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Annual Report 2015


Cover: SICAS Trainee Franck Boinay, Michael Kistler, M. Montavon of EST Porrentruy and Roman Niklaus


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Contents!

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Preface!

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Responsibilities and Actors!

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Benefit for the Canton Jura!

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Events and Courses!!

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SICAS Institute and MIC Lab!

SICAS Medical Image Repository (SMIR)!


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Preface! The year 2015 marks an intermediate consolidation of the SICAS institute after the support by the “Nouvelle Politique Régional” (NPR) had fully taken effect in 2014 by completing staff and infrastructure. The SICAS institute, installed in such a way, now in 2015 passed to a routine mode of operation with five employees, corresponding to 3.5 full time positions. An internship trainee from EST Porrentruy joined the team for three months.! Relying on the strong SICAS network, the team’s activity covered the full spectrum of the foundation’s objectives: Support of research collaborations, education, innovation and infrastructure based services.! The first edition of the SHAPE Congress at Courroux in 2014 bringing together leading scientists from all over the world was a great success. In 2015 we were able to top this marking it a highlight of the year. Again many scientists, industrials and medical doctors coming from five continents found their way to the Canton Jura and local business could substantially benefit from their spending. In 2015 SICAS events on site generated two Francs revenue in the local economy for every franc that was invested by SICAS/NPR funds, totaling about CHF 30’000.! The scenic trip to the Château de Pleujouse for the conference dinner, along with a talk on the Jurassica initiative not only attracted participant’s strong interest but also underlined the potential of the canton Jura as a great conference venue.! The SICAS Medical Image Repository SMIR data server operated by SICAS engineers and hosted by the Le Noirmont Data Center (CDROM SA) represents the SICAS core infrastructural platform. The institute is actively promoting its usage by research groups, research focused clinical units and the industry. In 2015 the platform has been part of the EU-CHIC cancer research project and SMIR has been used as the data and interaction hub of the ETH-Balgrist shape modelling project.! This project entitled “From Images To Statistical Shape Models: A Complete Pipeline” was granted by ETHZ with CHF 240’000 on behalf of the related research consortium in order to strengthen the SICAS network community, for which the SICAS platform serves as a common home base. The project, including Balgrist clinic and partners from

Bern, Basel and Zurich, was finalized in December 2015 and also found public interest by a full page contribution in NZZ am Sonntag.! As part of its educational program, the institute trained a student from EST (Ecole supérieure technique) Porrentruy for three months on SMIR related work for the EU-CHIC project. Very promising feedback was received from all involved, the trainee, his EST teacher and the SICAS instructor.! A number of educational events was organized or has been supported by the institute, for example an MD course in 3D surgical planning at the Medtech.Lab or the 2015 Endoscopic Paranasal Sinus and skull base hands-on course (PSSB) at the Institute of Anatomy, University of Bern. ! Various members of the foundation council have continuously been involved during the year in prominent innovation related agencies and initiatives, such as the federal innovation promotion agency CTI and the Swiss Innovation Park in Allschwil. With the support of FITEC, H.F. Zeilhofer achieved to create two start-up companies relying on SICAS technology: Di.Meliora in the field of Titan 3-D printing, Ad.Mirabiles in the area of cranial implants. They both plan to establish their offices at the Medtech.Lab Courroux (SIP Jura)! Several awards have been granted to SICAS technology companies throughout the year. We only mention the CTI Swiss Medtech Award 2015 given to AOT AG for their CARLO surgical robotic bone cutting technology, the Swiss Technology Award at the Swiss Innovation Forum for the start-up Mininavident AG addressing dental applications, and the Cancer League Award of the Canton Aargau given to H.F. Zeilhofer for innovative procedures and new technologies in facial reconstruction after tumor surgery.!

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Prof. Dr. Gabor Székely! Prof. Dr.-Ing. Lutz-P. Nolte! President ! ! !

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Vice President!!


Lutz-P. Nolte, Vice President


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Responsibilities and Actors!

! Foundation Council! !

Prof. Dr. Gabor Székely, ETH Zurich President and Member of the Board


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Prof. Dr.-Ing. Lutz-Peter Nolte, University of Bern Vice President and Member of the Board


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Dr. Bernhard Reber, ETH Zurich Member of the Board 


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Dr. med. Yves Rohner, Creapole SA
 Olivier Tschopp, Republique et Canton du Jura, Chef du Service de la formation


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Prof. Dr. Dr. h.c. Hans-Florian Zeilhofer ! University Hospital Basel!

