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General background

The Centre for Image Analysis (CBA) carries out research and graduate education in computerized image analysis and perceptualization. Our work ranges from the purely theoretical to methods, algorithms and systems for applications primarily in biomedicine and forest industry.

CBA is collaboration between Uppsala University (UU) and the Swedish University of Agricultural Sciences (SLU), which started in 1988. From an organizational point of view, 2011 was a transitional year for CBA, since it was the first year in which we were no longer a department at UU, but one of six divisions within the Dept. of Information Technology. New significant changes in the organization will take place in 2012 as outlined in Section 2. So far, these reorganizations have not prevented us from continuing and expanding our research. We expect that the future changes will not negatively affect our possibilities either.

During 2011, a total of 38 persons were working at CBA: 17 researchers, 17 PhD students, 3 visiting researchers or technical staff and one administrator. Additionally, 13 Master thesis students have finished their thesis work with supervision from CBA. This does not mean, however, that we have had 50 full-time persons at CBA: many have split appointments, part time at CBA and part time elsewhere. Last year, CBA had a work volume corresponding to about 15 full-time, full-year employees at UU and 8 at SLU, not counting undergraduate teaching or Master thesis students. Most of us at CBA also do some undergraduate teaching, which so far has been organized by other divisions, mainly at the Dept. of Information Technology at UU. This will change next year, when our new division also will handle undergraduate education.

As a result of the changed organization, we were able to recruit two new associate professors, Carolina Wählby in quantitative microscopy, and Anders Hast in computer graphics and visualization. We were pleased that Cris Luengo qualified as docent at SLU, bringing the total number of CBA docents to ten; and that Ingela Nyström was promoted and installed as professor in visualization at UU.

On average, 3-4 PhD dissertations are produced each year. In 2011, five PhD theses were defended: Filip Malmberg at UU in May, Hamid Sarve at SLU in September, Muhammad Khalid Khan Niazi in October, Amin Allalou in November, and Milan Gavrilovic in December, the latter three all at UU.

Image processing is highly interdisciplinary, with foundations in mathematics, statistics, physics, signal processing and computer science, and with applications in many diverse fields. We are working in a wide range of application areas, most of them related to life sciences and usually in close collaboration with domain experts. Our collaborators are found locally as well as nationally and internationally. For a complete list of our 49 national and 42 international collaborators see Section 5.6.

An important event this year was KOF11 - the evaluation of the quality of all research at Uppsala University carried out by international expert panels. It was a follow-up of the previous KoF07. The evaluators took part of our documented output, self evaluations and oral presentations. The result was summarized by the following statement under the heading Quality of research: ``The works of the CBA in the discrete approach applied to microscopic medical images, and of 3D display is remarkable and clearly of internationally high standard. In the overall field of image analysis, the activities of CBA are internationally recognized. The development of techniques of visualization are among the best current output of CBA.'' The full KoF11 report can be found at

This year, results from a very exciting CBA-industry collaborative research project was presented in the Royal Swedish Society of Engineering Sciences (IVA) annual adress about progress in industrial and academic research and technology. The project concerns automatic imaging and identification of viruses in transmission electron microscopy images.

We have for many years had a clear focus on developing image analysis for medical applications. This was recognized during 2011 by the Faculty of Medicine at UU with a direct permanent faculty grant of about 1.5 million SEK to support future research in that area, a very unusual measure. The large strategic program Science for Life Laboratory, SciLifeLab, also recognizes image analysis technology as essential for their fundamental biological research and supported the recruitment of Carolina Wählby, mentioned above, providing 3 million SEK per year for 3 years as a grant to strengthen the quantitative microscopy field.

A new multidisciplinary research area for CBA emerged towards the end of 2011. The Faculty of History and the Faculty of Languages with additional funds from the vice-Chancellor at UU will support this project concerning automatic reading of old handwritten documents.

Ingela Nyström, our deputy director, was appointed head of another major strategic research program in the e-science field, eSSENCE. As she assumed that position, she left the position as head of Uppsala Multidisciplinary Center for Advanced Computational Science, UPPMAX. She retains her position on the board of the Swedish University Computer Network, SUNET.

We are very active in international and national societies. Gunilla Borgefors was elected member of the Royal Swedish Society of Engineering Sciences (IVA) in 2011 and from 20110101, Borgefors is Editor in Chief for the journal Pattern Recognition Letters. Ingela Nyström served as secretary of the International Association of Pattern Recognition, IAPR. Ewert Bengtsson served as chair of the Evaluation Panel for Medical Engineering for the Swedish Research Council. At UU, he serves as senior advisor to the Vice-Chancellor on information technology and also as Chair of the University IT-council. Researchers at CBA also served on several other journal editorial boards, scientific organization boards, conference committees and PhD dissertation committees. In addition we took a very active part in reviewing grant applications and scientific papers submitted to conferences and journals. As part of our international research networks we were hosting workshops for delegations from Korea and India and in collaboration with SciLifeLab.

In addition to the more common ways of spreading information about our activites and work, such as seminars, publications, webpages etc., we have our ``CBA TV''. Short ``trailers'' on our projects and activities are presented on an LCD monitor facing the main entrance stairway where students and colleagues from other groups are passing by.

This annual report is also available on the CBA webpage, see

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