Numerical Methods of Cryo Electron Tomography
Group leader
Daniel Castaño
Address
Biofisika Institute (CSIC, EHU)
Science Park of the 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
Laura García Cornejo
PhD student
Andrés Molina
PhD student
Raffaele Coray
PhD Student
Daniel Castaño
CSIC Scientist
Publications
Coray R, Castaño-Díez D
Geometry-aware template matching for cryo-electron tomograms in Dynamo
Structure. 2025 Sep 4;33(9):1591-1602.e3
doi: 10.1016/j.str.2025.06.009
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