@builab.bsky.social
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builab.bsky.social
@builab.bsky.social
· Dec 23
Tired of drawing cilia or centrioles for slides and papers? I feel you.
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
I also started a MakerWorld page to share these files! There are only a few for now, but I’ll be uploading more as I go further down the 3D printing rabbit hole. 🕳️🐇
Grab the models here: makerworld.com/en/@user_763...
Grab the models here: makerworld.com/en/@user_763...
CiliaBuilder | Home - MakerWorld
MakerWorld is the leading 3D printing model community for designers and makers. Download thousands of free 3D models and STL files from the No.1 destination for multicolor designs.
makerworld.com
February 6, 2026 at 2:29 PM
I also started a MakerWorld page to share these files! There are only a few for now, but I’ll be uploading more as I go further down the 3D printing rabbit hole. 🕳️🐇
Grab the models here: makerworld.com/en/@user_763...
Grab the models here: makerworld.com/en/@user_763...
Ever wanted to hold a cilium in your hand? 🧬✨
Here is a look at how I’m using CiliaBuilder in @UCSFChimeraX to generate accurate 3D prints of centrioles and cilia. Perfect for teaching or lab displays!
Watch the process: youtu.be/IKnnp3ovptQ #CryoEM #CellBio #ChimeraX
Here is a look at how I’m using CiliaBuilder in @UCSFChimeraX to generate accurate 3D prints of centrioles and cilia. Perfect for teaching or lab displays!
Watch the process: youtu.be/IKnnp3ovptQ #CryoEM #CellBio #ChimeraX
February 6, 2026 at 2:25 PM
Ever wanted to hold a cilium in your hand? 🧬✨
Here is a look at how I’m using CiliaBuilder in @UCSFChimeraX to generate accurate 3D prints of centrioles and cilia. Perfect for teaching or lab displays!
Watch the process: youtu.be/IKnnp3ovptQ #CryoEM #CellBio #ChimeraX
Here is a look at how I’m using CiliaBuilder in @UCSFChimeraX to generate accurate 3D prints of centrioles and cilia. Perfect for teaching or lab displays!
Watch the process: youtu.be/IKnnp3ovptQ #CryoEM #CellBio #ChimeraX
Reposted
Very happy to say that our work on how axonemes are generated is now available on bioRxiv: www.biorxiv.org/content/10.6... - if you’ve ever wondered how the incredibly beautiful, complex structures within motile #cilia are constructed then this is for you!
www.biorxiv.org
February 6, 2026 at 11:20 AM
Very happy to say that our work on how axonemes are generated is now available on bioRxiv: www.biorxiv.org/content/10.6... - if you’ve ever wondered how the incredibly beautiful, complex structures within motile #cilia are constructed then this is for you!
I haven't tried the new version, but I followed the tutorial and no membrane thickness is measured despite the fact that other properties are measured, which is one of the main thing that I am interested
February 4, 2026 at 2:39 PM
I haven't tried the new version, but I followed the tutorial and no membrane thickness is measured despite the fact that other properties are measured, which is one of the main thing that I am interested
Reposted
Cilia alert! Stoked to have the new paper from Juyeon Hong about a new domain at the extreme distal tip of motile cilia! (The EDT, y'all!) It's out now @natcomms.nature.com.
Check it out!
#cilia
www.nature.com/articles/s41...
Check it out!
#cilia
www.nature.com/articles/s41...
A protein complex in the extreme distal tip of vertebrate motile cilia controls their organization, length, and function - Nature Communications
Here they combine in vivo imaging with proteomics to characterize a protein complex comprised of Ccdc78 and Ccdc33 that acts at the extreme distal tip of 9 + 2 motile cilia to control tip architecture...
www.nature.com
January 29, 2026 at 1:23 AM
Cilia alert! Stoked to have the new paper from Juyeon Hong about a new domain at the extreme distal tip of motile cilia! (The EDT, y'all!) It's out now @natcomms.nature.com.
Check it out!
#cilia
www.nature.com/articles/s41...
Check it out!
#cilia
www.nature.com/articles/s41...
The entire video list with Installation, Build Cilia, Centriole & 2D template
www.youtube.com/playlist?lis...
www.youtube.com/playlist?lis...
CiliaBuilder Tutorials - YouTube
CiliaBuilder Tutorials
www.youtube.com
December 28, 2025 at 4:40 PM
The entire video list with Installation, Build Cilia, Centriole & 2D template
www.youtube.com/playlist?lis...
www.youtube.com/playlist?lis...
