- We were at NEUBIAS2020.
- Nataša and Joakim participated in Imaging in Life Sciences, Vienna, November 21-22. Nataša co-organized the conference and chaired a session on Correlative software - Multimodal image analysis. COMULIS-specific meetings were organized on the 20th of November. Nataša lead WG4 and presented its activities. Joakim had a very active role in WG4.
- Bioimage Data Analysis Workflows is available online!
- Buda Bajić successfully defended her PhD thesis on the 16th of September 2019, at the Faculty of Engineering, University of Novi Sad. Congratulations for the excellent work done!
- We will be a part of the team, led by Tibor Lukić as a general chair, organizing the 20th IWCIA conference, this time in Novi Sad, Serbia! Nataša is a co-chair, Joakim is a program committee member, and Buda is a local organization committee member of this conference.
- Senate of University of Novi Sad approved the Evaluation Committee's report for Buda's thesis. The preliminary date for the defense is September 16!
- Our proposal for Master programme in Image Analysis and Machine Learning is approved by Rector's office and will be initiated at Uppsala University (Department of Information Technology) in 2020!
- Our proposal for a pedagogical development project, entitled "Computer assisted image analysis education in the era of deep learning and artificial intelligence - challenges and opportunities" is approved by Uppsala University. Nataša will, supported by Joakim Lindblad, Filip Malmberg, and Robin Strand, work in this project during 2019-2020.
- Nataša is co-organizing Imaging in Life Sciences, Vienna, together with the COMULIS team.
- Nataša was invited to talk at the Workshop on Mathematics for Complex Data at KTH, Stockholm, June 24-26, 2019. She discussed "Distance functions for robust image registration: Theory and applications".
- Tomas Majtner, our collaborator from the University of Southern Denmark, presented our study On the Effectiveness of Generative Adversarial Networks as HEp-2 Image Augmentation Tool at SCIA2019 in Norrköping, Sweden, June 11-13, 2019.
- Karl co-authored a paper presented at SSDL'19, Norrköping June 10-11. The paper is entitled CNNs on Graphs: A New Pooling Approach and Similarities to Mathematical Morphology.
- Johan presented our paper on Stochastic Distance Transform at DGCI2019 in Paris, March 25-29.
- Johan and Elisabeth participated at SSBA2019 in Göteborg, March 19-20 and presented our work on Stochastic Distance Transform, Fast and Robust Registration, and Oral Cancer Detection by Texture-Aware CNNs.
- Nataša and Joakim participated in the COMULIS meeting in Glasgow, colocalized with the EMIM- European Molecular Imaging Meeting. COMULIS organized a very successful Special session on Correlated Multimodal Imaging in Life Science at EMIM. In the continuation, Nataša organized a COMULIS WG4 meeting with focus on multimodal bioimaging ontology, data and software sharing platforms, and analysis of the available correlation software.
- Joakim (and Tibor) successfully supported our DIP group member Slobodan Dražić in the final part of his journey towards his PhD degree! Slobodan's thesis, entitled Shape based methods for quantification and comparison of object properties from their digital image representations was defended on February 20, 2019, at the Faculty of Technical Sciences, University of Novi Sad. Congratulations to all!
- Our paper Fast and Robust Symmetric Image Registration Based on Distances Combining Intensity and Spatial Information is now published by IEEE Trans. on Image Processing! Big congratulations to Johan for his excellent work on this framework!
- Jo Gay is our new master student. She will work on multimodal microscopy image registration. Considering that Jo and Hugo Harlin did excellent work on texture based image classification for oral cancer detection within their student project under Nataša and Joakim's supervision, we are very much looking forward to this continued collaboration. Welcome, Jo!
- Elisabeth, Nadia, Ida-Maria, Joakim, and Nataša participated in the 3rd NEUBIAS Conference organized in Luxembourg, February 2-8, 2019. As always, a very active and very rewarding week! Joakim and Nataša took part in the 7th taggathon, Feb 3-5. We then had four poster presentations: Nadia presented our work on Visualization of convolutional neural network class activations in automated oral cancer detection for interpretation of malignancy associated changes; Joakim presented our results on Texture-based oral cancer detection: A performance analysis of deep learning approaches; Elisabeth presented our work Towards automated multiscale Glomeruli detection and analysis in TEM by fusion of CNN and LBP maps, both orally and as a poster. Finally, Matuš Kalaš presented an updated version of our poster on EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats. Numerous interesting presentations and discussions during the whole week!