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Ruth Steinmann, Managing Director
 Dr. med. Jörg Beinemann, Medical Advisor
 Dr. Michael Kistler, Project Coordinator
 Roman Niklaus, Software Engineer
 Patrick Roth, Innovation Consultant! Franck Boinay, Trainee!

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
 Prof. Dr. Guoyan Zheng, University of Bern, ISTB!

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Members of the Foundation Council O. Tschopp, H.F. Zeilhofer and G. SzĂŠkely at the STRATE J site


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Benefit for the Canton Jura! Science and Innovation!

Swiss Innovation Park (SIP NWCH)!

SICAS’ mission in the Canton Jura is to establish science and innovation excellence in the field of Computer Assisted Medicine. The goal was to install SICAS at the medtech.lab in order to involve the Canton Jura on a hands-on level in Swiss and international research and innovation communities and hubs, for example the ARTORG Center in Bern, the Swiss Innovation Park (SIP) Allschwil or the EU RP7 Project CHIC (“Computational Horizons In Cancer), with research groups of 7 European countries.!

Foundation Council member Hans-Florian Zeilhofer and SICAS researcher Philippe Cattin are in leading roles in the SIP development and the new Department for Biomedical Engineering at the University of Basel. The SICAS foundation council is involved in related institutional processes (including CTI) of the Swiss Innovation Park, for example related to SIP-JU, or related to the creation of an Academy for Surgical Training, Technology, Education, Research and Innovation (ASTERI-S) with outreach to the canton JU.!

As a result, scientists from all over the world visited the Canton Jura. Furthermore Jura’s industry and authorities got direct access to leaders as for example from the Swiss Innovation Park (SIP) Allschwil or CTI. Successfull collaborations with Jura partners were continued in 2015, such as between the University Hospital Basel and BUSCH SA or between SICAS’s Medical Image Computing Lab and CDROM SA, Le Noirmont, hosting the SICAS Medical Image Repository (SMIR). !

Plans for a Master’s Course in CAS with it’s head office at the medtech.lab have now been put on the official agenda of the University Hospital Basel. !

Local innovation processes and science related procedures benefit from SICAS on a normative level in order to meet the proper standards. This for example by providing advice to Creapole and young MDs on how to access suitable expertise and join high level communities in the field of computer vision.! An innovation workshop was held at the medtech.lab in spring 2015 addressing the local industry. President Gabor Székely chaired the event with a number of experts of the SICAS network including CTI.!

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Cooperation with Local Education! SICAS trained a student from Ecole Supérieure Technique (EST, Porrentruy) by an internship of three months. He was selected form several candidates and successfully completed an ambitious task. The training and work was done in the context of the EU cancer project. EST confirmed that practical work and instructional benefit on a comparable level are usually not found in the region. In addition, valuable contacts beyond the canton have been highly appreciated by the trainee.!

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With the support of FITEC two start-up companies based on SICAS technology have been created: one in the field of 3-D Titan printing, the other one in the area of cranial implants. They both intend to install their head offices at the medtech.lab in Courroux (SIP Jura).!

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Events - Tourism - Economy! Workshops and educational events where held in the Jura bringing together Medical Doctors, scientists, industry and civil services. Alongside the networking, visitors got an impression of the canton and its amenities, landscape, outstanding gastronomy, places of interest and tourist attraction.! For the second time a large group of scientist from around the world attended the SHAPE Symposium at Courroux. They had dinner at Château de Pleujouse and were highly interested in the paleontologic excavations. Most of them would probably never have come to the Jura otherwise, or have taken notice of the Jurassica Project..! All these events, dominated by SHAPE, resulted in direct spending of around CHF 30’000 - half of it financed by SICAS/NPR, the rest by income and sposoring, Hence, each invested Franc resulted in two Francs flowing to the local economy.!


SHAPE participants on the tower of Château de Pleujouse


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Events and Courses! Shape 2015 Symposium!

Innovation and KTT Workshop !

The SHAPE Symposium was held from September 30 to October 2, 2015, again at the medtech.lab in Courroux. This conference in the new field of shape modelling which was notably embossed by early work of SICAS network researchers, was the outstanding event of the year. Some 70 attendees coming from Japan, USA, Canada, China, South Africa and from 11 European countries found their way to the Jura. International representation has increased compared to the previous year.!