CiliaBuilder Video Tutorial
www.youtube.com/watch?v=SJHo...
If your installation didn't work a few days ago, try again. I've fixed a few things, and let me know if it still doesn't work for you.
www.youtube.com/watch?v=SJHo...
If your installation didn't work a few days ago, try again. I've fixed a few things, and let me know if it still doesn't work for you.
ChimeraX CiliaBuilder - Modelling Cilia Basics
YouTube video by Bui Lab
www.youtube.com
December 28, 2025 at 4:40 PM
CiliaBuilder Video Tutorial
www.youtube.com/watch?v=SJHo...
If your installation didn't work a few days ago, try again. I've fixed a few things, and let me know if it still doesn't work for you.
www.youtube.com/watch?v=SJHo...
If your installation didn't work a few days ago, try again. I've fixed a few things, and let me know if it still doesn't work for you.
I just noticed that I did not put the proper dependency. Now, if you download version 1.0.6, it will install the dependency properly to run.
December 24, 2025 at 3:54 PM
I just noticed that I did not put the proper dependency. Now, if you download version 1.0.6, it will install the dependency properly to run.
I am planning to do the next release with ArtiaX style cilia in the near future :) You probably will like that a lot more.
December 23, 2025 at 8:13 PM
I am planning to do the next release with ArtiaX style cilia in the near future :) You probably will like that a lot more.
This was built in ~10 days of vibe-coding with Claude & Gemini. Now officially on holiday 😌
Video tutorial coming after the holidays
Video tutorial coming after the holidays
December 23, 2025 at 8:02 PM
This was built in ~10 days of vibe-coding with Claude & Gemini. Now officially on holiday 😌
Video tutorial coming after the holidays
Video tutorial coming after the holidays
Tired of drawing cilia or centrioles for slides and papers? I feel you.
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
December 23, 2025 at 8:02 PM
Tired of drawing cilia or centrioles for slides and papers? I feel you.
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
Check out CiliaBuilder for ChimeraX → cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Build custom 3D cilia & centriole models (tips + primary cilia included).
We also analysed SPEF1-KO cilia by cryo-ET to show that SPEF1 restricts C1 and C2 microtubule movement.
July 11, 2025 at 7:41 PM
We also analysed SPEF1-KO cilia by cryo-ET to show that SPEF1 restricts C1 and C2 microtubule movement.
In the final version, we included a lot more data and analysis compared to the previous biorxiv version. We achieved a 4.6 Angstrom resolution of the microtubule by subtomogram averaging of MT-SPEF1 complexes.
July 11, 2025 at 7:41 PM
In the final version, we included a lot more data and analysis compared to the previous biorxiv version. We achieved a 4.6 Angstrom resolution of the microtubule by subtomogram averaging of MT-SPEF1 complexes.
Our newest paper is now online in Current Biology. In short, we identified 7 proteins in the tip of the cilia and found SPEF1 is a seam-binding protein and important for cilia stability. Great work from my postdoc Thibault Legal and everyone involved!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1
Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The cil…
www.sciencedirect.com
July 11, 2025 at 7:35 PM
Our newest paper is now online in Current Biology. In short, we identified 7 proteins in the tip of the cilia and found SPEF1 is a seam-binding protein and important for cilia stability. Great work from my postdoc Thibault Legal and everyone involved!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
This seems great. I want to working on our picking using AI in the summer. Perhaps, I can ask you for an installation and usage guide if I have problems.
March 8, 2025 at 11:28 PM
This seems great. I want to working on our picking using AI in the summer. Perhaps, I can ask you for an installation and usage guide if I have problems.
I hated Amira with the $$. Need to try DragonFly but most of our processing is done on the cluster so anything using command line is a big advantage. Perhaps, my summer project :)
March 6, 2025 at 5:21 AM
I hated Amira with the $$. Need to try DragonFly but most of our processing is done on the cluster so anything using command line is a big advantage. Perhaps, my summer project :)
interesting I want to use dragonfly for segmentation but can we run dragonfly in command line for batch mode? Do you have a script to cluster and turn dragon fly into filament light?
March 5, 2025 at 4:32 AM
interesting I want to use dragonfly for segmentation but can we run dragonfly in command line for batch mode? Do you have a script to cluster and turn dragon fly into filament light?
Very nice preprint from the Wallingford lab. Seems like there is a common theme of tip proteins as these proteins seem to be in the tip of the ciliate cilia too.
