ISIDORE PROJECT “AUTOMATIC PIPELINE FOR BRAIN AUTORADIOGRAPHY IMAGE ANALYSIS”
Turku BioImaging, in collaboration with Zuzana Čočková (Charles University, Prague) and Francisco Lopez-Picón (Turku PET Centre) developed the Mouse Brain Alignment Tool (MBAT), a Python-based software for processing autoradiographic (ARG) images of mouse brain tissue sections and analyzing them using topographical data from the Allen Institute’s Mouse Brain Atlas. The ARG images of mouse brain were from a study that investigates brain damage caused by COVID-19. This project was funded by the ISIDORe project of Euro-BioImaging through the Finnish Advanced Microscopy Node. In June 2023, Zuzana visited Turku BioImaging (TBI) and developed the software together with Junel Solis, one of TBI’s image data analysts. The image is taken by Joanna Pylvänäinen. “The developed pipeline for analysis of ARG images will increase reliability and reproducibility as well as enable end-users to focus on image analysis without technical interruptions”, explains Junel. The source code repository will soon be made public and open source. The project results were…
Turku Imaging Day 2023, Turku, Finland
Turku BioImaging together with the Field of View Research Program organizes the 1st edition of Turku Imaging Day, which will take place on Tuesday 3rd of October, 2023! Turku Imaging Day brings together researchers interested in imaging and aims to strengthen and grow the imaging community in Turku. The main pillars of the Turku Imaging Day are: 1) Excellent, easy-to-follow, scientific talks all about imaging; 2) Networking and making new connections; 3) Evening Get-Together to turn your new connections to new friendships. There are different options to participate in the event: I) Flash Talk Competition: Are you an efficient and concise speaker? Introduce your research in two minutes using slides that only contain images; no text allowed. II) Poster Competition: You don’t fancy being on the stage? Present your research in a more relaxed setting during the lunch break. You can make brand new posters or recycle already used ones as long as they relate to imaging. III) Matchmaking Session: Do you miss a…
CytoData symposium 2023, Helsinki, Finland
CytoData symposium and hackathon brings together researchers interested in image-based profiling of biological phenotypes. The symposium including workshops, presentations and a poster session is scheduled for the first two days of the event (Oct 23-24) followed by a hackathon for developers during the last two days of the event (Oct 25-26). The themes of the symposium are Single-cell profiling and Spatial profiling. CytoData 2023 is the annual event of the CytoData Society hosted by Institute for Molecular Medicine Finland (FIMM), University of Helsnki and University of Turku. Symposium Dates & Venue: October 23-24, 2023. University of Helsinki City Center Campus, Main Building Hackaton Dates & Venue: October 25-26, 2023. University of Helsinki Meilahti Campus in the Biomedicum complex. Confirmed speakers Anne Carpenter, Broad Institute Berend Snijder, ETH Zurich Leeat Keren, Weizmann Institute of Science Loïc Royer, Chan Zuckerberg Biohub Wei Ouyang, KTH Royal Institute of Technology Symposium Chairs Lassi Paavolainen, Institute for Molecular Medicine Finland (FIMM), University of…
BNMI symposium 2023 in Denmark
The second meeting of the Bridging Nordic Microscopy Infrastructures (BNMI) network will take place at the University of Southern Denmark, Odense, Denmark at August 22-25, 2023. The aim of the meeting is to bring together scientists who develop or utilize biological imaging methods, the Nordic imaging core facilities, and representatives of industry to discuss projects and present the latest imaging technologies and processing methods. List of exciting topics and distinguished invited speakers includes: Super resolution microscopy, Christian Eggeling (Friedrich Schiller University Jena) Spatial transcriptomics, Kim Thrane (KTH Royal Institute of Technology in Stockholm) and Sinem Saka (EMBL) Electron Micoscopy and Correlative imaging, Christel Genoud (University of Lausanne) and Judith Klumpermann (UMC, Utrecht), SRS and Raman imaging, Andreas Zumbusch (University of Konstanz) and Val Brunton (University of Edinburgh) Light sheet microscopy, Jan Huisken (Georg-August-University Göttingen). Image analysis, Jon Sporring (University of Copenhagen). Registration and more information can be found here Venue: Univerity of Southern Denmark, Odense, Denmark Dates: August…
Euro-BioImaging All Hands Meeting 2023
Euro-BioImaging Nodes were gathering for their first in-person All Hands Nodes Meeting 2023 at EMBL in Heidelberg, April 17-19. There was great opportunity to know more about the Euro-BioImaging family with the presentations and poster sessions from Nodes and partner organizations. Our Finnish Advanced Microscopy (FiAM) Node was presented by Jiri Funda and Dado Tokic. It was a very nice meeting with the opportunities for discussion and networking. Looking forward to next meeting in Torino!
