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Simon F. Nørrelykke

@simonfn.bsky.social
980 followers 188 following 22 posts

EPFL Center for Imaging, Director imaging.epfl.ch

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Reposted by Simon F. Nørrelykke
Florian Jug @florianjug.bsky.social · 09/09/2026
Here we are, #BIC 2026 at @eccv.bsky.social is kicking off! Is this really the 11th time we’re doing this! 🥜 See full program here: bioimagecomputing.com
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Jean-Yves Tinevez @jytinevez.bsky.social · 03/09/2026
New version of #Mastodon-SC, the Fiji plugin to track and lineage cells in gigantic movies! What is Mastodon? 👉 in the preprint linked to the quote post What's new? 👇
liveimagetrackingtools.org
geff
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Gaëlle Letort @gaellel.bsky.social · 27/03/2026
I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social
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Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 02/09/2026
Job alert! This would be right up my alley which means it might be up *your* alley if you follow me: Software Engineer (Data Specialist) at the Australian National University's Centre for Advanced Microscopy: au.seek.com/job/94226839 #GetFediHired
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Joel Lüthi @joelluethi.bsky.social · 19/08/2026
Join the Open Bioimaging Practices Meetup all about OME-Zarr viewers on Monday, August 24th, 4pm CEST. Learn about ViZarr, napari & VolE & hear user stories on how they handle OME-Zarrs. More info here: www.biovisioncenter.uzh.ch/en/events/Up...
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napari @napari.fosstodon.org.ap.brid.gy · 31/07/2026
RE: fosstodon.org/@napari/1166165047810… And it's a wrap! The hackathon was a fantastic success! 🥳 You can look forward to a longer post about all we did, and one of our biggest releases yet in 0.9.0! Huge thanks to all the participants 🤩, and we hope to see you at the next one!
Hackathon participants discussing a new feature demo.Jules Vanaret shows off slicing of volumes with non-orthogonal transforms.The naPLari hackathon crowd: Wouter-Michiel Vierdag, Grzegorz Bokota, Tim Monko, Giannis Liaskas, Draga Doncila Pop, Lorenzo Gaifas, Aroj Hada, Brian Northan, Jules Vanaret, Zuzana Čočková, Curtis Rueden, Juan Nunez-Iglesias, and Margot Chazotte.Celebratory drink after the last full day of the hackathon. 🍻
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Constantin Pape @cppape.bsky.social · 16/07/2026
Segmenting individual cells in microscopy is much easier these days thanks to foundation models. Can we use these models for other tasks, such as cell classification? We investigate in our latest work, finding big improvements for object and pixel classification compared to classical approaches.
Evaluation of different methods for pixel classification (top) and object classification (bottom) on the LIVECell dataset. Dark green bars show the F1-Score, which measures the classification / segmentation quality (higher is better), light green bars show the runtimes. Five different settings are compared for each task: Ilastik features + random forest (RF), microSAM embeddings + RF, SAM2 embeddings + RF, and uSAM, SAM2 + attentive probing (DeAP and ObAP). microSAM feature perform best for RF based methods, attentive probing outperforms RF based approaches, but at a much higher runtime.
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Simon F. Nørrelykke @simonfn.bsky.social · 14/07/2026
New resource for teaching and learning BioImage Analysis, long in the making, from @tischi.bsky.social and friends, incl. @carpentries.carpentries.org. With roots in the material developed for NEUBIAS workshops.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026
1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org
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EMBL-EBI Training @training.ebi.embl.org · 30/06/2026
Introducing our new collection on imaging data management, designed to introduce researchers to the key concepts, standards, and community best practices for managing imaging data throughout the research lifecycle: www.ebi.ac.uk/training/onl... #Bioimaging #DataManagement #FAIR #OpenScience
Graphics image showing a collection about Imaging data management, a community effort to implement FAIR principles. Image credit: Karen Arnott and Rebecca Nicholl, EMBL-EBI
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Constantin Pape @cppape.bsky.social · 30/06/2026
Want to learn about the latest trends and developments in bioimage analysis? Join us for the GLOBIAS workshop in Dortmund this November! I will be hosting a session on foundation models / AI. www.globias.org/activities/g...
globias.org
GloBIAS2026 Workshop Dortmund
GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link! 10-13 November, 2026 - Tuesday to Friday Leibniz-Institut für Analytische Wissenschaften – ISAS – e. V. (https...
