the Co-Me Scientific Advisory Board at the Medtech.Lab, including an excursion to „franches montagnes“ in March 2012.

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Minister Elisabeth Baume-Schneider testing the hip navigation system developed by Dr. Guoyan Zheng (ISTB). The Ministers of health of the Canton Basel, Dr. Carlo Conti, and Michel Thenz of the Canton Jura are observing their encouraged colleague.

The members of the Scientific Advisory Board coming from five countries including overseas, completed by the head office and scientists from Bern, Basel and Zürich, as well as the president of Creapole SA

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RESEARCH WORKSHOP FOR PHD-STUDENTS"A research networking workshop with 35 PhD students of the field of Computer Assisted Surgery (CAS) took place on August 20th and 21st, 2012 at the medtech lab in Delémont. The local Radio  Fréquence Jura (RfJ) has followed the event broadcasting a feature on August 21st."

 “Science in the Media” was set as the focus of the workshop. Five teams of PhD students were expected to present their research projects in a

short video addressing the general public. Three movie professionals and a science editor from Swiss TV provided their support. The results were ranked in a competition by participant’s votes and were put on the SICAS website."

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Prof. Chuck Thorpe, robotics advisor to the US President Obama is throwing snow balls outside Montfaucon (left). "The distinguished englishman Prof. Chris Taylor from Manchester takes a sceptic look at the snow (right).

PhD students at work Leisure and dinner in a nearby adventure park and restaurant

SURGICAL ROBOTICS WORKSHOP IN DELÉMONT"

On November 30th, 2012, seven members of the SICAS network provided insight to their research activities and clinical experience in computer assisted surgery to an audience of Jura doctors and representatives of local companies. The event took place at the medtech.lab and was co-organized by SICAS, Dr. Yves Rohner of Hôpital du Jura and Creapole."Three medical professors presented clinical cases and ongoing research projects: Professor Marco Caversaccio, Head of the ORL Dept. at Inselspital Bern, informed on the current state of development of their hearing implant robot for cochlea implant surgery. "Prof. Daniel Jeanmonod, from Solothurn, reported on promising results of his latest clincial studies with MR-guided High-Intensity Focused Ultrasound treatments of patients with chronic pain and Parkinson. In 2009, the results of his first clinical study with this new method had raised worldwide attention."Three dimensional planning and navigation in cranio-maxillofacial reconstruction was reported by PD Dr. Philipp Jürgens, University Hospital Basel."Medical robotics specialists Dr. Charles Baur and Olivier Chappuis from EPF Lausanne presented a robotic assistance system, providing highly precise surgical solutions for spinal fusion surgeries."These specific lectures were completed by an overview on SICAS by its director Dr. Bernhard Reber, ETH Zurich, and a talk on knowledge and technology transfer by Vice President Prof. Lutz Nolte, University of Bern.

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Talk by Prof. Marco Caversaccio, The audience in the lecture hall and during apero time"Inselspital Bern"Dr. Yves Rohner operating the PC

self-sufficiency and consolidation of internal structures in 2013!

While Co-Me was about to phase out the activities until June 2013, SICAS and the NCCR together with the National Science Foundation (SNF), ETH Zürich and the Universities of Bern and Basel focused on finalising the legal and practical processes of mutual support and future synergy and sharing of forces."On the occasion of the formal closing event at ETH Zürich on April 17th, 2013, this regulation process was enhanced w i t h a m e e t i n g o f t h e S I C A S management and representatives of Creapole and the Government of the Canton Jura in order to set-up the implementation procedure of a service level agreement between SICAS and the C a n t o n J u r a a c c o r d i n g t o t h e parliament’s decision of December 14th, 2011. At the same time it was agreed on a proper representation of the Jura in the Foundation Council in the course of the year. Olivier Tschopp, head of the service of education of the Jura administration gave a closing talk, a video stream of the event may be found on the SICAS website.""""

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Co-Me Closing Event

17th April 2013

Olivier Tschopp conveys a message of the Canton Jura.

From left: Olivier Tschopp, Bernhard Reber, Wolf Zinkl, Cédric Koller and Yves Rohner on the roof of ETH Zürich.