“From Image Acquisition to Analysis and Data Storage” workshop in BioCity Turku
The Field of View Research Program, Turku BioImaging and Cell Imaging and Cytometry Core jointly organize the workshop “FROM IMAGE ACQUISITION TO ANALYSIS AND DATA STORAGE: available resources and good practices” on Wednesday 29.3. at 14:00 in BioCity Turku. At the workshop, you will learn how to navigate in the complex landscape of bioimaging techniques and how to properly execute all the steps of imaging workflow from image acquisition to data management. In addition, after the workshop, you will be familiar with the available resources at Cell Imaging and Cytometry Core and Turku BioImaging facilities and will know the responsible persons in the facilities. Please register latest by 21.03.23 here: https://link.webropolsurveys.com/S/E203560F01B43341 When: March 29th at 14:10 Where: BioCity Turku, Tykistökatu 6A, Turku
Light microscopy course organized by Helsinki BioImaging
Biomedicum Imaging Unit, Helsinki BioImaging organizes “Light Microscopy: From Basics to Advanced” course in February 2023. On-site lectures 09.02. – 10.02.2023 + demonstrations 13.02. – 17.2.2023 After completing this course the students should be able to explain the basic principles of light microscopy and microscopic image acquisition understand the most important steps of sample preparation for microscopy compare and contrast transmitted light and fluorescence methods compare and contrast widefield and optical sectioning microscopy methods know some basic and advanced research applications for the microscopy methods covered evaluate the suitability of covered microscopy methods for different research applications Detailed course content can be found here: https://www.helsinki.fi/en/news/life-sciences/dpbm-210-2023 Lectures are open for everyone. Register here by 31.01.23: https://studies.helsinki.fi/courses/cur/hy-opt-cur-2223-c1a91580-6159-4fbe-9b66-f8cc3b9492ec When: February 9th-17th, 2023 Where: Biomedicum, Haartmaninkatu 8, Helsinki
Image Analysis Basics course 2023
Turku BioImaging Image Data Team is organizing an Image Analysis Basics Course in 2023. This course will be organized in-person course with lectures and hands-on exercises mixed. Course Description: Image analysis course Feb-March 2023 Session 1 (24.2 / Pasi Kankaanpää): Friday 9-12 Basic concepts Session 2 (1.3 / Joanna Pylvänäinen): Wednesday 13-16 Image handling using Fiji Session 3 (3.3/ Junel Solis): Friday 9-12 Concepts and Hands-on exercises for segmentation, filters, particle analysis (shape and/or intensity analysis). Register here: https://link.webropolsurveys.com/S/2E24DD62253BA8A0
International Master´s Degree Programme in Biomedical Imaging in Turku, Finland
Call for applications for studies starting in August 2023 is opening on January 4th. Do you want to study in a stimulating research environment in a country with beautiful nature and high-tech innovations?Are you interested in studying Biomedical Imaging in the laboratories where Stefan Hell did his Nobel prize-awarded research with super-resolution?If your answer is YES, please read this email 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. The 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…
BioImage Informactics Finland Network Symposium 2022
3rd BioImage Informatics Finland symposium is organized by Helsinki Bioimaging at Biomedicum, Helsinki, Nov 14th 2022. The symposium brings together researchers and facility personnel working with analysis of microscopy images of cells and tissues to discuss the latest developments in bioimage informatics. The program includes four sessions focusing on applications, methods, software tools, and analysis services. After symposium dinner will be organized at participants own expense. The symposium is free but registration is required. The lecture hall holds room for 60 participants so we wish everyone who registers to also be present at the symposium. If you have registered but are unable to attend, please let the organizers know so that we can make room for other participants. For any inquiries, please contact Lassi Paavolainen (lassi.paavolainen@helsinki.fi). Registration deadline: November 6th, 2022 More information about the symposium can be found here: https://www.helsinki.fi/en/infrastructures/bioimaging/courses-and-news-archive/bioimage-informactics-finland-network-symposium-2022 When: November 14th, 2022Where: Biomedicum, sh.1-2 (bottom floor), Haartmaninkatu 8, 00290 Helsinki