Annual Report 2019 Centre for Image Analysis Centrum for¨ bildanalys Cover: Illustrations from the five PhD theses presented at Centre for Image Analysis (CBA) during 2019. Further information in Section 4.2. Cover design: Leslie Solorzano Edited by: Gunilla Borgefors, Filip Malmberg, Nadezhda Koriakina, Ingela Nystrom,¨ Ida-Maria Sintorn, Leslie Solorzano Centre for Image Analysis, Uppsala, Sweden Contents 1 Introduction 5 1.1 General background . 5 1.2 CBA research . 6 1.3 How to contact CBA . 7 2 Organisation 8 2.1 Finances . 9 2.2 People . 10 3 Undergraduate education 12 3.1 Undergraduate courses . 12 3.2 Bachelor thesis . 13 3.3 Master theses . 14 4 Graduate education 19 4.1 Graduate courses . 19 4.2 Dissertations . 21 5 Research 25 5.1 Medical image analysis, diagnosis and surgery planning . 25 5.2 Microscopy: cell biology . 31 5.3 Microscopy: model organisms and tissues . 37 5.4 Mathematical and geometrical theory . 42 5.5 Humanities . 47 5.6 Cooperation partners . 51 6 Publications 55 6.1 Edited conference proceedings . 56 6.2 Journal articles . 56 6.3 Refereed conference proceedings . 71 6.4 Other . 75 7 Activities 77 7.1 Conference organisation . 77 7.2 Seminars held outside CBA . 78 7.3 Seminars at CBA . 81 7.4 Conference participation . 85 7.5 Non-refereed conference presentations . 87 7.6 Attended conferences . 90 7.7 Visiting scientists . 94 7.8 Visits to other research groups . 94 7.9 Committees . 96 1 Introduction The Centre for Image Analysis (CBA) conducts research and graduate education in computerised image analysis and perceptualisation. Our role is to develop theory in image processing as such, but also to develop better methods, algorithms and systems for various applications. We have found applications primarily in digital humanities, life sciences, and medicine. In addition to our own research, CBA con- tributes to image technology promotion and application in other research units and society nationally as well as internationally. 1.1 General background CBA was founded in 1988 and was until 2014 a collaboration between Uppsala University (UU) and the Swedish University of Agricultural Sciences (SLU). From an organisational point of view, CBA was an independent entity within our host universities until 2010. Under the auspices of the Disciplinary Domain of Science and Technology at Uppsala University, CBA is today hosted by the Department of Information Technology (IT), where we belong to one of the five divisions, namely the Division of Visual Information and Interaction (Vi2). The organisational matters are further outlined in Section 2. A total of 38 persons within Vi2 were active in CBA research during 2019: 17 PhD students and 21 seniors (of which 3 are Professor Emeriti). Many of us have additional duties to research, for example, teaching, appointments within the Faculty, and leave for work outside academia, so the number 38 is not full-time equivalents. A complement to the CBA researchers are the 13 students who completed their Bachelor and Master thesis work with examination and/or supervision from CBA during 2019. The number of staff in the corridor fluctuates over the year thanks to that we have world class sci- entists visiting CBA and CBA researchers visiting their groups, for longer or shorter periods, as an important ingredient of our activities. A highlight during 2019 was that we hosted Guest Professor Fred Hamprecht from the Interdisciplinary Center for Scientific Computing, Heidelberg University, during his seven months sabbatical. Professor Hamprecht organised a much appreciated PhD course on combinato- rial problems in computer vision based on exact and approximate solvers, and their relevance in the age of deep learning. He also contributed to the TissUUmaps project with novel ideas on our image-based approaches for spatial transcriptomics — a collaboration continuing after his return to Germany. A fruitful example of collaboration we have is with the Department of Surgical Sciences; Radiology, where two of our staff members work part time at the Uppsala University Hospital in order to be close to radiology researchers and also have funding from there. The activity level continues to be high, for example, there were as many as five PhD defenses during 2019, see illustrations from them on the cover-page. All our PhDs can be recognised as the main product during the years. These young well-educated persons will contribute to our society and within academia for many years to come. Another way to measure our results is to acknowledge our 33 journal papers and 14 fully reviewed conference papers. The publication results stem from a total of 42 ongoing re- search projects during 2019. Our projects are involving as many as 70 international labs and companies, more than 20 national collaboration partners, plus not forgetting all the local collaborations we have in Uppsala. An outward-looking activity that is particularly noteworthy is the traditional annual national sympo- sium organised by the Swedish Society for Automated Image Analysis (SSBA) since late 1970’s, which