- A new edition of the Computer Assisted Image Analysis II course has started, with twice as many student as last year! More than half of them are international students. This strongly confirms that our new international master program comes in a right time and will meet real needs!
- COST project COMULIS organized MC and WG meeting in Porto. Joakim participated as an MC member and took an active role in the WG4 activities.
- Karl, Joakim and Nataša participated at the 3rd WASP Winter Conference which took place at Lindholmen in Göteborg, January 15-17 2019. The purpose of the event was to introduce new PhD students to WASP, give an update on WASP activities, and to give PhD students an opportunity to present their research in a friendly environment. This was indeed a very pleasurable experience!
- Our paper Stochastic Distance Transform, with Johan as the first author and a driving force of the project, is accepted for DGCI2019 in Paris. Congratulations!
- Martin Danelljan from Linköping University, and Postdoc at CVL ETH Zürich from January 2019, visited MIDA group and gave a CBA seminar Efficient Online Learning for Video Object Tracking and Segmentation on December 12. This was really inspiring! 2 hours of discussion with Martin afterwards, with many interesting ideas exchanged. Thanks, Martin!
- Our dear friends and colleagues, Ljiljana Teofanov (Faculty of Technical Sciences, University of Novi Sad) and Nenad Teofanov (Faculty of Science, University of Novi Sad), visited us December 8-11. We discussed approaches to diffeomorfic image registration, with an aim to extend our alpha_SMD based registration framework to accommodate elastic transformations. Nenad led a workshop on Wavelets, with focus on application of Haar wavelets to image processing.
- Joakim has been awarded a visiting professor grant from the Université Clermont Auvergne, France. Nataša and Joakim spent two weeks (November 6-17) with Antoine Vacavant's group. Interesting discussions related to collaboration on multimodal medical image registration!
- Nataša is appointed by the Educational Board of Science, Faculty of Science and Technology, Uppsala University, to prepare a proposal for initiating a new International Master Program in Image Anlysis and Machine Learning. This will strongly contribute to increased visibility and dissemination of the great work we are doing at the Centre for Image Analysis!
- Our colleague and friend, Antoine Vacavant, Université Clermont Auvergne, France, visited us at CBA Oct 22-23. He gave a talk within the CBA seminar and another one withing the CIM-CoSy seminar series. We discussed a number of possible joint research directions. Antoine's visit was supported by the TOR program.
- We have thoroughly enjoyed one more NEUBIAS TS&Taggathon session, Oct 16-19 in Edinburgh. As always, good work and good time!
- We have successfully initiated a new COST network - COMULIS - Correlated Multimodal Imaging in Life Sciences (17121). The kick-off meeting was in Brussels on Oct 12. Nataša is a leader of WG4 devoted to Correlated software. Both Joakim and Nataša represent Serbia in the MC of the project. Many friends from NEUBIAS involved, but also many new faces!
- Nadezhda Koriakina, our new PhD student, who will work under Joakim's supervision on development of novel methods of deep learning within computational microscopy, has joined our team. Warm welcome!
- We very much enjoyed the ECCV 2018 conference in Munich, Sept 8-14 - a very rewarding (and exhaustive) experience! Elisabeth had a poster presentation within the BioImage computing Workshop, (Sept 14), of our paper entitled "Towards automated multiscale imaging and analysis in TEM: Glomerulus detection by fusion of CNN and LBP maps", co-authored by Elisabeth Wetzer, Joakim Lindblad, Ida-Maria Sintorn, Kjell Hultenby, and Nataša Sladoje.
- We were represented at the 2nd Swedish Symposium on Deep Learning, SSDL2018 in Göteborg, Chalmers University of Technology. Elisabeth gave an oral presentation of our work entitled "Towards automated multiscale imaging and analysis in TEM: Glomeruli detection by fusion of CNN and LBP maps" co-authored by Elisabeth Wetzer, Joakim Lindblad, Ida-Maria Sintorn, Kjell Hultenby, and Nataša Sladoje.