The congress-like event with around 200 attendees provided a show case of the network’s achievements, including an exhibition of start-up companies and a booth of SICAS.""Based on intensive consultation within the Co-Me network, the SICAS developed a detailed activity plan for a period of three years. The first draft was discussed by B. Reber with JU-representatives O. Tschopp (JU administration), Y. Barth (Creapole) and C. Koller (NPR/Eco) on July 4th in Delémont. Participants agreed on this approach as the basis and integrated component of an agreement within NPR (“nouvelle politique régionale”).""DEFINITE TAKE OVER BY SICAS"The NCCR definitely closed down in summer 2013, and therefore, after summer vacation a Foundation Council (FC) Meeting was held on August 26th in order to take the necessary measures to organise future business. In a first instance, the FC elected Dr. Yves Rohner and Olivier Tschopp as new members of the council. "

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As at that time, the service level agreement with the Canton Jura was not yet ready for signature and by consequence a serious planning, such as hiring of personnel and purchase of IT-computer center infrastructure for the Media.Lab in Le Noirmont was not possible. Related decisions had to be postponed and a minimised procedure needed to be established. The decision had been taken to create a 60%-position for a chief operating officer (Geschäftsführerin) from October 1st on, and Ruth Steinmann from the former Co-Me Project Office could be hired. Additionally, with regard to the short term core activity of the foundation, the FC confirmed to fully integrate the VSD-Medical Image Repository into the Institute as an important Co-Me heritage (see related section of this report). The FC also agreed on taking first steps in view of IT-infrastructure purchase and to ask for respective offers. Preliminary negotiations should take place with former Co-Me PhD-students working on the Virtual Skeleton Database project in view of possible part-time hiring in 2014, provided the service level agreement with the Canton Jura would be signed. Furthermore, the realisation of a high-level international symposium on statistical shape modelling, called “SHAPE 2014”, was envisaged for the middle of 2014 and the SICAS operations were mandated to constitute a program board of young scientists who had built their career within Co-Me. Information material and a website should be created and first promotion activities should be launched on the occasion of important related international conferences. This was all achieved by the end of 2013, including committing six world leading researchers for keynote talks.

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EVENTS AND COURSES 2013"

In the course of the year SICAS supported two other events. Various demonstrations were given. Prof. Philippe Cattin and Jörg Beinemann at a booth exhibition of the World Medtech Forum (WMTF) in Luzern in September 2013. "

The Co-Me/ETH start-up company VIRTAMED AG provided a hands-on demonstration of its surgical training simulator for hysteroscopy at the Jura Health Day in October 2013 at Courroux.""Biomedical Engineering Day"

The SICAS network has been a back-bone in creating the Swiss Master’s Programs in Biomedical Engineering in Zürich and Bern. The Bern SICAS network partners ARtoRG Center for Biomedical engineering Research, the Institute for Surgical Technologies and Biomechanics as well as the Bern University of Applied sciences are running the Master’s program. Within this scope and since 2009 the industry, medical doctors, and engineers meet for the Biomedical engineering Day at the

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Jura health day at Courroux, October 5th, 2013" " World Medtech Forum at Lucerne,"The Virtamed Hysteroscopy Simulator in action " " September 9th - 11th 2013"" " " " " " " Philippe Cattin, MIAC, Basel explaining latest"" " " " " " " results of his medical image analysis research

Inselspital in Bern. The day takes place every year in May in the auditorium Ettore Rossi at the Inselspital in Bern and welcomes more than 250 participants. The event is an efficient platform in Switzerland for networking of Master and PhD graduates and swiss and international medical technology companies."

"Many SICAS researchers are involved as lectures and substantial content resulted and still results from the network’s collaboration projects. SICAS supported the Engineering Day by sponsoring the best Poster, best Master and best PhD thesis awards.

