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Department of Information Technology

Seminar series of the Centre for Image Analysis (CBA)

The seminar series hosted by the Centre for Image Analysis (CBA) is open to everybody interested. This is also the seminar of the Image Analysis Unit at Vi3. Join us in Theatrum Visuale, room 100155, building 10, Ångström Laboratory.

Each Monday at 14:15-15:00, seminars on current research in image analysis and related topics are given by internal and external speakers. See schedule below.

The CBA seminars are announced at the weekly internal Vi3 information meeting, and also on the Dept. of IT's newsletter LäsIT

Note that extra seminars may occasionally be held at other times than mentioned above.


Date Time Title Speaker
2023-01-16 14:15-15:00
Theatrum Visuale
Uncertainty Estimation of Semantic Segmentation of MR-Linac Prostate Cancer Images
Prostate cancer radiotherapy treatment makes use of medical deep learning methods in many steps of the workflow. Instead of focusing solely on the performance metrics of the deep learning model attention must also be given to the uncertainty of the model output. We applied the Monte Carlo dropout method for estimating the uncertainty of a semantic segmentation model of MR-Linac prostate cancer images. Concrete dropout was added to the middle layers of a simple U-Net to obtain multiple samples from a stochastic distribution for each input image. Epistemic uncertainty and predictive uncertainty were captured in uncertainty maps by using mutual information and predictive entropy. The predictive entropy maps revealed that the wrongly predicted pixels correspond to high estimated uncertainty values.
Marissa van Lente
Eindhoven University of Technology, The Netherlands
2023-01-23 14:15-15:00
Theatrum Visuale
Research in the micro-group
I will give an overview of the research that has been going on in the 'my' research group since I joined the Dept. of IT in 2011 as lecturer in Quantitative Microscopy. I will also talk a bit about efforts to find a way forwards, including both joys and disappointments. I will also try to include a bit of ideas for the future, and I'm hoping to give you some insights to my joy for being a researcher in the multi-disciplinary domain of bioimage informatics.
Carolina Wählby
2023-01-30 14:15-15:00
Theatrum Visuale
Uniform Polyhedra – or What’s in the Vitrines on Floor 4?
The history of the 75 uniform polyhedra starts with early humans and ends 1975. In this seminar, I will tell that story. Early efforts are attributed to Plato and Archimedes – doubtful – while Johannes Kepler 1600s, Louis Poinsot 1800s, Donald Coxeter et al., 1900s really did contribute to the story. Uniform polyhedra will be defined and sorted into different types. The construction of a number of uniform polyhedra will be discussed and presented. As an extra benefit, you will also understand that most mathematicians do not die young.
Gunilla Borgefors
2023-02-06 14:15-15:00
Theatrum Visuale
Towards an Improved Oral Cancer Classification via Multimodal Image Fusion of Brightfield and Fluorescence Micrographs
Diagnosis of oral cancer from brush biopsies combined with automatic detection has the potential to be a non-invasive cost-effective approach for early detection and intervention. In this project, we have investigated the potential for improving the accuracy of the automated classification of cancer in the individual cells by using multimodal imaging and analysis, incorproating both brightfield microscopy (which is commonly used) and also fluorescence microscopy of the Papanicolaou stained samples. We suggest an approach that involves the multimodal image acquisition, cell nuclei detection, cross-modal registration of cell nuclei to find matching image patches, and a multimodal deep learning classifier with fusion. We observe a substantial improvement in performance from incorporating the additional modality on a dataset of 8 cancer patients and 11 healthy people.
Johan Öfverstedt
2023-02-13 14:15-15:00 Title
Ankit Gupta
2023-02-20 14:15-15:00
Theatrum Visuale
Docentship lecture
Ultrasound Imaging: Fundamentals and Applications

Medical image analysis aims to generate value from medical images, and a fundamental understanding of the acquisition of such images is essential for devising processing methods and hypotheses utilized therein. Among such modalities, ultrasound imaging is a unique option being safe, real-time, portable, and affordable; and ultrasound is used in many clinical applications, including diagnostic decision making, pre-operative planning, surgical guidance, monitoring, and screening for diseases. This lecture will introduce the basics of ultrasound imaging and will present different ultrasound imaging techniques and contrast mechanisms; from conventional approaches to recent innovative methods such as in the fight against cancer, detecting aging muscles, and functional brain scans.
Orcun Göksel
2023-02-27 14:15-15:00 Title
Pol Del Aguila Pla
Biomedical Imaging Group, EPFL Lausanne
2023-03-06 14:15-15:00 Title
Joakim Lindblad
2023-03-13 No seminar
SSBA/SSDL Symposium
2023-03-20 14:15-15:00
Theatrum Visuale
Handwritten Text Recognition based on Attention Encoder-Decoder Networks for Historical Document Images
The pressing need for digitization of historical document collections has led to a strong interest in designing computerised image processing methods for automatic handwritten text recognition (HTR). Handwritten text possesses high variability due to different writing styles, languages and scripts. Training an accurate and robust HTR system calls for data-efficient approaches due to the unavailability of sufficient amounts of annotated multi-writer text. This seminar presents a recent work, called AttentionHTR, that leverages transfer learning to enable HTR in cases where training data is scarce. The proposed attention-based architecture is simple, modular, and reproducible; more data can be easily added in the pipeline, further strengthening the model’s accuracy. A case study on an ongoing project "Marginalia" will also be presented that utilizes AttentionHTR for recognition of Marginalia texts, i.e., text written in margins or handwritten notes. The data comes from early book collections found in the Uppsala University Library.
Ekta Vats
Centre for Digital Humanities
2023-03-27 14:15-15:00 Title
PhD rehearsal
Raphaela Heil
2023-04-03 14:15-15:00 Title
PhD rehearsal
Nicolas Pielawski
2023-04-10 No seminar
Easter Monday
2023-04-17 14:15-15:00 Title
Can Deniz Bezek
2023-04-24 14:15-15:00 Title
PhD rehearsal
Eva Breznik
2023-05-01 No seminar
May Day
2023-05-08 14:15-15:00 Title
Axel Andersson
2023-05-15 No seminar
EMBL-SciLifeLab Data Science Workshop
2023-05-22 14:15-15:00 Title
Nadezhda Koriakina
2023-05-29 14:15-15:00 Title
PhD rehearsal
Elisabeth Wetzer
2023-06-05 No seminar
Bridge Day for June 6
2023-06-12 14:15-15:00 Title
Petter Ranefall
Sysmex Astrego AB
2023-06-19 14:15-15:00 Title

Updated  2023-02-05 22:22:43 by Natasa Sladoje.