Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines.
🧵👇
doi.org/10.1002/pro.70578
Is the alt text AI generated? It is trolling Jurgen.
Oops, I forgot the preprint link
www.biorxiv.org/content/10.6...
Check out @lee in action, harvesting hindguts from termites! 🐜🔬. Massive credit for pionering work from @centriolelab.bsky.social and others for establishing the isolation of centriole from Trichonympha and earlier model for central hub. We significantly benefit from advances in cryo-ET & STA.
The cartwheel was first visualized ~70 years ago in the symbiont Trichonympha in the wood termite gut. We’ve discovered the cartwheel’s secret: a unique zigzag stacking of SAS-6 tetramers that facilitates the iconic 9-fold symmetry of cilia.
#cellbiology #teamtomo #SAS6 #cartwheel
I see. I just have a quick look through the figure. I can try it to see then.
Late to the thread,I wonder the difference to DeepDeWedge is due to CTF. When I used CTF corrected tomo to compare DeepDeWedge and IsoNet2, I saw no noticeable visual difference in my tomogram.
That looks sick :)
I used Tinkercad. Lots of tutorials on YouTube and it has very simple interface. The dimension I guessed a bit. A few trials and errors on print direction, design the join and groove.
The printing profile & the Stl file can be downloaded here:
makerworld.com/en/models/24...
You need an AMS to print with color or just a single black for everything.
3D printing is way too much fun 😄
Just made myself a Titan Krios G5 pen holder 🧊🔬
Now the only thing missing… is McGill getting the real one! 😉
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...
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
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
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...
The entire video list with Installation, Build Cilia, Centriole & 2D template
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.
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.
This was built in ~10 days of vibe-coding with Claude & Gemini. Now officially on holiday 😌
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).
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.
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...
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 :)
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.
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.