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Endoscopic Course for Paranasal Sinus and Skull Base Surgery and"Otological Microsurgery Course with Emphasis on Minimally Invasive Techniques""These annual courses are organised by the SICAS researcher Prof. Marco Caversaccio from University Hospital Bern; its content and instrumentation are strongly linked to SICAS research. The network partner ARtoRG Center is involved with latest technological development and demonstrations. The courses emphasise

anatomical whole-head dissection. Individual dissection sessions are framed by lectures and live anatomical demonstration. The events took place at Inselspital Bern on September 2-4 and 5-7, 2013, respectively. SICAS is supporting the courses by providing the cadaver specimens.

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Marco Caversaccio in a demonstration

medical image repository (VSD)! "INTRODUCTION "The “Virtual Skeleton Database” (VSD) has been a core project of Co-Me during four years. It was conducted under the lead of the Institute for Surgical Technology and Biomechanics (ISTB) of the University of Bern in cooperation with Berner Fachhochschule (BFH), Informatics of the University of Basel and the Computer Vision Lab of ETH Zürich. After the Co-Me closing in summer 2013, the ISTB supported the ongoing work with former Co-Me personnel, that was planned to be hired by SICAS when the related funding was secured, i.e. after signature of the service level agreement with the Canton Jura. This had not been the case until the end of 2013. "

The objective of the Virtual Skeleton Database is to provide a database system with tools for storing and sharing large amounts of annotated medical images and related information such as scientific models, biomechanical properties or clinical information. This enables researchers and companies to benefit from a large base of preexisting data to enhance, develop and test new applications as for examples for image analysis or implant manufacturing."

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System Achitecture

Although the focus is on the human skeleton, the system accommodates other types of data such as soft tissue, bone micro-architecture and animal data. Special attention is given to the storage of annotated medical images to build statistical shape models (SSM) to a specific clinical indications.""The solution provides the traditional functionalities of PACS systems. A WebDAV interface is implemented for a direct access to the content stored on the database. This method enables users to mount WebDAV shares directly on the computer file system and to interact with the files stored in the database in the same way as with local files.""ACHIEVEMENTS IN 2013"In 2013, 40 post-mortem full body CT-scans from the Forensic Institute at the Universities of Bern and Zurich (Prof. M. Thali) are uploaded. In addition, 300 chimpanzee skulls of the Senkenberg collection are stored and 65 multimodal sets of glioblastoma patients have been made available for download in the context of the for Multimodal Brain Tumor Segmentation Challenge (BRATS)."

In 2013, the system has been re-installed on a new hardware platform with better scalability and reliability. The graphical Web-interface was upgrade to a new modern interface using Bootstrap and Microsoft .NET technology. The existing functionality of upload, download and sharing was extended by the ontology powered search using the Foundational Model of Anatomy (FMA) ontology, a forum and a rating system. In June 2013, the SICAS Image Repository was presented on the Open Repository Conference in Charlottetown, Canada [3] and the journal article [2] was published. In the course of 2013, the following projects have been linked to the database, have been integrated and are carried on: "

1. CHIC-EU, a project of the European Union’s Seventh Framework Programme for research, technological development. CHIC proposes the development of clinical trial driven tools, services and infrastructures that will support the creation of multiscale cancer hypermodels. In CHIC, the VSD serves as a repository for clinical trial and image data. The SICAS Medical Image Repository

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integrated the single sign-on service in order to provide a flawless access to CHIC. Furthermore, we enabled the storage of CSDC files, a standard file format for clinical trial data."

2. BRATS [1, 6, 7, 8]: In 2013, the we hosted the NCI-MICCAI 2013 Grand Challenges in Image Segmentation. Such a challenge consists of several phases (training, leaderboard, challenge, and post-challenge). Initially, the contestants access training cases with annotations. Several weeks before the challenge, they have uploaded the segmentation of leaderboard cases to allow computation of scores as feedback. During the MICCAI meeting, the contestants were granted access to the sequestered challenge test data at the beginning of the workshop, then they processed, uploaded and evaluated them on our system. The submissions have been ranked and published [9]. It is important that the evaluation tool remains accessible (post-challenge) allowing researchers to continuously use it for benchmark for their algorithms. So far, almost 195 user registered to download the BRATS data, 16 are listed in the ranking, and over 14’000 datasets have been evaluated by the SICAS Medical Image Repository (VSD)."

