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 and 2012 were transitional years for CBA, since we joined other organizations at the two universities. At UU, we belong to one of five divisions within the Dept. of Information Technology, the Division of Visual Information and Interaction (Vi2). At SLU, we belong to the Dept. of Forest Genetics and Plant Physiology in Umeå. How these organizational changes have been performed is outlined in Section 2. The re-organizations have not prevented us from continuing and expanding our research. We now foresee opportunities for collaborations among our new close colleagues at UU and SLU.
During 2012, a total of 35 persons were working at CBA: 17 researchers, 16 PhD students, one technical staff and one administrator. Additionally, 17 Master thesis students completed their thesis work with supervision from CBA. This does not mean, however, that we have had more than 50 full-time persons at CBA: many have split appointments, part time at CBA and part time elsewhere. Most of us at CBA also undertake some undergraduate teaching. Previously this has been organized by other divisions, but with the organizational changes our new division now handles undergraduate education.
We are pleased that Robin Strand and Ida-Maria Sintorn qualified as Docents at UU bringing the total number of CBA docents to twelve.
On average, three PhD dissertations are produced each year at CBA. Nevertheless, in 2012 there was no PhD exam. This is not unexpected since 2011 was ``a year of harvest'' with five PhD theses defended. We also expect a number of PhD these to be defended in 2013.
Image processing is highly inter- and multi-disciplinary, 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 45 national and 49 international collaborators see Section 5.6.
We received three grants in the 2012 call from the Swedish Research Council (Vetenskapsrådet). Anders Brun and his collaborators Mats Dahllöf from the Dept. of Linguistics and Philology and Lasse Mårtensson from the University of Gävle received a 13.7 MSEK Framework Grant. The project is entitled ``Searching in Large Digitized Collections of Handwritten Text" and will enable a group of researchers to work on handwriting recognition for historical texts during the coming four years. The project is part of a larger strategic effort, supported by the Vice-Chancellor, also involving the Faculty of Languages, the Faculty of Science and Technology, and the Uppsala University Library. This represents a significant leap into the emerging field of digital humanities.
Carolina Wählby received a Project Research Grant for Junior Researchers for the project entitled ``A flexible automated cell tracking system optimized on an application basis by user-controlled feedback". The main goals of the project are to (i) make existing tracking algorithms available to the life sciences by reducing algorithmic insight required for parameter optimization, and (ii) validate developed tools on live cell experiments testing mechanistic hypotheses of molecular and cellular processes.
Ingrid Carlbom received a two-year Continuation Project Research Grant for the prostate cancer malignancy grading project. This new funding will allow the development of new classifiers from a combination of tissue morphology and immunohistochemical analysis that identify malignancy relative to long-term disease outcome. These classifiers could potentially improve upon the current Gleason grading system.
Ingela Nyström, our director, continues to coordinate the strategic research programme in the e-science field, eSSENCE. She retains her position on the board of the Swedish University Computer Network, SUNET.
Ewert Bengtsson has served as senior advisor on Information Technology at UU to the Vice-Chancellor since 1998. This role was terminated during 2012.
We are very active in international and national societies. Both Ewert Bengtsson and Gunilla Borgefors are elected members of the Royal Society of Sciences in Uppsala and the Royal Swedish Society of Engineering Sciences (IVA). In 2012, Ingela Nyström was elected member of Royal Society of Arts and Sciences of Uppsala. Gunilla Borgefors is Editor in Chief for the journal Pattern Recognition Letters and Cris Luengo is Area Editor for the same journal. Ingela Nyström was re-elected as Secretary of the International Association of Pattern Recognition, IAPR. 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 research networks we were hosting workshops in collaboration with SciLifeLab and hosted the 35th CERN School of Computing as well as arranged an AIMday Image.
In addition to the more common ways of spreading information about our activities and work, such as seminar series, publications, web-pages, 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 as a PDF, see http://www.cb.uu.se/annual_report/AR2012.pdf