Preprint Alert! Juyeon Hong in the lab has dissected the molecular organization of distal tips of vertebrate motile cilia. She even found a new compartment in the extreme distal tip marked by Ccdc78 and Ccdc33. Give it a read!
@biorxiv-cellbio.bsky.social
www.biorxiv.org/content/10.1...
@biorxiv-cellbio.bsky.social
www.biorxiv.org/content/10.1...
Molecular organization of the distal tip of vertebrate motile cilia
The beating of cilia on multi-ciliated cells (MCCs) is essential for normal development and homeostasis in animals. Unlike basal bodies or axonemes, the distal tips of MCC cilia remain poorly defined....
www.biorxiv.org
March 5, 2025 at 4:27 AM
Very nice preprint from the Wallingford lab. Seems like there is a common theme of tip proteins as these proteins seem to be in the tip of the ciliate cilia too.
Thanks. I found template matching is too slow for my need as I can manual pick microtubules much faster and more accurate. These tryout takes time so I 'd love to see people's experiences.
March 5, 2025 at 2:34 AM
Thanks. I found template matching is too slow for my need as I can manual pick microtubules much faster and more accurate. These tryout takes time so I 'd love to see people's experiences.
Reposted
Cryo-electron tomography of Tetrahymena #cilia by Sam Li, David Agard, Mark Winey provides insights into the intricate spatial organization of basal body inner junctions, compromised by loss of Poc1
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
February 24, 2025 at 2:48 PM
Cryo-electron tomography of Tetrahymena #cilia by Sam Li, David Agard, Mark Winey provides insights into the intricate spatial organization of basal body inner junctions, compromised by loss of Poc1
www.embopress.org/doi/full/10....
www.embopress.org/doi/full/10....
Reposted
We have posted our new #preprint regarding the track recognition mechanism of dynein-2 that works in #cilia on bioRxiv @biorxivpreprint.bsky.social!!
www.biorxiv.org/content/10.1...
1/8 🧵
www.biorxiv.org/content/10.1...
1/8 🧵
Dynein-2 is tuned for the A-tubule of the ciliary doublet through tubulin tyrosination
Eukaryotic cilia and flagella are thin structures present on the surface of cells, playing vital roles in signaling and cellular motion. Cilia structures rely on intraflagellar transport (IFT), which ...
www.biorxiv.org
January 28, 2025 at 7:05 PM
We have posted our new #preprint regarding the track recognition mechanism of dynein-2 that works in #cilia on bioRxiv @biorxivpreprint.bsky.social!!
www.biorxiv.org/content/10.1...
1/8 🧵
www.biorxiv.org/content/10.1...
1/8 🧵
Reposted
Excited to share our work on bioRxiv before my thesis defense! Together with my undergraduate mentee Diego, postdocs Wan and Jun, and my advisor Kai, we identified a novel dynein heavy chain subfamily, DNAHX, from sea urchin sperm axoneme.
Check out the details here: www.biorxiv.org/content/10.1...
Check out the details here: www.biorxiv.org/content/10.1...
DNAHX: a novel, non-motile dynein heavy chain subfamily, identified by cryo-EM endogenously
Ciliogenesis and cilia motility rely on the coordinated actions of diverse dyneins, yet the complexity of these motor proteins in cilia has posed challenges for understanding their specific roles. Tra...
www.biorxiv.org
January 21, 2025 at 3:34 AM
Excited to share our work on bioRxiv before my thesis defense! Together with my undergraduate mentee Diego, postdocs Wan and Jun, and my advisor Kai, we identified a novel dynein heavy chain subfamily, DNAHX, from sea urchin sperm axoneme.
Check out the details here: www.biorxiv.org/content/10.1...
Check out the details here: www.biorxiv.org/content/10.1...
Reposted
Best way to start 2025! Thrilled to share our Nature paper about the structures of axonemal components from sperm flagella and from epithelial cilia of the oviduct and brain ventricles. Great collaboration with Tzviya Zeev-Ben-Mordehai and @alanbrownhms.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 1, 2025 at 5:20 PM
Best way to start 2025! Thrilled to share our Nature paper about the structures of axonemal components from sperm flagella and from epithelial cilia of the oviduct and brain ventricles. Great collaboration with Tzviya Zeev-Ben-Mordehai and @alanbrownhms.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Amazing work. It is so useful for us working with Tetrahymena and for cilia in general.
December 17, 2024 at 11:13 PM
Amazing work. It is so useful for us working with Tetrahymena and for cilia in general.