Royer Lab at CZ Biohub

@royerlab
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How do organisms develop from a single cell?

The Royer Lab is a pluridisciplinary team of computer scientists, optical engineers, and biologists. Our goal is to build a time-resolved, multidimensional atlas of vertebrate development using zebrafish as a model organism. To attain this goal, we design, build, and implement novel state-of-the-art light-sheet microscopes, and employ and also design deep learning–based image processing and analysis algorithms.

Show threadRoyer Lab at CZ BiohubMar 8, 2023
This work would not have been possible without the amazing #team at @czbiohub sf, in particular, @Merlin_Lange who led this work, and a special shoutout to @ale_agranados, @Shruthi94Vijay, @jobragantini, and @Sarah_E_Ancheta for there wonderful contribution. 22/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
Thanks to last-minute help from @stardazed0 and the admirably twitter-less Jeremy Maitin-Shepard we managed to integrate github.com/google/neuroglancer in zebrahub.org/imaging Check it out! It's amazingly fast! 21/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
We are still trying to understand all this, and have some ideas in the preprint. We expect and hope for a robust and enthusiastic discussion with the community and welcome feedback, ideas, and suggestions! Reach out at [email protected] and [email protected] 20/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
To understand the relevant tissue kinematics, we applied the recently developed dynamic morphoskeletons framework from @Mattia__Serra et al. and found that pluripotent NMPs coincide with a strong repeller structure. For more details on the theory check the preprint đŸ˜‰ 19/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
Using the in-vivo experiment we can reconstruct the track of a single pluripotent presumptive NMP! 18/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
'in silico' fate mapping is great, but there is nothing better than a real experiment. Next, we performed similar in vivo photo-manipulation experiments directly in our multi-view light-sheet microscope. Again we find the same fate restriction. 17/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
Using the high-resolution image-based cell tracking together with our @napari_imaging plugin for in silico fate mapping we confirmed the NMP state transition in pluripotency. 16/n
Royer Lab at CZ BiohubMar 8, 2023
'in silico' fate mapping is great, but there is nothing better than a real experiment. Next, we performed similar in vivo photo-manipulation experiments directly in our multi-view light-sheet microscope. Again we find the same fate restriction. 17/n
Royer Lab at CZ BiohubMar 8, 2023
Using the high-resolution image-based cell tracking together with our @napari_imaging plugin for in silico fate mapping we confirmed the NMP state transition in pluripotency. 16/n
Show threadRoyer Lab at CZ BiohubMar 8, 2023
Going deeper we find that our RNA velocity data and a pseudotime analysis suggest that NMPs are pluripotent (give rise to mesodermal and neural progeny) only during early axis elongation before having their fate restricted to the mesoderm. 15/n