rotates between the active universities with Chalmers hosting in March 2019. The symposium gath- ered about 100 participants from academia and also several companies; CBA – today Sweden’s largest academic image analysis group – had 20 participants. We are very active in international and national societies and are pleased that our leaders are recog- nised in these societies. Ingela Nystrom¨ continues on new positions of trust within of the International Association of Pattern Recognition (IAPR) after having been a member of the IAPR Executive Commit- 5 tee during 2008–2018 (President 2014–2016). We are also closely involved in the Network of EUropean BioImage Analysis (NEUBIAS), where Natasaˇ Sladoje and Carolina Wahlby¨ serve as members of the management committee. Nationally, CBA has two board members in the Swedish Society for Automated Image Analysis (SSBA), Ida-Maria Sintorn as Chair and Robin Strand as Vice-Chair. Other examples of national com- mittee appointments are that Carolina Wahlby¨ serves on the Steering Group of the National Microscopy Infrastructure (NMI) and Ingela Nystrom¨ continued as Vice-Chair of the Council for Research Infra- structure (RFI) within the Swedish Research Council. During the last few years, we have been active on both national and local level to establish biomedical image analysis and biomedical engineering as more well-supported strategic research areas. The UU Faculties of Science and Technology, Medicine, and Pharmacy have formed the new centre Medtech Science and Innovation together with the UU Hospital. We are looking forward to the increased fund- ing and collaboration opportunities we expect to be the results of this new structure. For example, in December we arranged a joint workshop between Medtech and CBA to foster collaborations and grant applications. Our image analysis support for researchers within life science continues to develop with the national SciLifeLab facility within BioImage Informatics, with Carolina Wahlby¨ as director and Pet- ter Ranefall as head. CBA has several elected members of learned socities. Ewert Bengtsson, Gunilla Borgefors, Christer Kiselman, and Carolina Wahlby¨ are elected members of the Royal Society of Sci- ences in Uppsala. Christer Kiselman is elected member and Ingela Nystrom¨ is elected as well as board member of the Royal Society of Arts and Sciences of Uppsala. In addition, Ewert Bengtsson, Gunilla Borgefors, and Carolina Wahlby¨ are elected members of the Royal Swedish Academy of Engineering Sciences (IVA), and Christer Kiselman is an elected member of the Royal Swedish Academy of Sciences. Researchers at CBA also serve on several journal editorial boards, scientific organisation boards, con- ference committees, and PhD dissertation committees. In addition, we take an active part in reviewing grant applications and scientific papers submitted to conferences and journals. This annual report is available in printed form as well as on the CBA webpage, see http://www.cb.uu.se/annual_report/AR2019.pdf. 1.2 CBA research The objective of CBA is to carry out research in computerised image analysis and perceptualisation. We are pursuing this objective through a large number of research projects, ranging from fundamental mathematical methods development, to application-tailored development and testing in, for example, bio- medicine. We also have interdisciplinary collaboration with the humanities mainly through our projects on handwritten text recognition. In addition, we develop methods for perceptualisation, combining com- puter graphics, haptics, and image processing. Some of our projects lead to entrepreneurial efforts, which we interpret as a strength of our research. Our research is organised in many projects of varying size, ranging in effort from a few person months to several person years. There is a lot of interaction between different researchers; generally, a person is involved in several different projects in different constellations with internal and external partners. See Section 5 for details on and illustrations of all our research projects on the diverse topics. 6 1.3 How to contact CBA CBA maintains a home-page (http://www.cb.uu.se/). There you can find the CBA annual report series is in existence since 1993 (approximately 100 pages each), lists of all publications since CBA was founded in 1988, and other material. Note that our seminar series is open to anyone interested. Please, join us on Mondays at 14:15. Staff members have their own homepages, which are found within the UU structure. On these, you can find some detailed course and project information, etc. The Centre for Image Analysis (Centrum for¨ bildanalys, CBA) can also be reached by visiting us in the corridor at Campus Polacksbacken or by sending mail. Visiting address: Lagerhyddsv¨ agen¨ 2 ITC, building 2, floor 1 Uppsala Postal address: Box 337 SE-751 05 Uppsala SWEDEN 7 2 Organisation In the early years, CBA was an independent entity belonging equally to Uppsala University (UU) and the Swedish University of Agricultural Sciences (SLU).