Acta Crystallographica Section D Structural Biology
Image-processing software has always been an integral part of structure determination by cryogeni... more Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionali...
We have developed a new data collection method and processing framework in full field cryo soft X... more We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.
Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells ... more Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells preserved under cryo conditions. Images obtained in these X-ray microscopes can be combined by tomographic reconstruction to quantitatively estimate the three-dimensional (3D) distribution of absorption coefficients inside the cell. The impulse response of an imaging system is one of the factors that limits the quality of the X-ray microscope reconstructions. The main goal of this work is to experimentally measure the 3D impulse response and to assess the optical resolution and depth of field of the Mistral microscope at ALBA synchrotron (Barcelona, Spain). To this end we measure the microscope apparent transfer function (ATF) and we use it to design a deblurring Wiener filter, obtaining an increase in the image quality when applied to experimental datasets collected at ALBA.
We have developed a new data collection method and processing framework in full field cryo soft X... more We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.
One of the most recent tools currently used to understand the mechanisms that take place within t... more One of the most recent tools currently used to understand the mechanisms that take place within the cell is cryo cellular soft X-ray tomography (cryo-SXT). Usually, tomograms are reconstructed by processing the data with software originally developed for electron microscopy data, such as SPIDER, BSOFT, IMOD or XMIPP. Because the reconstruction algorithms in these packages do not take into account the cryo-SXT image formation model, the results are not optimal. Cryo-SXT projections deviate from ideal data due to the limited depth of field (DOF) of the microscope optical system. This limited DOF produces images where the contribution of the different planes of the specimen is different, leading to images where certain parts of the sample are blurred. In this communication we present: 1) an experimental measurements of the cryo-SXT DOF of the Spanish synchrotron ALBA and 2) an in depth analysis on how artifacts associated to DOF can be reduced by multiplexing focal series. The optimal ...
Acta Crystallographica Section D Structural Biology
Image-processing software has always been an integral part of structure determination by cryogeni... more Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionali...
We have developed a new data collection method and processing framework in full field cryo soft X... more We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.
Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells ... more Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells preserved under cryo conditions. Images obtained in these X-ray microscopes can be combined by tomographic reconstruction to quantitatively estimate the three-dimensional (3D) distribution of absorption coefficients inside the cell. The impulse response of an imaging system is one of the factors that limits the quality of the X-ray microscope reconstructions. The main goal of this work is to experimentally measure the 3D impulse response and to assess the optical resolution and depth of field of the Mistral microscope at ALBA synchrotron (Barcelona, Spain). To this end we measure the microscope apparent transfer function (ATF) and we use it to design a deblurring Wiener filter, obtaining an increase in the image quality when applied to experimental datasets collected at ALBA.
We have developed a new data collection method and processing framework in full field cryo soft X... more We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.
One of the most recent tools currently used to understand the mechanisms that take place within t... more One of the most recent tools currently used to understand the mechanisms that take place within the cell is cryo cellular soft X-ray tomography (cryo-SXT). Usually, tomograms are reconstructed by processing the data with software originally developed for electron microscopy data, such as SPIDER, BSOFT, IMOD or XMIPP. Because the reconstruction algorithms in these packages do not take into account the cryo-SXT image formation model, the results are not optimal. Cryo-SXT projections deviate from ideal data due to the limited depth of field (DOF) of the microscope optical system. This limited DOF produces images where the contribution of the different planes of the specimen is different, leading to images where certain parts of the sample are blurred. In this communication we present: 1) an experimental measurements of the cryo-SXT DOF of the Spanish synchrotron ALBA and 2) an in depth analysis on how artifacts associated to DOF can be reduced by multiplexing focal series. The optimal ...
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Papers by Joaquín Otón