This half-day event took place at the medtech.lab in Courroux on April 14 with some 30 participants from within and outside the Canton Jura, including companies like BienAir. It targeted the economic tissue of the Jura area with regard to the role of the Federal Commission for Technology and Innovation (CTI) in innovation and start-up processes and with regard to collaboration between companies and universities. !

The intense 3-days program included oral and poster presentations on state-of-the-art as well as cutting edge research. Keynote presentations by experts from leading academic and industrial institutions, and a panel discussion marked the schedule. Tutorials on dedicated software for shape modelling and shape analysis completed the scientific program. Beyond science, participants were taken to a scenic bus ride to Château de Pleujouse where they enjoyed the exquisite cuisine and the great views. A talk on the palaeontological excavations presented by an expert of the Jurassica initiative attracted great interest.! The second edition of this congress gave evidence that SHAPE has definitely established as an important platform for the international shape modelling community. The SHAPE Symposium is a major initiative of SICAS and a pillar of the centre to further promote the field. The next SHAPE conference is scheduled for 2017.!

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BME Day! SICAS supported the BME Day 2015, held on May 29 at the University Hospital Bern. This career day offers companies the opportunity to meet Master and PhD students from the Biomedical Engineering Master program of the University of Bern and the Bern University of Applied Sciences.! Yves Mermoud received the SICAS Award 2015 for the best Master thesis “On-Chip Impedance Analysis to Monitor Epithelial Barrier Integrity”. The SICAS Award 2015 for the best PhD thesis was handed over by CEO Ruth Steinmann to Jakob Johann Schwiedrzik for his work “Experimental, theoretical and numerical investigation of the nonlinear micromechanical properties of bone”. !

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Gabor Székely, SICAS president and head of CTI MedTech, depicted various supporting initiatives. SICAS medical consultant Jörg Beinemann reported on the collaboration with Busch SA and University Hospital Basel. Stefan Weber, director of the ARTORG Center at University Hospital Bern, highlighted the development of liver navigation technology within former SICAS collaboration research. He exemplified the creation of the related start-up CAScination and its development to an internationally successful company. In a similar way Charles Baur of EPFL gave evidence of medical robotics development and start-up creation. The event was chaired by the SICAS KTT consultant Patrick Roth.!

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Surgical Skills Training! A Medical Doctor’s 3-D Software Planning course was organized at the medtech.lab. These piloting courses have a promising potential given the pronounced demand by assistant MDs and international fellows of the University Hospital Basel. Prospects for sponsoring by software manufactures need to be examined.!

! 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 2015 at the University Hospital Bern. These international courses are organised by SICAS member Marco Caversaccio. SICAS technology was involved through ARTORG, Stefan Weber. SICAS further supported the courses by providing the cadaver specimens.!


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SICAS Institute and MIC Lab! The Institute located at the medtech.lab in Courroux hosts the Head Office (HO) and the Medical Image Computing Lab (MIC Lab). The HO manages the general administration, the Foundation Council’s business, events and corporate communication, including social media and various websites. In particular the HO supports subgroups, as for example the Shape Modelling steering committee and the SHAPE group. The HO staff provided technical and logistic support for the SHAPE 2015 congress. It coordinated the event’s overall organisation and was in charge of finance and administration.! The MIC Lab constitutes the infrastructure part of the Institute’s activity in acquisition, hosting and processing of medical image data. The purpose is to provide the infrastructure and environment for the development of tools for visualisation and operation planning. These developments are mostly done within collaboration projects, for example the ETH-Balgrist Application Pipeline (p.18). These collaborations, by the majority, rely on well known network partners from universities, clinics and companies. They represent the "SICAS community" and are the network part of the MIC Lab.! The SICAS Medical Image Repository SMIR (p. 14) is operated by SICAS engineers. Our own server infrastructure is hosted by the Le Noirmont Data Center (CDROM SA) and represents the SICAS core infrastructural platform. The Institute promotes and supports its usage by research groups, as well as research focused clinics and industry. The SMIR staff offers tailored services and training of personnel. In 2015 this was exemplified within the ETH-Balgrist Appliation Pipeline Project.! Facilities of the MIC Lab were used in 2015 for Medical Doctor’s training. Various software tool kits have been enhanced in the course of the year, for example within the EU CHIC project for cancer research.! The Institute's arrangement together with the so far available medtech.lab environment, such as the lecture hall, provided a perfect venue for the SHAPE congress. Given this special character it was highly appreciated by the younger audience. ! There is some evidence, that more experienced attendees prefer a more traditional venue style. This provides promising prospects for the SHAPE symposium 2017, to eventually take place at the

new STRATE J building near the railway station of Delémont, the future tertiary campus.!

