Anna Foix
@afoix.bsky.social
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
Pinned
Anna Foix
@afoix.bsky.social
· Sep 23
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)
📄 arxiv.org/pdf/2507.01009 (1/N)
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/...
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/...
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.,
www.janelia.org
December 28, 2025 at 7:06 PM
🚨 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/...
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
Reposted by Anna Foix
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
December 1, 2025 at 8:27 AM
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
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
December 2, 2025 at 9:40 PM
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 Foix
If 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
December 2, 2025 at 6:35 AM
If 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
December 1, 2025 at 8:27 AM
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
Reposted by Anna Foix
Next to @afoix.bsky.social from @virginieuhlmann.bsky.social lab @ebi.embl.org talking about data-driven shape qualification for 2D microscopy Images
November 25, 2025 at 10:18 AM
Next 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.
ShapeEmbedLite stay tuned for a new preprint coming out soon.
November 25, 2025 at 10:31 AM
#CBIAS2025
ShapeEmbedLite stay tuned for a new preprint coming out soon.
ShapeEmbedLite stay tuned for a new preprint coming out soon.
Reposted by Anna Foix
Day 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
November 25, 2025 at 9:40 AM
Day 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 Foix
Had 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!
November 25, 2025 at 11:33 PM
Had 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!
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.
November 25, 2025 at 3:56 PM
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
November 25, 2025 at 11:52 AM
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
November 25, 2025 at 11:37 AM
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
Reposted by Anna Foix
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
November 24, 2025 at 11:31 AM
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
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
November 24, 2025 at 11:31 AM
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
Reposted by Anna Foix
November 24, 2025 at 9:12 AM
Reposted by Anna Foix
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! 😃
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...
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...
September 23, 2025 at 12:17 PM
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! 😃
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! 😃
Reposted by Anna Foix
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
@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
🍻TLM Pub Talks are back! 🍻
Join us for an evening of interesting talks to discuss over a drink in a social environment. All those interested in the intersection of biology and theory are welcome!
Join us for an evening of interesting talks to discuss over a drink in a social environment. All those interested in the intersection of biology and theory are welcome!
November 21, 2025 at 2:14 PM
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
@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
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
@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
🍻TLM Pub Talks are back! 🍻
Join us for an evening of interesting talks to discuss over a drink in a social environment. All those interested in the intersection of biology and theory are welcome!
Join us for an evening of interesting talks to discuss over a drink in a social environment. All those interested in the intersection of biology and theory are welcome!
November 21, 2025 at 2:14 PM
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
@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
Reposted by Anna Foix
📢 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
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
November 6, 2025 at 6:56 PM
📢 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
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📢 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
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
November 6, 2025 at 6:56 PM
📢 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
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
Reposted by Anna Foix
My 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.
Sometimes I’ll see a paper that implements an idea I’ve had but implements it poorly for engineering reasons. But then it’s hard to write a follow up paper because it’s not “novel” anymore
October 9, 2025 at 2:13 PM
My 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.
Reposted by Anna Foix
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🌺
October 22, 2025 at 8:23 PM
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🌺
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🌺
October 22, 2025 at 8:23 PM
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 👩💻
October 19, 2025 at 7:56 PM
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 👩💻