November 11, 2024 at 11:59 AM
November 22, 2024 at 4:15 PM
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Icecream: High-Fidelity Equivariant Cryo-Electron Tomography
Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...
www.biorxiv.org
October 23, 2025 at 11:13 AM
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
Software Updates: April's software push was big one, with new releases pushed for AWS CLI, BCFtools, breseq, cryoCARE, cryoDRGN, CryoSieve, Foldseek, Ghostscript, Infernal, LightDock, Phenix, Qt, SAMtools, and Spring.
May 10, 2024 at 11:04 PM
Software Updates: April's software push was big one, with new releases pushed for AWS CLI, BCFtools, breseq, cryoCARE, cryoDRGN, CryoSieve, Foldseek, Ghostscript, Infernal, LightDock, Phenix, Qt, SAMtools, and Spring.
I have been using CryoLithe recently as DeepDeWedge and cryoCARE erase many of the periplasmic complexes that I want to pick.
arxiv.org/abs/2501.15246
If you are unfortunate and have to manually pick particles. I have had the most success using the WARP deconvolution filter.
arxiv.org/abs/2501.15246
If you are unfortunate and have to manually pick particles. I have had the most success using the WARP deconvolution filter.
End-to-end localized deep learning for Cryo-ET
Cryo-electron tomography (cryo-ET) enables 3D visualization of cellular environments. Accurate reconstruction of high-resolution volumes is complicated by the very low signal-to-noise ratio and a rest...
arxiv.org
July 11, 2025 at 12:01 AM
I have been using CryoLithe recently as DeepDeWedge and cryoCARE erase many of the periplasmic complexes that I want to pick.
arxiv.org/abs/2501.15246
If you are unfortunate and have to manually pick particles. I have had the most success using the WARP deconvolution filter.
arxiv.org/abs/2501.15246
If you are unfortunate and have to manually pick particles. I have had the most success using the WARP deconvolution filter.
Sobre los últimos días de Timothy Leary, sale este documento en Ulises
El extraño caso de Timothy Leary - ulises.online
Cuando Timothy Leary se unió a CryoCare en noviembre de 1994, dejó en claro que quería ser más que “un miembro más”. Durante un tiempo (hasta que le explicamos los problemas legales y prácticos) llevó...
ulises.online
January 8, 2025 at 8:27 AM
Sobre los últimos días de Timothy Leary, sale este documento en Ulises
Scipion ... Doppio 😅
For TS alignment, reconstruction, CTF estimation and correction and denoising (cryoCARE/IsoNET), Scipion has really been great for us. For STA though we go out usually (STOPGAP, RELION4, WARP/M).
But I feel Scipion is nice for organizing projects.
For TS alignment, reconstruction, CTF estimation and correction and denoising (cryoCARE/IsoNET), Scipion has really been great for us. For STA though we go out usually (STOPGAP, RELION4, WARP/M).
But I feel Scipion is nice for organizing projects.
a picture of a bat with the words " which one " below it
ALT: a picture of a bat with the words " which one " below it
media.tenor.com
November 10, 2024 at 10:15 PM
Scipion ... Doppio 😅
For TS alignment, reconstruction, CTF estimation and correction and denoising (cryoCARE/IsoNET), Scipion has really been great for us. For STA though we go out usually (STOPGAP, RELION4, WARP/M).
But I feel Scipion is nice for organizing projects.
For TS alignment, reconstruction, CTF estimation and correction and denoising (cryoCARE/IsoNET), Scipion has really been great for us. For STA though we go out usually (STOPGAP, RELION4, WARP/M).
But I feel Scipion is nice for organizing projects.
Thanks @tibuch_ for the nice visit and great talk on #DeepLearning-based denoising of light and electron microscopy images🔬🤖. #CryoCARE is a core part of our #CryoET workflow. Also thanks @rdrighetto for hosting!
@biozentrum @FMIscience @humantechnopole @mpicbg @helmholtz_ai
@biozentrum @FMIscience @humantechnopole @mpicbg @helmholtz_ai
November 23, 2024 at 6:15 AM
Thanks @tibuch_ for the nice visit and great talk on #DeepLearning-based denoising of light and electron microscopy images🔬🤖. #CryoCARE is a core part of our #CryoET workflow. Also thanks @rdrighetto for hosting!
@biozentrum @FMIscience @humantechnopole @mpicbg @helmholtz_ai
@biozentrum @FMIscience @humantechnopole @mpicbg @helmholtz_ai
Probably not so inventive but we use cryoCARE and IsoNet. We like them both, but it's important to know a bit about how they function. Basically, IsoNet can sometimes, on some samples, "invent" features, or rather place recurring features in places they are not. CryoCARE is more conservative.
July 10, 2025 at 2:38 PM
Probably not so inventive but we use cryoCARE and IsoNet. We like them both, but it's important to know a bit about how they function. Basically, IsoNet can sometimes, on some samples, "invent" features, or rather place recurring features in places they are not. CryoCARE is more conservative.
when using cryoCARE. I used the default settings on the Train tab. But how does changing the “number of sub-volumes per tomogram” or “sub-volume dimensions” change the training data? Is increasing it make more prone to producing artifacts or completely dampening low contrast structural features?
July 10, 2025 at 3:37 PM
when using cryoCARE. I used the default settings on the Train tab. But how does changing the “number of sub-volumes per tomogram” or “sub-volume dimensions” change the training data? Is increasing it make more prone to producing artifacts or completely dampening low contrast structural features?