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Press Release

Press Release

Doctoral thesis in Cell Biology presents three user-friendly image analysis tools tailored for quantifying live microscopy videos

Joanna Pylvänäinen.
Joanna Pylvänäinen

Lic.Phil. Joanna Pylvänäinen’s doctoral thesis in Cell Biology will be put forth for public defence at the Faculty of Science and Engineering at Åbo Akademi University.

The thesis is entitled Bioimage analysis for life scientists: tools for live cell imaging.

The public defence of the doctoral thesis takes place on 26 April 2024 at 1.15 PM in Auditorium Argentum, Aurum, Henrikinkatu 2, Turku. Professor Carolina Wählby, Uppsala University, Sweden will serve as opponent and Associate Professor, Guillaume Jacquemet, Åbo Akademi University, as custos.


The imaging of living cells is crucial for visualizing dynamic biological processes such as tissue development, wound healing, and cancer progression. Optical microscopy, in conjunction with digital cameras, facilitates the magnification, visualization, and capture of these events in videos. However, extracting meaningful insights from live videos poses several challenges. Living cells are fragile and require imaging in controlled environments with minimal light exposure, often resulting in noisy videos. Moreover, microscope or sample movements introduce drift in captured videos, further complicating analyses. While various tools exist to enhance video analysis, many are inaccessible to researchers due to a lack of programming skills or inadequate documentation and user interfaces.

Addressing these challenges, this doctoral thesis presents three user-friendly image analysis tools tailored for quantifying live microscopy videos. Fast4DReg rapidly corrects drift in 3D videos, DL4MicEverywhere enables deep learning implementation across multiple computational platforms, enhancing video quality, and TrackMate v7 integrates cutting-edge segmentation algorithms to improve tracking. Extensive documentation and openly available datasets accompany these tools to ensure usability.

To emphasize their usability, two case studies are presented: one examining the interaction between pancreatic cancer cells and the endothelium during metastasis, and another focusing on drug resistance in cancer cells. The tools developed in this thesis offer accessible solutions for biological video processing and analysis, thus benefiting researchers in various fields in understanding cell behavior and disease mechanisms.

Joanna Wiktoria Pylvänäinen was born in 1984 in Tampere. She can be reached by phone +358 44 012 3436 or email joanna.pylvanainen@abo.fi.

The doctoral thesis can be read online through the Doria publication archive.

Click here for a press photo of the doctoral student.