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Anna Klemm

@ahklemm.bsky.social
1K followers 409 following 7 posts

BioImage Analyst Head of BioImage Informatics, SciLifeLab NBIS, Sweden www.scilifelab.se/units/bioimage-in…

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Reposted by Anna Klemm
Ting @huanting-ong.bsky.social · 01/09/2026
Excited to share what I've been up to in @jennyoung.bsky.social lab! Bringing #Mechanobiology & #SpatialBiology together, we ask: How does local tissue stiffness relate to the molecular state of that same region? Spatial Mechanomics preprint here! 👇 @nusingapore.bsky.social @mbisg.bsky.social
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Guillaume Jacquemet @guijacquemet.bsky.social · 16/06/2026
Shamelessly sharing this here in case it is useful bioimagingai.janelia.org/9-train-mode...
bioimagingai.janelia.org
9  How to Train and Use Deep Learning Models in Microscopy – AI in Microscopy: A BioImaging Guide
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 10/06/2026
At the Special Edition #VirtualPub on #SpatialTranscriptomics, Jonathan Enriquez, Institut de Génomique Fonctionnelle de Lyon (IGFL), will share his work with 3D MERFISH. 🗓️ Friday, June 12 at 1 pm CEST Join us! www.eurobioimaging.eu/news/making-...
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NBIS @nbis.se · 08/06/2026
Unsure how to analyse your biological or biomedical data? 🔈 Registration is now open for the course Statistical Methods for Life Sciences. 📅 When: 7–11 September 2026 📍 Where: BMC, Uppsala 🗓️ Apply by: 26 June 2026 🔗 Course webpage: training.scilifelab.se/events/stati...
training.scilifelab.se
Statistical Methods for Life Sciences
<p>This national course is open to PhD students, postdocs, and staff in the life sciences who need biostatistical skills in their research. Using real research examples, the course introduces core ide...
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Universität Jena @uni-jena.de · 05/06/2026
New pedestrian traffic lights in front of the main building at #UniJena and at two other locations highlight Jena's status as a centre for science and research; instead of the traditional traffic light figure, they feature a walking microscope. ➡️ rathaus.jena.de/en/citizens-b…
The pedestrian traffic light in front of Jena's Main University Building displays a walking microscope instead of the traditional traffic light figure when the light is green.
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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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Utz Ermel @uermel.bsky.social · 20/04/2026
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578
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Damian Dalle Nogare @damiandn.bsky.social · 07/04/2026
🚨🚨🚨JOB ALERT🚨🚨🚨 The Image Analysis Unit at Human Technopole in Milan is recruiting for two positions to join our growing team: 1) Bioimage Analyst 2) Research Software Engineer (RSE) Read on to learn why one of these two people should be you!
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Damian Dalle Nogare @damiandn.bsky.social · 23/03/2026
Been a while since I did this so I'm behind, but here's another batch of tools (somewhat) fresh from the bioRxiv)
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Jean-Yves Tinevez @jytinevez.bsky.social · 24/02/2026
One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇
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GloBIAS @globias.bsky.social · 25/11/2025
Looks like someone is misusing GloBIAS and its president name to approach people for money transfers. Please note - GloBIAS will always send proper payment requests and has no need for members and volunteers to transfer money on their behalf.
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Nature Methods @natmethods.nature.com · 13/11/2025
Our November issue is now live! 🎉 www.nature.com/nmeth/volume... On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 13/11/2025
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
A fluorescent embryo on black text, with the words 
Halfway to I2K: Virtual Tutorials on Image Analysis
November 17-19, 2025
Virtual Conference for beginners to developers
i2kconference.org
Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024
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Reto Fiolka @retof.bsky.social · 12/11/2025
Felix Zhou's u-Segment3D is out: www.nature.com/articles/s41... It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation. It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.
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Turku BioImaging @turkubioimaging.bsky.social · 10/10/2025
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️ jobs.helsinki.fi/job/Helsinki... #jobopening
jobs.helsinki.fi
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
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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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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 02/10/2025
Great to see Node staff, #i4A training grantee hernanmn.bsky.social & others at the EMBO "Advanced Methods in BioImage Analysis" course! @ahklemm.bsky.social @perrinegil.bsky.social @jytinevez.bsky.social @france-bioimaging.bsky.social @iemcas.bsky.social More🔽 www.eurobioimaging.eu/news/success...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/09/2025
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
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Jean-Yves Tinevez @jytinevez.bsky.social · 18/09/2025
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)? Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
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Ignacio Arganda-Carreras @iarganda.eurosky.social · 18/09/2025
Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org @tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
Christian Tischer addresses the online participants of the EMBO Advanced methods in biomage analysis course before starting his tutorial on OME-Zarr.Christian Tischer gets prepared to start his tutorial on OME-Zarr in front a full classroom.Christian Tischer gives the first intructions to the onsite and the online participants of the EMBO Advanced methods in biomage analysis course for his tutorial on OME-Zarr.
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Ignacio Arganda-Carreras @iarganda.eurosky.social · 17/09/2025
Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University! So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩‍💻 in image facility projects 🔬
Panoramic view of the classroom during the round table discussion
led by Anna Klemm and Suganya Sivagurunathan from Scilifelab & Uppsala University, Sweden.
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Ignacio Arganda-Carreras @iarganda.eurosky.social · 16/09/2025
What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜
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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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Kyle Harrington @kyleharrington.com · 26/08/2025
Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: community models beat expert tools. Read more in the @natmethods.nature.com article that just came out: 🔗 doi.org/10.1038/s415...
doi.org
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