- Karl Bengtsson Bernander, our new PhD student with the Wallenberg AI, Autonomous Systems and Software Program (WASP), AI-Math has joined our team. Warm welcome!
- Our MIDA (Methods for Image Data Analysis) research group has a new web-page.
- Nataša and Joakim were lecturers at SSIP2018 - as always, a very pleasant experience.
- Nataša is, from July 1, appointed as Senior Lecturer in Computerized Image Analysis, Department of Information Technology, Uppsala University.
- We have joined a recently accepted COST Action CA 17121 COMULIS - "Correlated Multimodal Imaging in Life Sciences". We are looking forward for its kick-off in October!
- We were at the IEEE International Symposium on Biomedical Imaging - ISBI2018 in Washington, D.C., USA, April 4-7. Buda and Amit presented our joint paper entitled "Denoising of Short Exposure Transmission Electron Microscopy Images for Ultrastructural Enhancement", co-authored by B. Bajić, A. Suveer, A. Gupta, I. Pepić, J.Lindblad, N. Sladoje, and I.-M. Sintorn.
- We are looking forward to a new collaborative project with Moritz Kirschmann, University of Zurich, Center for Microscopy and Image Analysis! Buda is awarded a STSM (Short Term Scientific Mission) within NEUBIAS and will visit Moritz in March, to jointly work on "Denoising of low signal-to-noise scanning electron micrographs by energy minimization and deep learning". We hope to be able to extend our good results which will be presented at ISBI2018 to this new imaging modality.
- We were at the 36th Annual Swedish Symposium on Image Analysis, SSBA, organized at KTH, Stockholm, March 7-9. Johan gave an oral presentation of our joint work on "Distance Between Vector-valued Images based on Intersection Decomposition with Applications in Object Detection".
- We were at the very successful NEUBIAS conference and found it really inspiring (Jan 27 - Feb 2). Nataša gave an invited talk "Improved distance measures between images and their performance in biomedical applications". Our well performing distance attracted quite some attention!
Nataša and Joakim participated in Tagathon#4, focusing mostly on EDAM bioimaging onthology. Our EDAM-bioimaging team presented a poster at the symposium.
- We had a poster presenting "Denoising of short exposure Transmission Electron Microscopy images for ultrastructural enhancement" (B. Bajic, A. Suveer, A. Gupta, I. Pepic, J. Lindblad, N. Sladoje, I.-M. Sintorn) at NEUBIAS conference in Szeged (Jan 31 - Feb 2).
- Nataša has been awarded a visiting professor grant from the Université Clermont Auvergne, France. Nataša and Joakim spent two weeks (November 2-16) with Antoine Vacavant's group.
- Nataša gave an invited talk "Tackling a major bottleneck in the BioImage Computing community – Network of European BioImage Analysts (NEUBIAS)" at the Bioimage Computing @ ICCV 2017 workshop, October 23. A very successful workshop, and impressive main ICCV conference in Venice, Italy.
- Elisabeth Wetzer, our new PhD student with the Centre for Interdisciplinary Mathematics, has joined our team. Warm welcome!
- Nataša is an invited speaker at the 2nd NEUBIAS Conference in Szeged, Hungary.
- Nataša and Joakim participated at the Neubias workshop 2 in Gothenburg, September 11-14, 2017. Two training schools, one for the facility staff, the other for early career investigators, and one more Taggathon are organized.
- Buda Bajić, our PhD student from Novi Sad, visited us at CBA. She staying with us from August 15 to October 28, 2017.
- Nataša participated at the Workshop Big Data for Life Sciences, organized by COST Action CHARME in Uppsala, September 18-22, 2017. She presented and promoted NEUBIAS activities.
- DIP group@FTN Novi Sad successfully organized the 25th Summer School on Image Processing, SSIP 2017. More than 30 students and 18 teachers from 10 countries participated. Congratulations to Tibor and the whole organizing team!
- Nataša, Joakim, Johan, Amit, Anind, and Ida-Maria participated at the 20th Scandinavian Conference on Image Analysis SCIA2017, in Tromsö, Norway. Two papers of our team presented! "Enhancement of Cilia Sub-structures by Multiple Instance Registration and Super-resolution Reconstruction" co-authored by Amit, Nataša Joakim, Anka, and Ida-Maria and "Convolutional Neural Networks for False Positive Reduction of Automatically Detected Cilia in Low Magniffcation TEM Images" co-authored by with Anind, Amit, Joakim, Ida-Maria, Anca, and Nataša.
