Finnish Advanced Microscopy Node

🎆 We are excited to share that Cell Imaging and Cytometry Core and Turku BioImaging are organizing the Practical Super-Resolution Microscopy course in Turku. Places are limited, registration is open until the end of the summer! 📅 September 23-27, 2024 📍 BioCity, Tykistökatu 6, 20520 Turku, Finland ☑ Register by August 31, 2024 via https://lnkd.in/du-3Ghbt 🔗 More info: https://lnkd.in/dM7FfUgR Finnish Advanced Microscopy Node Turku Bioscience Turun yliopisto - University of Turku Åbo Akademi University

The rapid innovation in imaging technology has led to the creation of hundreds of proprietary file formats, posing significant challenges for the #interoperability of imaging data in the pursuit of making scientific data #FAIR (1). foundingGIDE main aim is to enable bioimage data sharing and #community efforts around biological and preclinical open image data by enhancing the interoperability across image data resources. Traditionally, working with large-scale image data has required managing file format heterogeneity and downloading extensive datasets to local machines, a process that is both ⏳ time-consuming and ⚡ resource-intensive. OME-Zarr, a next-generation file format (NGFF) developed by the Open Microscopy Environment (3) community not only addresses these challenges by enabling users to interact with bioimaging data directly in the cloud, but also significantly enhances interoperability across diverse imaging platforms. By standardizing how data is stored and accessed, OME-Zarr paves the way for more seamless data sharing and collaboration across the scientific community. A prime example of OME-Zarr's impact can be seen in the European Bioinformatics Institute | EMBL-EBI BioImage Archive selection of studies (2), where interactive images can be explored directly in the browser. This advancement not only improves efficiency and accessibility but also ensures that data can be more easily integrated and utilized across various systems and research projects. As OME-Zarr cloud-native technologies continue to shape the future of bioimaging, we are particularly excited about the upcoming OME 2024 NGFF Challenge. This challenge aims to convert a significant volume of existing bioimaging data into the next major version of OME-Zarr, based on Zarr v3 (4). The results of the OME 2024 NGFF Challenge will be showcased at the back-to-back events of Global BioImaging EoE (5) and the foundingGIDE Community Event (6), taking place from October 29 to November 1 in Okazaki, Japan. (1) https://lnkd.in/eVBwdBPr (2) https://lnkd.in/eddfxGvQ (3) https://lnkd.in/eVpkBJwE (4) https://lnkd.in/eTxjfa8U (5) Global BioImaging EoE https://t.ly/y7FDA (6) foundingGIDE Community Event https://lnkd.in/eH476niF

📢 Excellent opportunity for those who are working in imaging facility/lab and would like to visit our Finnish Advanced Microscopy Node. Find more information below ⤵

We are delighted to share the Euro-BioImaging Annual Report 2023 with you! It includes numerous highlights, such as the celebration of two new consortium members (Spain & Belgium), an overview of our Strategic Plan, a selection of user stories, multiple indications of our impact and a glimpse at the amazing research & innovation happening at Euro-BioImaging Nodes. The Annual Report 2023 captures an exciting, pivotal year with significant progress and growth - don't miss it! https://lnkd.in/diSHCsMn

📣 We need your feedback! If you're working at a #EuroBioImaging Node, please help us tailor the opportunities that will be available within the EVOLVE project by filling in our Node staff survey. EVOLVE is a new EU-funded initiative designed to strengthen and grow the Euro-BioImaging community. Our survey covers four key areas: ✅ Training for Node staff, ✅ User communities, ✅ Image data, ✅ Green and sustainable research infrastructures. Please take a few moments to help us fine-tune our plans within this project for your needs!   All Node staff are asked to fill in this survey. You can find the link for the survey in June’s version of the Nodes Newsletter and on our Slack channel. Or, reach out to us at [email protected] and we'll make sure you get the link! Thanks for your help!

We believe in #FAIRdata sharing! Here's a BY-COVID project success story for data mobilisation featuring #EuroBioImaging FAIR Image Data Steward Isabel Kemmer & our Node colleague Lassi Paavolainen Institute for Molecular Medicine Finland, part of our Finnish Advanced Microscopy Node. Check out the huge COVID-19 #dataset shared in the European Bioinformatics Institute | EMBL-EBI's BioImage Archive ⤵ https://lnkd.in/d3AVhG5e

Great news 🎆 Professor Teng-Leon Chew from Janelia Research Campus will visit Turku next week! Professor Chew will give a talk at InFLAMES Research Flagship minisymposium and lead a one-day microscopy 🔬 workshop!   ▶ InFLAMES Visiting Professor minisymposium 💡 Topic: “Microscopy technologies: today and tomorrow”, Professor Teng-Leong Chew, Director of Advanced Imaging Center, Janelia Research Campus, USA 📅 Monday, June 17, 2024, 12-14 📍 Lauren 1, Medisiina D, Turku, Finland 🔗 More info: https://lnkd.in/dCQ4F8dy   ▶ InFLAMES mini microscopy workshop 💡 Topic “Experimental design for hypothesis-driven quantitative fluorescence microscopy” by Professor Teng-Leong Chew 📅 Tuesday, June 18, 2024, 9-16 📍 Lauren 2, Medisiina D, Turku, Finland ☑ Registration link: https://lnkd.in/dpk4qnUJ 🔗 More info: https://lnkd.in/diAyyz-a

📰 Fantastic work showcasing our Finnish Advanced Microscopy Node technologies in practice: Serial Block Face-Scanning Electron Microscopy/SBF-SEM and Microscopy Image Browser (MIB) were used at Electron Microscopy Unit (EMBI), University of Helsinki to study the principles underlying the generation of micrometric and submicrometric structures using the larval bristles of Platynereis as a model. The unique feature of this collaboration was that the EMBI has done the whole project remotely. Congratulations to the authors Kyojiro N Ikeda, Ilya Belevich, Luis Zelaya-Lainez, @Lukas Orel, Josef Füssl, Jaromír Gumulec, @Christian Hellmich, Eija Jokitalo, and @Florian Raible 🎉 Read more in the article ⤵️ https://rdcu.be/dHSWM

Volume electron microscopy (vEM) datasets are extensively rich of information, waiting to be used for scientific discovery beyond their original research context. Check out our recent Nature Cell Biology Comment where we discuss exciting possibilities of data reuse and sharing (https://lnkd.in/dFvPp4BT). To empower the concept, we are releasing a beautiful FIB-SEM dataset of a U2OS cell that includes a segmentation model for various organelles (ER, Golgi, Mitochondria, etc). Moreover, we’ve supplemented the dataset with pre-trained neural networks and instructions on how to perform similar segmentations. Special thanks to my colleagues Kirk Czymmek, Johanna Bischof, Aastha Mathur, Lucy Collinson, Eija Jokitalo for the great collaboration!   Links: More videos: https://lnkd.in/dTzevBkz Dataset and models: https://lnkd.in/dZmQPFGt Segmentation instructions: https://lnkd.in/dG3-5pfY

💡 Highly recommend attending this online workshop for all who want to make the bioimage data FAIR (• Findable • Accessible • Interoperable • Reusable) ⤵ https://lnkd.in/dQvuENdM