Anna Foix
PhD candidate at EMBL-EBI and the University of Cambridge (Uhlmann Group). Turning bioimages into numbers and finding the stories they hide. Loves math, climbing, and anime
- Reposted by Anna FoixLast call! This is a great opportunity for those interested in learning and applying SOTA ML/DL models to microscopy data with the leading experts in the field. Personally super excited to be a lead TA along with the amazing @afoix.bsky.social and @edhirata.bsky.social! Hope to see you there :)
- 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/...
- All the tiredness and travel are worth it if it means showing the world what D’Arcy taught us. Thanks to @aibio-uk.bsky.social and the local organisers for yesterday’s event in Bristol. It was a pleasure to engage in such stimulating discussions 👩🏻💻🦇. #AI #Morphology #ResearchCommunity #EarlyCareer
- Reposted by Anna FoixJacqueline Chalakova, @afoix.bsky.social and @denzibubs.bsky.social share their highlights from #CBIAS2025 @cbias.bsky.social, with all three emphasising the welcoming atmosphere. Check out the reasons that #CBIAS2026 should be in your calendar⤵️ focalplane.biologists.com/2026/01/12/c...
- Very much looking forward to this tomorrow 🎉 I’ll be sharing my journey from pure CS to tackling multidisciplinary challenges in biology using AI, and how crossing disciplines opens up cool scientific questions. Grateful to @aibio-uk.bsky.social 👩🏻💻🔬✨ #interdisciplinary #AIinBiology #AIforLifeSciences
- 🤖 AI + Biosciences 📍 Join our workshop @ BristolUni, 13 Jan 2026! ✨ Learn how AI transforms genomics, imaging & biotech 🗓 Register by 4 Jan: aibio.ac.uk/events/bridg... #AI #Biosciences #Research
- Reposted by Anna Foix🚨 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/...
- Reposted by Anna Foix
- Maria gave such an excellent and much-needed talk linking transcriptomic data with morphology at @neuripsconf.bsky.social 🔬👩💻 and showing how AI shapes biomedical discovery, and vice versa. @wimlworkshop.bsky.social always brings brilliant speakers! 👩💻👏 #InterdisciplinaryML
- Reposted by Anna FoixIf you are attending @neuripsconf.bsky.social in San Diego, go check out Anna's beautiful work on learning shape representations!
- We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
- We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
- Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)
- Reposted by Anna FoixNext to @afoix.bsky.social from @virginieuhlmann.bsky.social lab @ebi.embl.org talking about data-driven shape qualification for 2D microscopy Images
- Reposted by Anna Foix#CBIAS2025 ShapeEmbedLite stay tuned for a new preprint coming out soon.
- Reposted by Anna FoixDay two of #CBIAS2025 kicked off by @lankylaste.bsky.social from @crick.ac.uk and the first session is on physical and mathematical modelling chaired by @natalieah.bsky.social , with the first presenter Ewa Paluch from @cam.bsky.social
- Reposted by Anna FoixHad a blast at #CBIAS2025! Great science (like the incredible ShapeEmbed talk from @afoix.bsky.social), amazing people and obviously tons of beautiful images :) Already looking forward to coming back next year!
- Amazing talk by my dear colleague and friend @albertdm.bsky.social and his supervisor @maweigert.bsky.social showing the cool things you can do with Spotiflow at #CBIAS2025. Look at this beautiful learned spot detection in 3D! 👩🏻💻👩🏻💻🔬 #bioimageanalysis #spotdetection
- Congratulations to @aafkegros.bsky.social for winning the Best Poster Award at #CBIAS2025! 🎉 Their Microscopy Nodes Blender plugin not only makes visualisation easier, but also shines as a brilliant link between computer vision, mathematics, and biology.
