Three-dimensional electron and X-ray microscopies: image processing challenges

JM Carazo

 Carlos Oscar Sorzano

José María Carazo

Group Leader



Carlos Oscar Sorzano

Group Leader





Research summary

We focus in understanding how the three-dimensional structure of macromolecular machines together with its flexibility is linked with their function. We use three-dimensional electron microscopy (3D EM) to study systems characterized both by its flexibility and its vital role in the cell, such as replicative helicases and the centrosome.



Ljubetič A, Lapenta F, Gradišar H, Drobnak I, Aupič J, Strmšek Ž, Lainšček D, Hafner-Bratkovič I, Majerle A, Krivec N, Benčina M, Pisanski T, Veličković TĆ, Round A, Carazo JM, Melero R, Jerala R. Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Nat Biotechnol. 2017 Nov;35(11):1094-1101.

Koning RI, Gomez-Blanco J, Akopjana I, Vargas J, Kazaks A, Tars K, Carazo JM, Koster AJ. Asymmetric Cryo-Em Reconstruction of Phage Ms2 Reveals Genome Structure in Situ. Nat Commun 2016; 7: 12524

Vargas J, Otón J, Marabini R, Carazo JM, Sorzano CO. Particle alignment reliability in single particle electron cryomicroscopy: a general approach. Sci Rep 2016; 6: 21626

Otón J, Pereiro E, Pérez-Berná AJ, Millach L, Sorzano CO, Marabini R, Carazo JM. Characterization of transfer function, resolution and depth of field of a soft X-ray microscope applied to tomography enhancement by Wiener deconvolution. Biomed Opt Express 2016; 7: 5092-5103

Sorzano CO, Alcorlo M, de la Rosa-Trevín JM, Melero R, Foche I, Zaldívar-Peraza A, del Cano L, Vargas J, Abrishami V, Otón J, Marabini R, Carazo JM. Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revised. Sci Rep 2015; 5: 14290




The 2013-2014 biennium was particularly important for the field of cryogenic electron microscopy (cryo EM). Thanks to key technological developments in instruments and software, it became obvious in 2013 that cryo EM had indeed matured as a technique, such that we can now systematically produce quasi-atomic structural information for a wide range of very challenging macromolecular complexes. The need to re accommodate all image processing workflows to address the new challenges in the field consequently became the target of the group. This goal fitted very well with our focus on methods and software development in our role as the image processing infrastructure providers for Instruct, the structural biology project of the European Strategic Forum for Research Infrastructures.

We have explored new areas of cryo EM image processing within our traditional software suite XMIPP (downloaded in recent years by thousands of researchers from all over the world). We addressed a number of topics central to enhanced microscope performance and optimal image processing, such as accurate, parameter-free optical characterization, automatic analysis of micrographs, or image-ranking procedures, all critical to render cryo EM a high throughput technique for structural biology. With regard to software, we introduced the beta version of our key development, Scipion, a graphic image-processing workflow integrator that assures full tracking of all analytic results, while offering an environment that integrates most of the best known software packages in the field.

With respect to X-microscopy, using the X-ray microscope at the Spanish synchrotron ALBA, we produced the first detailed optical characterization with this type of instrument, while advancing in automation and image processing capabilities.




José M. Carazo Principal investigator
Carlos Oscar Sorzano Sánchez Principal investigator
Joan Segura Mora Postdoctoral scientist
Roberto Melero del Rio Postdoctoral scientist
Marta Martinez Postdoctoral scientist
Tomas Majtner Postdoctoral scientist
Amaya Jiménez Postdoctoral scientist
Erney Ramirez Aportela Postdoctoral scientist
David Maluenda Postdoctoral scientist
Peter Horvath Postdoctoral scientist
Ruben Sanchez García Predoctoral scientist
Jose Luis Vilas Predoctoral scientist
Javier Mota Predoctoral scientist
David Strelak Predoctoral scientist
Pablo Conesa Mingo Technician
Blanca E. Benítez Technician
Laura del Caño Technician

ComFuturo Vertical

La Fundación General CSIC, financia a través del Programa ComFuturo el contrato del investigador Javier Vargas Balbuena para la realización del proyecto "Procesamiento de imagen en criomicroscopía electrónica con impacto en la industria farmacéutica".

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