3. HEAR-EU, a project of the European Union’s Seventh Framework Programme for research, technological development. The overall goal is to improve hearing restoration. The SICAS Medical Image Repository enables to streamline the process of statistical shape model building for accurate population-based models in a multidisciplinary project setting. All parties have access to the same dataset and the metadata. The individual processing tasks can be distributed while the research data is stored on the repository. A partner with access to high resolution medical data can provide researchers with medical image analysis background for segmentation. Once these segmentations are available on the repository, the statistical shape model can be engineered and provided by means of the database. Since every processing step is stored on the system, this approach ensures a high level of reproducibility of the model building and of quality control."

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4. Statismo [5], is a software framework for statistical shape model building (SSM) emerging from long-term Co-Me research. The Co-Me special interest group for SSM had decided to collaborate for integrating important software developments in a modular way for future shard (open source) use. Statismo was developed under the lead of the GRAVIS Institute of the University of Basel. In order to integrate Statimso into the SICAS Medical Image Repository, we developed a prototype Representational State Transfer Application Programming Interface (REST API) for the exploration of the connectivity between Statismo and our database. Based on this, the full REST API was defined as an initial version.

"OUTLOOK"According to the decision of the SICAS Foundation Council and in agreement with the former carriers Co-Me and ISTB Bern, the virtual skeleton database project was fully taken over by the SICAS Foundation to be re-launched under the notion of “SICAS Medical Image Repository”, virtual skeleton database for research and development, with a special focus on statistical shape modelling."

This re-launch includes to hire the necessary personnel on a part-time basis (from the former Co-Me project) and to install a SICAS owned data center at the Media.Lab in Le Noirmont, hosting a 24 TB Server system and making use of the former Server at ISTB for mirroring."

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The future host of the SICAS computing center for the Medical Image Repository

References [1] Bauer, S., Wiest, R., Nolte, L.-P., & Reyes, M. (2013). A survey of MRI-based medical image analysis for brain tumor studies. Physics in Medicine and Biology, 58(13), R97–129. doi:10.1088/0031-9155/58/13/R97"

[2] Kistler, M., Bonaretti, S., Pfahrer, M., Niklaus, R., & Büchler, P. (2013). The Virtual Skeleton Database: An Open Access Repository for Biomedical Research and Collaboration. Journal of Medical Internet Research, 15(11), e245. doi:10.2196/jmir.2930"

[3] Kistler, M., Pfahrer, M., Niklaus, R., Tomas, V., & Büchler, P. (2013). The Virtual Skeleton Database: An open access repository for biomedical research and collaboration. In OpenRepository. Charlottetown, PEI, Canada."

[4] Kjer, H.M., Fagertun, J., Vera, S., González-Ballester, M.A., Paulsen, R.R.. Shape modelling of the inner ear from micro-ct data. Shape Symposium 2014. Delémont."

[5] Lüthi, M., Albrecht, T., Gass, T., Goksel, O., Kistler, M., Bousleiman, H., … Vetter, T. (2012). Statismo - A framework for PCA based statistical models. The Insight Journal, 1–18. Retrieved from http://hdl.handle.net/10380/3371"

[6] Menze, B. H., Jakab, A., Bauer, S., Kalpathy-cramer, J., Farahani, K., Kirby, J., … Leemput, K. Van. (n.d.). The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS), 1–32."

[7] Menze, B., Jakab, A., Bauer, S., Reyes, M., Prastawa, M., & van Leemput, K. (2012). BRATS 2012 - MICCAI 2012 Challenge on Multimodal Brain Tumor Segmentation. In Preceedings of MICCAI-BRATS 2012. Nice. Retrieved from http://www.imm.dtu.dk/projects/BRATS2012"

[8] Porz, N., Bauer, S., Pica, A., Schucht, P., Beck, J., Verma, R. K., … Wiest, R. (2014). Multi-Modal Glioblastoma Segmentation: Man versus Machine. PLoS ONE, 9(5), e96873. doi:10.1371/journal.pone.0096873"

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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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