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Rita Strack @ritastrack.bsky.social · 17/06/2026
If you love imaging metadata, do I have something for you -- Search, organize, aggregate and share image data with BioFile Finder (BFF) | Nature Methods share.google/9UxsAcpaWhbu...
share.google
Search, organize, aggregate and share image data with BioFile Finder (BFF) - Nature Methods
Nature Methods - Search, organize, aggregate and share image data with BioFile Finder (BFF)
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epflimaging.bsky.social @epflimaging.bsky.social · 11/06/2026
📸 🚞 A successful summerschool is not only about exploring cutting-edge imaging methods but also about creating memorable experiences. Short mountain excursion with breathtaking views over Lake Geneva . #EPFLImaging #EPFLImagingSummerschool @simonfn.bsky.social @jules-vanaret.bsky.social
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epflimaging.bsky.social @epflimaging.bsky.social · 09/06/2026
💻🔬☀️ Our 6th Imaging Summerschool has officially started! Welcome to our motivated group of PhD students from a wide range of disciplines. Beautiful environment=perfect setting for learning and new connections. #EPFLImaging #EPFLImagingSummerschool @simonfn.bsky.social @jules-vanaret.bsky.social
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Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026
📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...
jobs.uzh.ch
UZH: Bioimage Analyst
The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...
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epflimaging.bsky.social @epflimaging.bsky.social · 07/05/2026
Proud to have contributed to this exciting work on programmable metamaterials led by Flexlab at EPFL, Universiteit Leiden and AMOLF. Our team helped design a spline-based computer vision approach to track beam evolution during rotation. 📖 lnkd.in/eP-8RVFq
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Simon F. Nørrelykke @simonfn.bsky.social · 06/05/2026
The SwissBIAS Annual Meeting is taking place on June 3rd in Bern. Registration deadline: Friday, May 15th, so make sure to secure your spot now! We look forward to seeing you all there for a fantastic day of science, networking, and inspiration. @swissbias.bsky.social tinyurl.com/SwissBIAS2026
eventbrite.com
SwissBIAS annual meeting 2026
It is the time of the year to make veterans meet new members, discuss to foster feedback on existing activities and promote new initiatives.
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Simon F. Nørrelykke @simonfn.bsky.social · 01/05/2026
Very glad to see this out in Nature Cell Biology. A genuinely rewarding collaboration. We contributed some image analysis and spatial statistics via @antoineruzette.bsky.social in the @hms-iac.bsky.social. Super strong work by @nina-kozlova.bsky.social and a large, impressive team. rdcu.be/fgsjv
rdcu.be
Cancer-associated fibroblasts regulate DNA repair in pancreatic cancer through NDRG1-mediated R-loop processing
Nature Cell Biology - Kozlova et al. report a functional role for NDRG1 in regulating R-loops and DNA repair, thereby linking cancer-associated fibroblast-derived extracellular matrix to...
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epflimaging.bsky.social @epflimaging.bsky.social · 28/04/2026
Wrapping up our 4-day microcredential on imaging in the age of IA with Formation Continue UNIL-EPFL 👏 Special thanks to the speakers and industry experts who contributed to making this course both practical and impactful. Looking forward to seeing how these new skills will be applied.