- Our very own @teunhuijben.bsky.social from the @loicaroyer.bsky.social lab at the Biohub gave a brilliant overview of their journey to improve tracking and visualisation (and our lives in general 😝) at #CBIAS2025 👩🏻💻🔬👩🏻🔬 #tracking #interdisciplinary #bioimageanalysis
- It’s wonderful when a venue feels like home. Thanks to #CBIAS2025 organisers for welcoming established researchers and supporting so many early-career scientists year after year. Grateful for the amazing bioimage analysis community in the UK, Europe and beyond 🔬👩🏻💻👩🏻🔬. #bioimage #interdisciplinary
- Next to @afoix.bsky.social from @virginieuhlmann.bsky.social lab @ebi.embl.org talking about data-driven shape qualification for 2D microscopy Images
- Amazing talk by my dear colleague and friend @albertdm.bsky.social and his supervisor @maweigert.bsky.social showing the cool things you can do with Spotiflow at #CBIAS2025. Look at this beautiful learned spot detection in 3D! 👩🏻💻👩🏻💻🔬 #bioimageanalysis #spotdetection
- And how cool is it that Albert also shared in his #CBIAS2025 talk our Deep Learning course at Janelia this June, directed by @janfunkey.bsky.social @computingnature.bsky.social and @mattersoflight.bsky.social! 🎉🔬 More info: shorturl.at/j4sgY
- Reposted by Anna FoixT-minus 1 hour #CBIAS2025
- Super grateful to the organisers of @tlmcambridge.bsky.social for inviting me 🤩 It’s great to see in-person events coming back strong and helping rebuild a solid scientific community around Cambridge. Come have a drink and enjoy some exciting science!👩🔬🔬👩💻 #bioimageanalysis #interdisciplinary #theory
- 📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee 📍 Janelia Research Campus, VA 🗓️ Apply by Jan 15, 2026 🔗 shorturl.at/j4sgY
- Reposted by Anna FoixMy take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
- Don’t miss Elena’s (from @ilastik-team.bsky.social lab) brilliant work @ #ICCV2025 with @anwaiarchit.bsky.social & @cppape.bsky.social poster 292 @ 11:15AM 🔬They tackle segmentation of massive 3D microscopy images & show how BatchRenorm removes tiling artifacts boosting transferability and clarity🌺
- Attending BISCUIT workshop at #ICCV2025 🌺 — the first talk by @mariavak.bsky.social on quantifying biases in foundation models was fantastic! Exciting to see interdisciplinary efforts focused not just on prediction but on understanding why — and ViTs seem to be the trend in biomedical vision 👩💻
- Reposted by Anna FoixThank you, @afoix.bsky.social! I am really happy I could be part of this one. Everybody, please enjoy the new ShapeEmbeding goodness!
- We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...
- We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...
- We’ll be presenting at the #BIC workshop at @iccv.bsky.social! This year’s BIC has amazing speakers 🌺 — join us on 19 October at the Honolulu Convention Center to explore cutting-edge methods at the intersection of computer vision and biology 🔬 #ICCV2025 More details: www.bioimagecomputing.com
- Reposted by Anna FoixAlso don’t miss: 🧬👯 @epetsalaki.bsky.social’s talk “From Data to Digital Twins” (Wed, Digital Twin Models) 📊🧬 My poster P03.14 – Towards Data-Driven Executable Models (Wed) 🧩🤖 @alussana.bsky.social’s poster P18.13 – Data-Driven Inference of Functionally Coherent Gene Modules (Mon)
- Thrilled to be speaking at #CBIAS2025! 🥳 CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD. Join us if you get the chance! 😃
- The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live! Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions. Space is limited - register now! www.crick.ac.uk/whats-on/cri...
- Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)
- ShapeEmbed encodes Euclidean distance matrices relying on a novel encoder design and a new indexation-invariant loss. Through this, it learns highly-informative shape features that surpass classical approaches and current SotA learning methods. (2/N)
- ShapeEmbed is performant even with very limited data — a huge advantage in biological context where images are scarce and may be costly to acquire. Small microscopy sets are enough to learn useful shape descriptors. (3/N)
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View full threadA huge thank you 💙 to my supervisor @virginieuhlmann.bsky.social, my co-advisor @alex-krull.bsky.social and my colleague Craig Russell who shared feedback and ideas. And to the community already using ShapeEmbed — it’s inspiring to see it applied in different biological contexts! (N/N)
- Reposted by Anna FoixThanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell
- It’s crucial that the bioimage community joins spaces long dominated by computer vision/CS to highlight challenges in microscopy data and how we tackle them. Brilliant talk from @aafkegros.bsky.social showing how biology is both exciting and challenging👩🏻💻🔬🧬🦠 #bioimage #microscopy #interdisciplinary
- I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
- Reposted by Anna FoixThe abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions. In fact, we have slightly more submissions from women than men.
- Reposted by Anna FoixSnake-in-the-Box Problem xkcd.com/3125/
- Reposted by Anna Foix"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪
- Reposted by Anna FoixCan robots in a swarm act like the cells of an organism? Thanks to Sedeer El-Showk for the new article in @nature.com, which highlights the work of a number of research groups, including our own, on how “Robots demonstrate principles of collective intelligence”. www.nature.com/articles/d41...
- Reposted by Anna Foix🔬API-first feature extraction for image-based profiling workflows If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle. 1/6
- Reposted by Anna FoixAnd just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be: www.youtube.com/watch?v=8t8R...