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The Staff! The Institute’s core staff comprises the managing director (CEO), a scientific coordinator, a software engineer and a part-time advisory medical doctor. A KTT consultant was mandated for innovation issues on request, for example for the innovation workshop. ! SICAS staff trained a student from Ecole Supérieure Technique (EST) in Porrentruy in the course of an internship of three months. The substantial success of the trainee encourages us to continue this internship program.!


SICAS Medical Consultant Jรถrg Beinemann giving a talk at the innovation workshop for local companies


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SICAS Medical Image Repository (SMIR)! The SMIR is a specialised database for medical images. It includes an anatomy ontology and is linked to various computations tools, such as for statistical shape modelling of image segmentation. It provides a database system and image content for specific use by researchers, clinicians and industrials. The SMIR provides tools for storing and sharing large amounts of images and related information such as scientific models, biomechanical properties or clinical information. ! In 2015, the SMIR could consolidate its running mode due to the experienced and qualified SICASSMIR team, that has been hired in the beginning of 2014. It comprises a software engineer and a project coordinator. They run our hardware infrastructure in the Le Noirmont data center CDROM SA, provide programming assistance and offer specific services to users and customers. Since late 2015, they are also in charge of the trainee’s program.! The transformation from the VSD (Virtual Skeleton Database, a former 4 years Co-Me project of the University of Bern) into SMIR has been completed in 2015 with a domain change to fully identify the database system as a SICAS product integrated in the Institute. The domain smir.ch has been registered. On this occasion, an Extended Validation SSL certificate for this domain has been acquired to increase confidence and trust. ! The SICAS infrastructure with cloud environment at the data center in Le Noirmont has proved to be a reliable setup with an uptime of 99.79%. A blog, advanced hardware monitoring and the RICORDO ontological framework have been added.! The core framework has been optimized and now includes support for clinically relevant data formats. CDISC-ODM, a standardized format to store clinical trial information has been added together with the possibility to store standardized genomic datasets as MINiML files. And finally, SMIR now supports the Stereolithography format STL for surface models. In addition, the search algorithm and interface have been updated as a modular structure. The underlying search builder Angular Query Builder has been published on Github.! In 2015, the member statistics have increased by about 100%. SMIR collected around 20'000 visits and 78'000 page views, 1'229 users accounts, and 60 research units are registered on SMIR. On behalf of the challenges about 1'250 datasets of 250 subjects

have been added in 2015. A challenge data collection has been downloaded 2'250 times and SMIR evaluated about 10'000 related user segmentations. In total, SMIR now hosts more than 50'000 datasets. Some 80 percent are segmentations, mostly created by challenge participants. Additional 6'000 image sets, 1'250 surface models, and a small set of statistical models are hosted. Depending on the data type, between 97 (segmentations) and 75 percent (images) are downloadable for registered SMIR users.!

SMIR related projects! EU-CHIC! The European Union's Seventh Framework project CHIC (“Computational Horizons In Cancer: Developing Meta- and Hyper-Multiscale Models and Repositories for In-Silicon Oncology) includes 16 research groups from seven European countries and one from the USA.! The focus is on the development of clinically driven, multi-scale cancer models. The SMIR software is running as a clinical data repository in the CHIC private cloud environment. After defining the desired data formats for clinical and genetic data, the CIDISC-ODM and MINiML standard were integrated into the SMIR core and deployed to the clinical data repository.!

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BRATS 2015! The 2015 edition of the NCI-MICCAI Grand Challenge in Image Segmentation was hosted by SMIR. Such segmentation challenges are becoming an integral part in the work of researchers to compare and benchmark their algorithms. The challenge again consisted of a training and a testing phase. During the training phase, researchers have access to both the multi-modal MR images and ground truth segmentations. During the challenge phase, only the image data is available to the participants. The BRATS 2015 data collection consists of data of about 100 patients (4 MR and 1 segmentation). 300 researchers have registered to the BRATS 2015 challenge, 13 users finally submitted their results to the SMIR. The evaluation tool and access remains available to allow continuous benchmark of algorithms.!