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Damian Dalle Nogare @damiandn.bsky.social · 28/04/2026
Roughly two weeks (until May 15th) left to apply and join our team! Bioimage Analyst: careers.humantechnopole.it/job/Bioimage... Rsearch Software Engineer: careers.humantechnopole.it/job/Research...
careers.humantechnopole.it
Fondazione Human Technopole - Viale Rita Levi-Montalcini, 1 - Area MIND - 20157 Milano Italy - C.F. 97821360159 - PEC: htechnopole@pec.fondazioneht.it
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epflimaging.bsky.social @epflimaging.bsky.social · 01/04/2026
👩‍💻🔬 First part of the image analysis continuing education program for industry organized by @foco-unil-epfl.bsky.social and the Center for Imaging ✔️ Great energy, hands-on learning, and inspiring discussions Thanks to all participants 🙌🏼 Looking forward to what’s next! #ImageAnalysis
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Jan Funke @janfunkey.bsky.social · 05/03/2026
We opened 4 PhD positions at @humantechnopole.bsky.social together with Polimi (see 👇). My lab offers a PhD project on "Computational Morphogenesis": use state-of-the-art machine learning methods together with realistic simulations to build digital twins of developing tissue. Apply by March 26.
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Guillaume Jacquemet @guijacquemet.bsky.social · 09/01/2026
I am looking for two postdocs to join our lab - One (bio)image analyst - One cell biologist interested to work on lymphatics! The positions will open soon, be in touch!
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Jan Funke @janfunkey.bsky.social · 17/11/2025
We moved the AI@MBL course "Deep Learning for Microscopy Image Analysis" to HHMI Janelia (@hhmijanelia.bsky.social). Join us for two weeks of intense lectures, exercise, and hands-on project work! Course dates: June 4-18 2026 Application by: January 15 2026 www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Jean-Yves Tinevez @jytinevez.bsky.social · 07/10/2025
Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
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Ignacio Arganda-Carreras @iarganda.eurosky.social · 30/09/2025
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...
cvpd.github.io
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
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Wolfgang Huber @wkhuber.bsky.social · 29/09/2025
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems? Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
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Florian Jug @florianjug.bsky.social · 12/09/2025
🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮 www.scilifelab.se/news/ready-t...
scilifelab.se
Ready to shape the future of AI in life science?
The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...
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Guillaume Jacquemet @guijacquemet.bsky.social · 10/09/2025
Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030 abo.rekrytointi.com/paikat/index...
abo.rekrytointi.com
University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030
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Eva de la Serna @sciencedoodles.bsky.social · 29/07/2025
Check out our amazing #bobiac2025 cohort! Was a joy to teach this group! Thanks @bioimagingna.bsky.social for generously supporting this 6 week bioimage analysis w/Python course!
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HMS Image Analysis Collaboratory @hms-iac.bsky.social · 14/07/2025
Day 1 of #bobiac2025 🐍 The day started strong with @talley.codes speaking about the Python ecosystem and uv. Students then gave short talks about their research (#coolscience). It was then time to code in Python with @sciencedoodles.bsky.social!
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Simon F. Nørrelykke @simonfn.bsky.social · 14/07/2025
First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social - "This will be a long week, but it will change your life". iac.hms.harvard.edu/bobiac/2025/
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Sten Linnarsson @sten.linnarsson.org · 25/06/2025
A major KI initiative to recruit new assistant professors with outstanding proposals in all areas of medicine, biomedicine and public health. We offer an amazing research environment, great colleagues and generous startup packages. Check it out and get working on your applications! (repost please!)
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Guillaume Jacquemet @guijacquemet.bsky.social · 23/06/2025
Are you looking for a postdoc? I will be looking for 2-4 people after the summer to join the lab !! Do not hesitate to reach out and disseminate !!
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Florian Jug @florianjug.bsky.social · 09/06/2025
Come and work with us! Super exciting and relevant projects! Become an #AI pro and do something positive for the 🌍! 👩‍🎓 🧑‍🎓 If you know someone who might be interested… please repost and/or forward this! 🙏
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HMS Image Analysis Collaboratory @hms-iac.bsky.social · 30/05/2025
‼️3 days left to apply to the Boston Bioimage Analysis Course (BoBiAC)! 💻 Get started w/Python & learn to analyze fluorescence microscopy images — no programming experience required! Fee waivers available! 🗓️ Apply by June 1st! 🌐 iac.hms.harvard.edu/bobiac/2025/
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GloBIAS @globias.bsky.social · 15/05/2025
Deadlines extended - you can still register for the GloBIAS conference! We have extended most deadlines. Please check our webpage: tinyurl.com/mr3kx5a5! Looking forward to welcoming you to Kobe, for training, developing and discussing a broad range of BIA topics!