- Reposted by Anna FoixSpotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com! Since the pre-print, we have added many features, notably native 3D detection! @maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social Paper: rdcu.be/epIB7 (1/N)
- Reposted by Anna FoixOut today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social www.nature.com/articles/s41... rdcu.be/epIB7
- Reposted by Anna FoixAnother year, another #BIC Workshop! This year at #ICCV 2025 in Honolulu, 🌺 🏄♀️ 🍹 🌼 Check it here: www.bioimagecomputing.com Submission deadline: July 4th Hey, you have a month left to submit your work!!! 👍
- Another year, another #BIC Workshop! This year at #ECCV 2024 in Milan, 🇮🇹. Check it out here: bioimagecomputing.com Submission Deadline: July 19th Get your computational work out, we are looking forward to meet you in October! 🍕 🍷 👩🎓 👨🎓 ☀️
- Reposted by Anna FoixVery happy and proud to announce that the first preprint of my PhD is out: arxiv.org/abs/2504.20710 We developed an R package to translate mathematical models in SBML format into executable odin models and visualise models from @biomodels.bsky.social on our website Menelmacar biomodels.bacpop.org
- Reposted by Anna FoixHow can AI help you to analyze your microscopy images? Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6! Applications are due 🚨 April 30 🚨 Read on for more! 👇 www.mbl.edu/education/ad...
- Reposted by Anna FoixBioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
- Reposted by Anna Foix📢 Just published! Introducing Isopeptor: a computational tool for detecting intramolecular isopeptide bonds in protein structures with high precision and recall. academic.oup.com/bioinformati...
- Reposted by Anna FoixBe a part of groundbreaking research! 🔬 Help us study immune cells & fight transplant rejection: www.zooniverse.org/projects/h-s... Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse (6/6) ✅
- Reposted by Anna FoixShare this with everyone you know and help us hunt the immune cells!!!
- Reposted by Anna FoixKudos to Matthew Hartley of the @bioimagearchive.bsky.social for his message of global collaboration in the #bioimaging community @ #TiM2025 👏👏👏
- Reposted by Anna Foix@virginieuhlmann.bsky.social talked @tlmcambridge.bsky.social online seminar series about: Turning morphology into numbers across microscopy scales and modalities; a perforce ride from imaging to image analysis to model generation to prediction. bio-mat-sketches-mor.blogspot.com/2025/03/virg...
- Reposted by Anna FoixThe "E" in FEGA might stand for European, but FEGA is for Everyone! 🌐 Thrilled that Canada has officially joined the FEGA family with the first 7 national FEGA nodes. An important step towards a global network supporting secure human data sharing. Read about FEGA 👉 www.nature.com/articles/s41...
- To mark the recent news that Canada has joined the Federated European Genome-phenome Archive (FEGA), we take a look at FEGA's achievements so far, what’s in store for the future, and the collaborative effort that has led to its success. @egaarchive.bsky.social 🖥️🧬 www.ebi.ac.uk/about/news/t...
- Reposted by Anna Foix🚨Next week, Wed 05/03 | 16:00 UK - Online Seminar🚨 "Turning morphology into numbers across microscopy scales and modalities" by Dr Virginie Uhlmann. To attend online please register to our 📧 for the zoom link: lists.cam.ac.uk/sympa/subscr...
- Congrats for such an amazing paper to my friend Lau!
- Congratulations Laura Avinyo! @lauavinyo.bsky.social and Heura Cardona! First paper of your PhD 🎉. doi.org/10.1242/dev.... Beautiful quantified trajectory of how the skeletal pattern of the gene Sox9 emerges during limb development. @embl.org @barcelonacollaboratorium.com
- It’s so cool to be at EMBL again to TA in the new Advanced Deep learning course 🙂🎉 #EMBLDeepLearning
- ‼️🔬 We start!!! 🎉🤖 Super exciting!!! After years of teaching courses for #DeepLearning for Microscopy and Life Science application, we start today our first “advanced course” @embl.org! #EMBLDeepLearning
- Reposted by Anna Foix🔬🎤 As pre-announced a few days ago... please let us proudly present to you: 𝑴𝒊𝒄𝒓𝒐𝕊𝒑𝒍𝒊𝒕 - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. 🔬 doi.org/10.1101/2025... Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏
- Immagine you could image two cellular structures in the same fluorescent channel and still reliably get them separated afterwards… What would you do with this? Now… what would you do if that also worked with 4 structures at once? 👇 #MicroSplit #preview🧵
- Reposted by Anna FoixDifferent year, different conference, same vibe.
