uermel.bsky.social
Scientist at Chan Zuckerberg Imaging Institute, Redwood City, CA
I like to make open source cryoET things.
11 posts
290 followers
644 following
Prolific Poster
Conversation Starter
comment in response to
post
Exciting news! Are you planning to eventually release these beautiful segmentations as well?
comment in response to
post
Here is a direct link to @mgflast.bsky.social's and @thomsharp.bsky.social's deposition: cryoetdataportal.czscience.com/depositions/10314
comment in response to
post
How about pieces of virus capsids? For example this HIV capsid pentamer: www.rcsb.org/3d-view/5MCY/1
comment in response to
post
10302 is a very large dataset of FIB-lamellae from C. reinhardtii that was used for a couple of recent studies, e.g.:
doi.org/10.1093/micmic/ozad067.480
doi.org/10.1101/2024.09.03.610704
cryoetdataportal.czscience.com/datasets/10302
comment in response to
post
10007 is a dataset of S. cerevisiae FIB-Lamella that was used to validate cryoDRGN-ET. (doi.org/10.1038/s41592-024-02340-4)
cryoetdataportal.czscience.com/datasets/10007
comment in response to
post
10004 includes tomograms of C. Elegans created using Serial Lift-Out sectioning. (doi.org/10.1038/s41592-023-02113-5)
cryoetdataportal.czscience.com/datasets/10004
comment in response to
post
There is a whole bunch of data over at the cryoET data portal. Would be very happy to see more manual/curated segmentations--contributions are always welcome and would be made publicly available!
For great FIB-milled datasets that need more annotations, check out datasets 10004, 10007 or 10302.
comment in response to
post
Depends on your definition of 'observe', 'raw', and the type of sample, I'd say. Observe visually? Does raw include CTF deconv?
e.g. one can easily spot single DNA strands in tomograms of in vitro chromatin. In cellular cryoET it's harder, but sometimes you can spot the turns in nucleosomes.
comment in response to
post
Always wondered what these were!
I've also seen them in HUVEC data on the cryoET data portal.
e.g.
cryoetdataportal.czscience.com/runs/9234
cryoetdataportal.czscience.com/runs/9124
comment in response to
post
Using interactive web-viz for sharing results lossless is always an option! In this case it's as easy as clicking "View Tomogram" here: cryoetdataportal.czscience.com/runs/14185