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Simon F. Nørrelykke @simonfn.bsky.social · 08/05/2025
Thanks to generous support from @bioimagingna.bsky.social we now have even more fee-waivers for our workshop. No funds, but want to learn? Apply below.
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 01/05/2025
BIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
Ad for the Bioimage Analysis Beginnings Bootcamp at the Broad Institute. 

Where & When
Broad Institute, 415 Main Street, Cambridge MA (in-person only)
Monday–Friday, August 4–8, 20259:00 AM – 5:00 PM

About the Bootcamp
Learn core bioimage analysis skills using open-source tools for light
microscopy in this hands-on, in-person course. The Bootcamp
covers annotation, segmentation, and deep learning fundamentals.

Fee: $600 (Academic/Non-Profit) | $1000 (Industry/For-Profit)
For more information email ImagingAdmin@broadinstitute.org
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HMS Image Analysis Collaboratory @hms-iac.bsky.social · 22/04/2025
‼BREAKING‼ We’ve secured new funding for the Boston Bioimage Analysis Course (BoBiAC) this July at Harvard Med School! Course fees down 37%, with fee waivers for academic applicants, for an intensive hands-on intro to bioimage analysis with Python! Apply by June 1st! iac.hms.harvard.edu/bobiac/2025
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Simon F. Nørrelykke @simonfn.bsky.social · 15/04/2025
Please join in-person if you are nearby, or by Zoom if not.
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Marco Dalla Vecchia @marcodv.bsky.social · 09/04/2025
In the past 2 days, we had the great pleasure to host an in-person workshop at @istaresearch.bsky.social with the collaboration of @globias.bsky.social, @carpentries.carpentries.org and @istaustria-iof.bsky.social. We wanted to create a go-to course for image analysis in Python. Info in the thread!
GloBIAS and Data Carpentry members group picture
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Rita Strack @ritastrack.bsky.social · 10/04/2025
Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.
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Joanna Pylvänäinen @jwpylvanainen.bsky.social · 08/04/2025
We wrote an opinion with simple, practical advice for building data exploration workflows in quantitative cell biology with @guijacquemet.bsky.social and @hanna09.bsky.social . I hope you find it useful!
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/04/2025
Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)
youtube.com
Ask Erin, Dear Beth
On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...
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Simon F. Nørrelykke @simonfn.bsky.social · 08/04/2025
www.globias.org/activities/u...
globias.org
Update the Data Carpentries Bioimage Analysis with Python Curriculum
Data Carpentry BioImage Analysis Curriculum - update with Python Join us to update the Data Carpentry Bioimage Analysis Curriculum with Python! The participant list has been finalised, more informat...
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GloBIAS @globias.bsky.social · 08/04/2025
Another in-person event from #GloBIAS Together with #Data Carpentry. Thanks to the GloBIAS volunteers at ISTA for organising and hosting us! #BioImageAnalysis #Python
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Jean-Yves Tinevez @jytinevez.bsky.social · 31/03/2025
Preprint (update) alert! F-BIAS: Towards a distributed national core facility for Bioimage Analysis. (arxiv.org/abs/2409.15009) 0/ In this paper we discuss our experience in federating ourselves and delivering bioimage analysis services to the scientific community in France. 👇 a short thread
arxiv.org
F-BIAS: Towards a distributed national core facility for Bioimage Analysis.
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Florian Jug @florianjug.bsky.social · 28/03/2025
Now that looks like a great new course to check out! More python 🐍 heavy than other courses I know… which is great to have! 👍 Check it out, sign up, learn!!! 🤩
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