Ryan Savill
@cryaaa.bsky.social
PhD Student with the Jesse Veenvliet Group at the @mpicbg.bsky.social . Interested in all things Data and 3D bioimage analysis, organoids and development!
This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!
📢 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 11:06 PM
This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!
Reposted by Ryan Savill
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 Ryan Savill
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains
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doi.org/10.1101/2025...
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doi.org/10.1101/2025...
October 8, 2025 at 1:05 PM
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains
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doi.org/10.1101/2025...
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doi.org/10.1101/2025...
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
September 12, 2025 at 12:44 PM
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
Reposted by Ryan Savill
FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging
Let's have a look 👇🧪💻🔬
Let's have a look 👇🧪💻🔬
June 17, 2025 at 10:54 PM
FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging
Let's have a look 👇🧪💻🔬
Let's have a look 👇🧪💻🔬
Reposted by Ryan Savill
Check out our "In Preprints" @dev-journal.bsky.social w/ Yonit Maroudas-Sacks & Marc Trani Bustos @mpi-cbg.de @poldresden.bsky.social, putting recent #gastruloid work from @viktri08.bsky.social @thomasgregor.bsky.social @amartinezarias.bsky.social labs in broader perspective: doi.org/10.1242/dev....
In preprints: exploring developmental robustness and timing with gastruloids
How developmental processes are coordinated in time and space to ensure the robust formation of complex, functional patterns during embryogenesis remains an outstanding question. Investigating this in...
doi.org
May 19, 2025 at 11:42 AM
Check out our "In Preprints" @dev-journal.bsky.social w/ Yonit Maroudas-Sacks & Marc Trani Bustos @mpi-cbg.de @poldresden.bsky.social, putting recent #gastruloid work from @viktri08.bsky.social @thomasgregor.bsky.social @amartinezarias.bsky.social labs in broader perspective: doi.org/10.1242/dev....
Reposted by Ryan Savill
Thoughtful preview article by María Rodríguez Colman & @sonnenlab.bsky.social on recent papers from our lab and @jesseveenvliet.bsky.social lab! Grateful for their in-depth analysis of the papers and their big-picture perspective on the role of metabolism in development.
doi.org/10.1016/j.st...
doi.org/10.1016/j.st...
Signaling switches: Metabolism regulates gastruloid self-organization
Metabolic regulation of embryonic development is increasingly recognized. Villaronga-Luque
et al. and Stopornwongkul et al. show that metabolic activity influences gastruloid
formation from mouse embr...
www.cell.com
May 2, 2025 at 10:43 AM
Thoughtful preview article by María Rodríguez Colman & @sonnenlab.bsky.social on recent papers from our lab and @jesseveenvliet.bsky.social lab! Grateful for their in-depth analysis of the papers and their big-picture perspective on the role of metabolism in development.
doi.org/10.1016/j.st...
doi.org/10.1016/j.st...
This my first big project during my PhD and I couldn’t be happier about it being out! Please give it a read if you’re interested in embryo models, data fusion, machine learning, image analysis, metabolism, scSeq…. because a lot of great people made this project possible! 🚀
😱 A very hungry #PacManoid ate the original post 🍬🍬🍬
Here’s the 🧵 on our latest in @cp-cellstemcell.bsky.social again!
Gastruloids w/ a sweet tooth better model natural embryos: doi.org/10.1016/j.st...
Spearheaded by @cryaaa.bsky.social & Alba Villaronga-Luque @mpi-cbg.de @poldresden.bsky.social
Here’s the 🧵 on our latest in @cp-cellstemcell.bsky.social again!
Gastruloids w/ a sweet tooth better model natural embryos: doi.org/10.1016/j.st...
Spearheaded by @cryaaa.bsky.social & Alba Villaronga-Luque @mpi-cbg.de @poldresden.bsky.social
April 22, 2025 at 8:20 AM
This my first big project during my PhD and I couldn’t be happier about it being out! Please give it a read if you’re interested in embryo models, data fusion, machine learning, image analysis, metabolism, scSeq…. because a lot of great people made this project possible! 🚀
Reposted by Ryan Savill
📢 Fresh off the press and featuring new exciting experiments! 🧪
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
April 16, 2025 at 5:40 PM
📢 Fresh off the press and featuring new exciting experiments! 🧪
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
Reposted by Ryan Savill
Festive times with @mpi-cbg.de predocs Ryan Savill @cryaaa.bsky.social & Alba Villaronga Luque! What were we celebrating? More tomorrow!
Supported by @sumoconsortium.bsky.social, part of @ec.europa.eu European Innovation Council Engineered Living Materials Portfolio #EUeic #EICPathfinder #ELMs
Supported by @sumoconsortium.bsky.social, part of @ec.europa.eu European Innovation Council Engineered Living Materials Portfolio #EUeic #EICPathfinder #ELMs
April 15, 2025 at 4:27 PM
Festive times with @mpi-cbg.de predocs Ryan Savill @cryaaa.bsky.social & Alba Villaronga Luque! What were we celebrating? More tomorrow!
Supported by @sumoconsortium.bsky.social, part of @ec.europa.eu European Innovation Council Engineered Living Materials Portfolio #EUeic #EICPathfinder #ELMs
Supported by @sumoconsortium.bsky.social, part of @ec.europa.eu European Innovation Council Engineered Living Materials Portfolio #EUeic #EICPathfinder #ELMs
Reposted by Ryan Savill
Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀
github.com/BiAPoL/napar...
github.com/BiAPoL/napar...
April 12, 2025 at 12:56 PM
Some new additions for the upcoming @napari.org clusters-plotter version 👉0.9.0 around the corner! Powered by some work from @mazoc.bsky.social, it casually turns into a pretty neat tool for feature map creation 😀
github.com/BiAPoL/napar...
github.com/BiAPoL/napar...