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Agustin Corbat @acorbat.bsky.social · 26/08/2025
Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects! My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally. Check out my portfolio and contact: acorbat.github.io
acorbat.github.io
iPortfolio Bootstrap Template - Index
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Virginie Uhlmann @virginieuhlmann.bsky.social · 25/08/2025
Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
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GloBIAS @globias.bsky.social · 20/08/2025
Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden Wednesday, 27th of August, 2pm CEST
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Dave Barry @david-j-barry.bsky.social · 26/08/2025
The #CBIAS2025 abstract deadline is this Sunday, August 31st. Submit your #BioImageAnalysis work, whether it’s a new tool or a biological discovery. #EarlyCareerResearchers, this is for you! Short and flash talk slots are up for grabs. www.crick.ac.uk/whats-on/cri...
Crick BioImage Analysis Symposium 2025 Poster
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BioVoxxel (Jan Brocher) @biovoxxel.de · 14/08/2025
I am stunned! First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers. If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE on LinkedIn buff.ly/cLPh8eZ #bioimageanalysis #biovoxxel #fiji
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Nicolas Chiaruttini @nkiaru.bsky.social · 12/08/2025
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3) forum.image.sc/t/qupath-ext...
forum.image.sc
QuPath extension Spotiflow is now available
Hello @qupath team & users, We are pleased to announce a new qupath-spotiflow-extension to handle spotiflow in QuPath 🎉 ! This extension reproduces the logic behind the qupath-extension-cellpose to ...
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Robert Haase @haesleinhuepf.bsky.social · 12/08/2025
My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess. Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩 scads.github.io/embo-lsm-bia...
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OME @openmicroscopy.org · 06/08/2025
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
idr.openmicroscopy.org
IDR: Image Data Resource
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Virginie Uhlmann @virginieuhlmann.bsky.social · 21/07/2025
Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)! More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥
swissuniversities.ch
Funded Projects - swissuniversities
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 10/07/2025
Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):
arxiv.org
GloBIAS: strengthening the foundations of BioImage Analysis
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...
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Laurent Guerard @lguerard.bsky.social · 08/07/2025
Day 2 of #Zidas2025 is happening! After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !
Day 2 of #Zidas2025
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Nav @naveed-ishaque.bsky.social · 02/07/2025
Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths". More in our preprint: www.biorxiv.org/content/10.1...
biorxiv.org
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...
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EPFL Brain Mind Institute @epfl-brainmind.bsky.social · 30/06/2025
New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis - paper: elifesciences.org/articles/99848 news: tinyurl.com/y2hpmbb9
actu.epfl.ch
Self-supervised, label-free 3D cell imaging is here
EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...
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Jean-Yves Tinevez @jytinevez.bsky.social · 11/06/2025
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology! 🎉✌️ journals.plos.org/ploscompbiol... So happy about this paper and how the work turned out. A small thread 👇 #bioimageanalysis #corefacility
journals.plos.org
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...
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Anna Klemm @ahklemm.bsky.social · 03/06/2025
Deadline approaching tomorrow!
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GloBIAS @globias.bsky.social · 28/04/2025
Second round of hashtag#GloBIAS Free Help (previously Call4Help) is happening in May. You can register for the sessions on our webpage: www.globias.org/activities/g... Registration deadline is 7. May 2025.
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Anna Klemm @ahklemm.bsky.social · 06/05/2025
So much looking forward to this! 🤩 We're thrilled to be running a new instance of our "Advanced Methods in Bioimage Analysis" course. It's going to be a blast! Apply by June 4th.
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Anna Klemm @ahklemm.bsky.social · 17/04/2025
Ready to step into bioimage analysis in Python? The course mastermind 🧠 has just launched a new course:
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Constantin Pape @cppape.bsky.social · 12/02/2025
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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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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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 20/03/2025
🌌 Missed the presentation on “Image Analysis Using Galaxy” by Beatriz Serrano-Solano, Leonid Kostrykin, Anne Fouilloux and Riccardo Massei as part of the #GloBIAS Seminar Series? Watch it now on the GloBIAS YouTube channel: www.youtube.com/watch?v=wAHO... To the slides: zenodo.org/records/1494...
youtube.com
Image Analysis using Galaxy by B. Serrano-Solano, A. Fouilloux, L. Kostrykin, R. Massei
YouTube video by GloBIAS
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AI4Life @ai4life.bsky.social · 07/03/2025
End-of-week news! The selected projects for the 3rd AI4Life Open Call are here: 🔹 Phase 1: Consultation – 10 projects received expert guidance 🔹 Phase 2: Deep Learning Support – 8 projects selected for in-depth AI-driven bioimage analysis 🔍 More at: ai4life.eurobioimaging.eu/third-ai4lif...
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Retro Tech Dreams @retrotechdreams.bsky.social · 09/02/2025
Lemmings (1991)
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SciLifeLab @scilifelab.se · 14/02/2025
“We love #microscopy and thanks to the infrastructures at SciLifeLab we can develop new methods and establish original views on human #CellBiology” says Bennie Lemmens (SciLifeLab & @ki.se) 🧪 Image: #SuperResolutionMicroscopy image of replicating human epithelial cell with two nascent #DNA labels
The image shows a microscopy image of a replicating human epithelial cell with two different nascent DNA labels in cyan and magenta, which was imaged with super resolution microscopy (3D-SIM) at the SciLifeLab Advanced Light Microscopy unit.
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Constantin Pape @cppape.bsky.social · 11/02/2025
Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.
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AI4Life @ai4life.bsky.social · 28/01/2025
🚨 Save the Date! 🚨 AI4Life & @globias.bsky.social are hosting a 4-part webinar series to showcase AI4Life services and lessons learned. 📅 When: Feb 13, Apr 10, Jun 12, Aug 14 🖥️ How: Online | 🎥 Recorded 🔗 Registration: bit.ly/registration...
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