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Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization.
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http://dx.doi.org/10.3390/ijms241713375 | DOI Listing |
Aberration correction is critical for obtaining sharp images but remains a challenging task. Owing to its ability to record both spatial and angular information of light rays, light field imaging is a powerful method to measure and correct optical aberrations. However, current methods need extensive calibrations to obtain prior information about the camera, which is restrictive in real-world applications.
View Article and Find Full Text PDFACS Appl Mater Interfaces
December 2024
Group of Characterization of Materials, Departament de Física, Universitat Politècnica de Catalunya, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, Barcelona 08019, Spain.
Hybrid organic-inorganic perovskites (HOIP) have emerged in recent years as highly promising semiconducting materials for a wide range of optoelectronic and energy applications. Nevertheless, the rotational dynamics of the organic components and many-molecule interdependencies, which may strongly impact the functional properties of HOIP, are not yet fully understood. In this study, we quantitatively analyze the orientational disorder and molecular correlations in archetypal perovskite CHNHPbI (MAPI) by performing comprehensive molecular dynamics simulations and entropy calculations.
View Article and Find Full Text PDFJ ISAKOS
December 2024
Gelenkpunkt-Sports and Joint Surgery FIFA Medical Centre of Excellence, Innsbruck, Austria; Research Unit for Orthopaedic Sports Medicine and Injury Prevention (OSMI), Private University for Health Sciences Medical Informatics and Technology, Innsbruck, Austria.
Importance: The management of posterior cruciate ligament (PCL) injuries in children is complex and varies depending on the specific nature of the injury. Avulsions of the PCL can often be addressed with proximal or distal repair, while intra-substance tears and cases with persistent instability generally require more extensive reconstruction. Despite the prevalence of such cases, the literature is predominantly composed of case reports, indicating a lack of comprehensive research in this area.
View Article and Find Full Text PDFNanophotonics
February 2024
Shaanxi Key Laboratory of Artificially-Structured Functional Materials and Devices, Air Force Engineering University, Xi'an, Shaanxi 710051, China.
Vortex beams carrying orbital angular momentum (OAM) are considered to hold significant prospects in fields such as super-resolution imaging, high-capacity communications, and quantum optics. Therefore, the techniques of vortex beam generation have attracted extensive studies, in which the development of metasurfaces brings new vigor and vitality to it. However, the generation of reconfigurable vortex beams by metasurfaces at the incidence of arbitrary polarized electromagnetic (EM) waves holds challenges.
View Article and Find Full Text PDFNanophotonics
November 2023
Key Laboratory of Ultrafast Photoelectric Technology and Terahertz Science in Shaanxi, Xi'an University of Technology, Xi'an, 710048, China.
As a high-degree-of-freedom approach to manipulate the electromagnetic wave, metasurfaces are widely used in high-capacity information technology. Extensive investigations have explored multiplexing techniques using polarization, incident angle, wavelength, and infinite-dimensional multiplexing through Orbital Angular Momentum (OAM). However, due to the limited spatial resolution and array size of the metasurface, the number of multiplexing channels that can be actually realized is limited.
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