Ryan Savill

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!

106 followers99 following18 posts

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Albert Dominguez Mantes
@albertdm.bsky.social

Last 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 :)

Jan Funke@janfunkey.bsky.social

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/...

janelia.orgDeep Learning for Microscopy Image AnalysisTopics 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.,

Ryan Savill reposted

Florian Jug
@florianjug.bsky.social

🚨 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/...

janelia.orgDeep Learning for Microscopy Image AnalysisTopics 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.,
Ryan Savill
@cryaaa.bsky.social

This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!

Anna Foix@afoix.bsky.social

📢 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

Ryan Savill reposted

Anna Foix
@afoix.bsky.social

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...

Ryan Savill reposted

Miki Ebisuya
@ebisuyamiki.bsky.social

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 1/ doi.org/10.1101/2025...

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Ryan Savill
@cryaaa.bsky.social

(14/14) Thanks to Allyson Q Ryan whose ToSkA method inspired SpinePy. Thanks to @jesseveenvliet.bsky.social for supervision, @campaslab.bsky.social & @carldmodes.bsky.social for input and guidance, the @mpi-cbg.de & @poldresden.bsky.social and the #EIC for funding @sumoconsortium.bsky.social

arxiv.orgToSkA: Topological Skeleton Analysis for Network-Based Shape Representation and Evaluation of Objects from Cells to Death StarsShape analysis and classification are popular methods for biologists, biophysicists and mathematicians investigating relationships between object function and form. Classic shape descriptors, such as ...
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Ryan Savill
@cryaaa.bsky.social

(11/14) Building on this we can identify features that correlate with the observed patterning classes. The 3D patterning maps thus provide framework to systematically investigate gastruloid patterning spaces!

Ryan Savill
@cryaaa.bsky.social

(12/14) If you want to find out more about the synthetic data generation, see comparisons to 2D patterning approaches, or just want to dive into the details give the preprint a read and contact me or @jesseveenvliet.bsky.social if you’re interested in using the method!

biorxiv.orgSpinePy enables automated 3D spatiotemporal quantification of multicellular in vitro systemsOrganoids and stem-cell-based embryo models such as gastruloids are powerful systems to quantitatively study morphogenesis and patterning. This requires 3D analysis in reference frames that emerge dyn...
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Ryan Savill
@cryaaa.bsky.social

(9/14) With this normalized reference frame in hand we can use data with multiple developmental markers and quantify patterning maps using SLIC segmentation. Maps are a 2D representation of 3D patterning data, allowing comparison of patterning types in a unified reference frame.

Ryan Savill
@cryaaa.bsky.social

(10/14) Alba Villaronga Luque generously shared her data investigating how initial cell number (N0) influences patterning. We extracted patterning maps of 54 gastruloids and were able to detect distinct patterning phenotypes using dimensionality reduction and clustering.

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Ryan Savill
@cryaaa.bsky.social

(7/14) Another neat feature is the quantification of scalar fields along the axis. We use density as an example but any signal of interest could be used to generate profiles along the AP axis. Again, the synthetic data facilitates verification of the pipeline!

Ryan Savill
@cryaaa.bsky.social

(8/14) A core feature of SpinePy is the generation of a common reference frame, no matter the gastruloids size, shape, or orientation under the microscope. We define the AP and core-to-surface (CS) position and can use it to map the signals into a common space!

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Ryan Savill
@cryaaa.bsky.social

(5/14) This allowed me to create hundreds of gastruloids in silico, with defined spines and thickness profiles to benchmark SpinePy. We show that the spine detection performs well with low relative errors compared to the ground truth!

Ryan Savill
@cryaaa.bsky.social

(6/14) One core biological feature to quantify is gross morphology. Using optimized, non-intersecting planes, we measure radial profiles over the AP axis for fixed and live gastruloids giving insights into 3D morphodynamics. Big thanks to @mtrani.bsky.social who provided data and insight!

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Ryan Savill
@cryaaa.bsky.social

(3/14) The first step is detecting the anteroposterior (AP) axis in gastruloids, based on gross morphology. We can either use a skeletonization approach using segmentation or a surface mesh approach using Non-linear PCA, which was important for timelapse data.

Ryan Savill
@cryaaa.bsky.social

(4/14) Using manual annotations to benchmark the spine is a crucial but in 3D annotation can be challenging. To have a second method of verification I generated synthetic gastruloids with some Perlin noise to generate realistic structures (like this wobbly gastruloid)

Ryan Savill
@cryaaa.bsky.social

(2/14) Its modular architecture allows it to plop into pre-existing workflows. This means you can map any signal of interest into a common reference frame across gastruloids!

Ryan Savill reposted

Jesse Veenvliet
@jesseveenvliet.bsky.social

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....

doi.orgIn preprints: exploring developmental robustness and timing with gastruloidsHow 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...

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Kristina Stapornwongkul
@kstapornwongkul.bsky.social

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...

cell.comSignaling switches: Metabolism regulates gastruloid self-organizationMetabolic 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...
Ryan Savill
@cryaaa.bsky.social

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! 🚀

Jesse Veenvliet@jesseveenvliet.bsky.social

😱 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

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