Newsletter Winter 2022

Such  hardware is especially suitable for performing tasks from the image processing where one needs to work with large dataset, high resolution data, or time-lapse sequences. The common tasks solved in our servers include cell segmentation, tumor segmentation, detection of specific regions in organs and their classification, and biomedical image synthesis. The most frequent application area is currently oncology (cancer cell image analysis and tumor image analysis) in the frame of newly established Centre for Artificial Intelligence in Oncology coordinated by Masaryk University.

Our core facility is proud of a high user comfort. The servers are located in the university data center which guarantees the non-stop service and avoidance of blackouts. The broadband connection to the internet, the graphical user interface for each user, and full interactive control without the necessity of creating the batches and scheduling make the use of our service as easy and comfortable as possible. The stable OS Linux Ubuntu 20.04 is installed on both servers. The users of MS Windows operating system are nevertheless not expelled as we can prepare MS Windows desktop environment as well.

A detailed description of the servers and services provided by the Centre of Biomedical Image Analysis can be found at https://cbia.fi.muni.cz/services/. The services are provided to both internal and external users. In case of interest, please contact the support team at cbia-supp@fi.muni.cz.

The MRI protocol for 3 Tesla human MRI scanners optimized by the group allowed the acquisition of high-resolution diffusion MRI, MR spectroscopy, and structural MRI data. Data were collected on a large cohort of patients with different stages of degenerative cervical spinal cord compression and were related to healthy volunteers. Acquired images allowed to reveal micro- and macro-structural damage of the spinal cord in patients with compression and its relationship to the clinically used measures. Findings serve as a starting point for the follow-up longitudinal study with the aim to identify the predictive MRI-based biomarkers of spinal cord damage.

Moreover, our group participated in an international project focused on the development of reproducible MRI protocol for human spinal cord imaging. The protocol was published in the Nature Protocol journal and is widely adopted by researchers all around the world. Over forty centers worldwide have already acquired MRI data with this protocol and published them freely online in line with open-access practices.

The conference is traditionally dedicated primarily to the Czech-BioImaging users and scientists interested in biological and medical imaging and this year was not an exception. Five scientific sessions were mixed of lectures from fields of electron microscopy, light microscopy and medical imaging, some including an industrial presentation introducing advances in manufacturing. To express in numbers, 31 high-quality scientific talks were given in total. Five of the talks related to the industrial sector and were either given by the company representatives or associated users. The audience reached around 100 participants, which is considered a very satisfactory number for the conference of its kind.

Although all of the lectures presented research of very high-quality, three of them stood out in particular. Two international lecturers accepted the invitation to join the conference and give an invited lecture – Julia Fernandez-Rodriguez, University Gothenburg, Sweden introduced the “Centre for Cellular Imaging – a Research Infrastructure for Correlated Multimodal Imaging” in her talk and Claus Lamm, University of Vienna, Austria focused on “Novel multi-method neuroimaging approaches to unravel the complexities of the human social brain“. Highly acclaimed was the lecture given by Ivan Rektor, Masaryk University, Brno titled “The lifelong impact of extreme stress on the human brain: a three-generation study of Holocaust survivors”.

An integral part of the conference was the poster session in which around 20 scientific posters were displayed. The conference was supported by the Ministry of Education, Youth and Sports of the Czech Republic and commercial sponsors: Abberior Instruments GmbH, Carl Zeiss spol. s.r.o., HPST s.r.o., Měřicí technika Morava s.r.o. and Pragolab s.r.o., who participated in a commercial exhibition introducing their newest microscopic equipment and offering services to the participants.

We are pleased to announce that we are already making arrangements to hold the conference in October 2023. All of you are kindly invited to join us. You can expect more information to appear soon on our website
czech-bioimaging.cz, or in your mailbox.

If your answer is YES, please read this message carefully!

International Master´s programme in Biomedical Imaging is a two-year (120 ECTS) programme jointly administrated by the Faculty of Science and Engineering at Åbo Akademi University, Turku, Finland, and the Faculty of Medicine at the University of Turku (Masters programme in Biomedical Sciences). Close cooperators are the national Turku PET Centre, Turku Center for Disease Modeling, Turku Centre for Biotechnology, and the Turku University Hospital.

Programme is aimed at students with a B.Sc. degree in the Life Sciences or applicable areas of biomedical sciences, physics, chemistry, or engineering. The interdisciplinary curriculum provides the graduates with a broad spectrum of the most recent knowledge in biomedical imaging related to many application areas in cell biology, medicine, and nanotechnology. One of the great examples of our diverse success is the 2014 Nobel Prize in Chemistry shared by Prof. Stefan W. Hell, who has made his original publications on STED microscopy in Turku.

The programme is tuition free for European students and non-EU/EEA students the tuition fee is 12 000€ / year. Scholarships are available!

The language of instruction is English. Book and take the language test well in advance before the application period!

Please find more info in:

• http://www.bioimaging.fi/programme/
• Biomedical Imaging | Åbo Akademi University (abo.fi)
• Master's Degree Programme in Biomedical Sciences: Biomedical Imaging | University of Turku (utu.fi)
• Studying in Finland: http://www.studyinfinland.fi/
• https://www.turku.fi/en/study-turku

Application period: 4-18 January 2023.

We are more than happy to answer if you have any questions about the Master´s Degree programme in Biomedical Imaging! Please contact us: bima-office@bioimaging.fi

We are proud to have been a part of the International Conference on Research Infrastructures (ICRI) 2022 held on 19-21 in Brno with the Imaging Principles of Life being the ICRI Satellite event.

Euro-BioImaging ERIC was one of the 3 partners, who joined a new, promising collaborative agreement among top-class life science research infrastructures during ICRI 2022. The trilateral Memorandum of Understanding was signed by 2 other parties - Instruct-ERIC and EU-OPENSCREEN ERIC. The initiative is designed to benefit the life science research community by building common pipelines for user access, and joining forces in training, external communication, FAIR data management, and funding opportunities.