Numerical Methods of Cryo Electron Tomography
Group leader
Daniel Castaño
Address
Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)
Research goal
We develop software and algorithmic methods for cryo-electron tomography (cryoET). Our inhouse package Dynamo covers all stages of this computational pipeline: alignment of tilt series, reconstruction of tomograms, particle extraction and subtomogram averaging and classification. Using constitutive exocytosis in yeast cells as experimental example, we ultimately aim at building a numerical infrastructure for the combined use of cryoET, intracellular nanotools and live cell imaging to resolve dynamic cellular processes with atomic resolution.
Group members
Publications
Vivas-Lago A, Castaño-Díez D
Few-shot learning for non-vitrified ice segmentation
Sci Rep. 2025 Feb 14;15(1):5501
doi: 10.1038/s41598-025-86308-0
Coray R, Navarro P, Scaramuzza S, Stahlberg H, Castaño-Díez D
Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo
Structure. 2024 Oct 3;32(10):1808-1819.e4
doi: 10.1016/j.str.2024.07.003
Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A
Architecture of the ESCPE-1 membrane coat
Nat Struct Mol Biol. 2023 Jul;30(7):958-969
doi: 10.1038/s41594-023-01014-7
Talledge N, Yang H, Shi K, Coray R, Yu G, Arndt WG, Meng S, Baxter GC, Mendonça LM, Castaño-Díez D, Aihara H, Mansky LM, Zhang W
HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation
J Mol Biol. 2023 Aug 1;435(15):168143
doi: 10.1016/j.jmb.2023.168143
Zivanov J, Otón J, Ke Z, von Kügelgen A, Pyle E, Qu K, Morado D, Castaño-Díez D, Zanetti G, Bharat TAM, Briggs JAG, Scheres SHW
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
Elife. 2022 Dec 5;11:e83724
doi: 10.7554/eLife.83724
S Scaramuzza, D Castaño-Díez
Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo.
PLoS Biol. 2021 Aug 26;19(8):e3001318.
DOI: 10.1371/journal.pbio.3001318
PP Navarro, H Stahlberg, D Castaño-Díez.
Protocols for subtomogram averaging of membrane proteins in the Dynamo software package.
Front Mol Biosci. 2018 Sep 4:5:82
DOI: 10.3389/fmolb.2018.00082
D Castaño-Díez, M Kudryashev, H Stahlberg
Dynamo catalogue: geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms.
J Struct Biol. 2017 Feb;197(2):135-144
DOI: 10.1016/j.jsb.2016.06.005