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ISLES 2015! The Ischemic Stroke Lesion Segmentation (ISLES) Challenge was hosted for the first time on SMIR. The aim and setup of the ISLES challenge follows the one of BRATS. However, this challenge consisted of two sub sections: Sub-acute ischemic stroke lesion segmentation (SISS) and the stroke penumbra estimation (SPES). A data collection of 500 MR images and 250 segmentations was added to SMIR. Over 150 researchers were interested in this challenge. Finally, 20 users have submitted their results for this MICCAI challenge. As for BRATS, this challenge remains open and available on SMIR for continuous benchmarking.!

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SHAPE 2015 Challenge ! The SMIR hosted the second challenge for statistical shape models as part of the SHAPE 2015 conference in Courroux (JU). 50 participants downloaded the training dataset from the SMIR and 6 submitted their results to the repository where they were evaluated. The task was to build a model from the training data and use it to predict the shape of an incomplete structure. The results were displayed online and the challenge remains available on SMIR for the broad R&D community.!

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Statismo! A secondary goal of the SMIR repository is to support the building of statistical shape models. To this end, an important complement to the image repository is the Statismo software tool kit. Statismo, which is used under the name “Scalismo� by GRAVIS Basel, is an open source project, whose main goal is to substantially simplify the use and exchange of statistical shape models. Hence, Statismo provides state-of-the-art methods for building and using statistical models. Furthermore, it defines and implements an open file format for storing models that is also supported by SMIR. In 2015 Statismo (Scalismo) was significantly extended with functionality for model-based image segmentation, which is one of the main application areas of statistical models. Scalismo is used for the SSM open course (online) teaching to be launched in spring 2016 by GRAVIS Basel.!

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An Application Pipeline for Statistical Shape Models This project fully entitled “From Images To Statistical Shape Models: A Complete Pipeline” spans from data acquisition to image processing, operation planning and the surgical intervention. ETH has granted CHF 240’000 on behalf of the related research consortium in order to strengthen the SICAS network community, for which the SICAS platform serves as a home base. SMIR was used as the data hub of the project, to store and exchange patient image data, intermediate results and related information. In addition, SICAS operated as a facilitator for processes and for securing the legal (ethical) framework.! Beyond SICAS, the partners of the research alliance were: Graphics and Vision Research Group (GRAVIS) , University of Basel; Institute for Surgical Technolgy and Biomechanics (ISTB), University of Bern; Computer Vision Lab (CVL), ETH Zürich and the Balgrist University Hospital including its startup company CARD AG.!

CVL, ETH Zurich:! “A big challenge in research is that expertise is frequently located in different teams, both for specific technical knowledge and clinical challenges. This project brought together distributed knowledge, summing up to achievements exceeding the sum of the parts, in particular with regard to bring shape models closer to clinical practice.! The prominent advantage of the SMIR has been its availability as a independent “third party” platform for the exchange of clinical and research data, providing strong guarantees with regard to data security, access rights and hence, IPR. This has made it possible to make more than 200 images and segmentations available for joint research.”!

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80 abdominal MR of 20 patients, CT of the forearm of 65 patients, 102 lower extremity CT and 100 Caucasian pelvis CT have been uploaded to the SMIR. The results (segmentations and 6 shape models) have been stored on the SMIR. !

GRAVIS, University of Basel:!

The project was finalised in the end of 2015. In a follow-up evaluation, the project partners were asked to give their feedback on the collaboration. !

ISTB, University of Bern:!

The SMIR provides a very well defined way to store the images and intermediate result for the processing. Thanks to the possibility to automate data download and upload, the data processing can be automated even though it is distributed to several groups. Furthermore, it imposes a common, well defined structure to organise the data.!

“This collaboration was extremely useful for the development of the lower extremities shape model. We have access to a large collection of CT datasets and have several concrete applications of a SSM for orthopedic/biomechanical applications. However, we didn’t have competences to build shape models without extensive manual work (i.e. manual segmentations). In this context, this collaboration represents a good example of efficient interactions towards fast model building for specific applications. The SICAS database was very useful and allowed to easily share the data amongst different groups located at separate institutions.”!

The SMIR now contains a set of images for different organs with annotated meta-data (such as sex/age known pathologies, etc.), validated segmentation and a statistical shape model that was built from the data. Such data can be used for many applications and is immensely more valuable than random collection of images, for which no metadata and/or defined segmentations are available. The development of the SMIR Client provides a convenient means to access the SMIR programmatically, which makes it possible to integrate the SMIR directly into custom software, or to build additional tools to interact with the SMIR.”!

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Testimonies of Project Partners!

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“The involvement of several groups to contribute images and help process and analyse them resulted in a good set of high quality data that could be used for building shape and intensity models. !

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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 annual report 2015