To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻 www.ebi.ac.uk/empiar/EMPIA... A little thread about what's new... 🧵 1/n - ThreadSky

lifeonthewedge.bsky.social • 10 hours ago

To all #TeamTomo #CryoET and #Chlamydomonas aficionados: we have updated EMPIAR-11830 with a bug fix concerning some cryo-CARE denoised tomos as well as additional files and metadata! 🎉👩🏽‍💻

https://www.ebi.ac.uk/empiar/EMPIAR-11830/

A little thread about what's new... 🧵 1/n

Comments

lifeonthewedge.bsky.social•10 hours ago

First, we had accidentally uploaded cryo-CARE tomograms that were calculated using an outdated version of the tilt series alignments. In most cases the differences were small, but noticeable. This concerns all tomograms numbered <= 712, or 464 tomograms
(bad tomos were not uploaded, hence the skips)

lifeonthewedge.bsky.social•10 hours ago

IMPORTANT: this error only concerns these specific cryo-CARE tomos. The raw data and alignments deposited have not changed, and if you already used those to calculate your own reconstructions, they are fine!
But if you picked particles on the "bad" denoised tomos, they may not match the aligned TS!

lifeonthewedge.bsky.social•10 hours ago

Additionally, we have now included bin4 3D-CTF-corrected versions of all 1829 tomograms, ready for you to template match ✨🔍

Furthermore, we added improved defocus estimations from TILTCTF:
https://www.biorxiv.org/content/10.1101/2024.10.10.617684v1 4/n

lifeonthewedge.bsky.social•10 hours ago

Finally, we have added a STAR file version of the tomolist containing the full metadata, as well as information concerning excluded tilts, defocus, etc as STAR files in each tomogram folder.

Full tomolist:
https://ftp.ebi.ac.uk/empiar/world_availability/11830/data/chlamy_visual_proteomics/tomolist.star
Correspondence tomo num vs name:
https://ftp.ebi.ac.uk/empiar/world_availability/11830/data/chlamy_visual_proteomics/tomolist_num_dir.star

lifeonthewedge.bsky.social•10 hours ago

I'd like to point out that a spreadsheet is also available on Zenodo containing annotations of some organelles and short comments per tomo: https://doi.org/10.5281/zenodo.13941456

If you would like to know more about the dataset, make sure to read our #preprint: 📜🤓

https://www.biorxiv.org/content/10.1101/2024.12.28.630444v1 6/n

lifeonthewedge.bsky.social•10 hours ago

Some cool applications of this dataset are emerging, such as the awesome voxel-dense annotations generated by @mgflast.bsky.social @thomsharp.bsky.social with Ais and Pom:

https://cryopom.streamlit.app/

https://www.biorxiv.org/content/10.1101/2025.01.16.633326v1 7/n

uermel.bsky.social•5 hours ago

Exciting news! Are you planning to eventually release these beautiful segmentations as well?

lifeonthewedge.bsky.social•4 hours ago

These were made by @jessheebner.bsky.social on selected tomograms for the paper and yes, we can deposit them as well! Not sure what's the best approach but we can discuss that 😉

jessheebner.bsky.social•3 hours ago

I'm in the process of segmenting all of the tomograms as well! We should look into the best way for sure!

lifeonthewedge.bsky.social•3 hours ago

oh that sounds amazing!!

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