- Nataša and Joakim's paper on "Distance Between Vector-valued Representations of Objects in Images with Application in Object Detection and Classification" is accepted for the 18th International Workshop on Combinatorial Image Analysis, IWCIA2017. Nataša presented the paper at the conference in Plovdiv, Bulgaria.
Joakim, as a program committee member, supported IWCIA2017.
- Johan, Joakim and Nataša's paper on "Distance Between Vector-valued Fuzzy Sets based on Intersection Decomposition with Applications in Object Detection" is accepted for ISSM2017. Johan presented the paper at the conference at the Center for Mathematical Morphology, MINES ParisTech, in Fontainebleau, France.
- Nataša, as a program committee member, supported the 13th International Symposium on Mathematical Morphology, ISMM2017.
- Johan Öfverstedt is our new PhD student. Warm welcome! Johan will work on development of methods for analysis of multi-modal, multi-layer, and multi-scale images.
- Feb 12-17 Joakim and Nataša participated at NEUBIAS2020 in Lisbon, Portugal.
This was the first Annual meeting of NEUBIAS, gathering the whole Bioimage Analysis Community into a multi-faceted event - Training schools, a Working Meeting (Taggathon) and a Large Symposium dedicated to Open Tools in BioImage Analysis.
We have presented our work on "Detection and enhancement of objects in low resolution transmission electron microscopy images for multi-scale imaging and structural analysis."
- Jan 16 Joakim and Nataša participated at NETDELIVER project team meeting in Paris, France.
- Dec 12-15 Buda, Joakim and Nataša participated at IPTA2016 in Oulu, Finland.
Our paper Single image super-resolution reconstruction in presence of mixed Poisson-Gaussian noise, is among six best reviewed papers at the conference.
- Nov 14-15 our collaborator Zoltan Kato, University of Szeged, is visiting CBA. He will give a talk at CBA seminar series on November 14, and within CIM CoSy-seminar series on November 15.
- Nov 8-11 Joakim and Nataša visiting Department of Image Processing and Computer Graphics at the University of Szeged, Hungary.
- Oct 31 New PhD position in Computerized Image Processing
Latest application date: 2016-12-01
- Oct 27 Kick-off meeting of our project A smart and easy platform to facilitate ultrastructural pathologic diagnoses held at Vironova.
- Oct 25 Sebastian Bas Kanå started a master project with Joakim and Nataša. We had a kick-off meeting of the collaborative project Automatic landmark identification in digital images of Drosophila wings for improved morphometric analysis at EBC. Our host was Zorana Kurbalija Novičić who suggested the study.
- Oct 24-25 Our collaborator Antoine Vacavant visited CBA. He gave a presentation at CBA seminar series and within CoSy-Seminar at the Centre for Interdisciplinary Mathematics (CIM).
We discussed a joint project application, NETDELIVER, which is led by Antoine.
- Oct 7 Nataša is now elected Full Professor in pure and applied mathematics at the Faculty of technical sciences, University of Novi Sad.
- Sept 26-30 Nataša spent a week with DIP group in Novi Sad. We had several fruitful meetings. Buda successfully presented her research work to the evaluation committee and is now officially approved to start preparing her PhD thesis.
Nataša acted as a committee member at a defense of the PhD thesis of Stefana Janićijević. The thesis "Variable Formulation and Neighborhood Search Methods for the Maximum Clique Problem in Graph" is successfully defended at the Faculty of Technical Sciences, on September 29.
- Sept 13-16 Joakim and Nataša participated in the 1st NEUBIAS training school and Taggathon in Barcelona, at the Universitat Pompeu Fabra. Joakim gave a lecture/tutorial on Matlab to an international group of 25 selected Bioimaging facility staff members.
- Aug 15-19 Joakim and Nataša spent a week with DIP group in Novi Sad. We had several fruitful meetings. Slobodan successfully presented his research work to the evaluation committee and is now officially approved to start preparing hir PhD thesis.