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
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- 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
- 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/...
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- 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
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- 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)
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- 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
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- 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
- 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
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- 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 👩💻
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- 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...
- 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)
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- 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
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- 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 🧪
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- 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
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- 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! 🍕 🍷 👩🎓 👨🎓 ☀️
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- 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...
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- 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...
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- 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
- 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! 🙏
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