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
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 👩💻
Reposted by Anna Foix
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
BioImage Computing
a truly interdisciplinary workshop
www.bioimagecomputing.com
October 17, 2025 at 7:35 AM
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 Foix
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...
October 17, 2025 at 7:35 AM
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 Foix
Thank you, @afoix.bsky.social!
I am really happy I could be part of this one. Everybody, please enjoy the new ShapeEmbeding goodness!
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...
October 17, 2025 at 11:43 AM
Thank you, @afoix.bsky.social!
I am really happy I could be part of this one. Everybody, please enjoy the new ShapeEmbeding goodness!
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...
October 17, 2025 at 7:35 AM
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 Foix
Also 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)
🧬👯 @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)
October 5, 2025 at 5:59 PM
Also 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)
🧬👯 @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)
Reposted by Anna Foix
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)
September 23, 2025 at 8:32 AM
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)