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Svensson, Lennart, 1980-, et al.
(författare)
Rigid template registration in MET images using CUDA
2012
Ingår i: VISAPP 2012. - Rome : SciTePress. - 9789898565037 ; 2, s. 418-422
Konferensbidrag (refereegranskat) abstract
Rigid registration is a basic tool in many applications, especially in Molecular Electron Tomography (MET), and also in, e.g., registration of rigid implants in medical images and as initialization for deformable registration. As MET volumes have a low signal to noise ratio, a complete search of the six-dimensional (6D) parameter space is often employed. In this paper, we describe how rigid registration with normalized cross-correlation can be implemented on the GPU using NVIDIA's parallel computing architecture CUDA. We compare the performance to the Colores software and two Matlab implementations, one of which is using the GPU accelerated JACKET library. With well-aligned padding and using CUDA, the performance increases by an order of a magnitude, making it feasible to work with three-dimensional fitness landscapes, here denoted scoring volumes, that are generated on the fly. This will eventually enable the biologists to interactively register macromolecule chains in MET volumes piece by piece.
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Coufalova, Eva, et al.
(författare)
Low Voltage Mini TEM
2014
Ingår i: Proceedings.
Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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Sintorn, Ida-Maria, et al.
(författare)
Automated Image Acquisition and Particle Size Distribution in the MiniTEM Instrument
2015
Konferensbidrag (refereegranskat) abstract
The MiniTEM instrument is a desktop-top low-voltage easy to use TEM that was introduced last year. It has a high degree of automation in the microscope alignment, image acquisition, and analysis process.The microscope runs at 25 keV, which enables imaging of biological (negative stain and tissue sections) as well as inorganic samples prepared with standard methods. It is small, robust, requires only one standard wall socket, and can be hosted in any lab or office. The GUI is developed for Windows 8, and designed for a touch screen, allowing convenient search through the sample with pinch-zooming (changing magnification). The instrument has an integrated image processing and analysis library, which allows the user to design and apply analysis scripts. A graph based interface is used to create scripts which can be saved for future use and applied to multiple images, either acquired on the fly or manually acquired and stored in a folder.Here, we show how the MiniTEM instrument can be used to extract a user independent size distribution of particles in a sample in a highly automated manner. We designed analysis scripts for automatic image acquisition followed by segmentation and extraction of characteristic measures of individual particles. As a final step, obvious false-positives are manually removed which simultaneously updates the extracted measures. In the first example we image (at 1.46 nm/pixel) and analyze influenza viral vectors kindly provided by Max Planck Institute for Dynamics of Complex Technical Systems. The resulting size distribution was compared to and does agree with the distribution derived from corresponding analysis in high-voltage images (Tecnai G2 Spirit, 1.85 nm/pixel, 100 keV), see fig. 1. In the second example, we investigate the size distribution of mixtures of two differently sized polystyrene spheres (at 1.46 nm/pixel). The measured distribution (fig. 2) again coincides with the expected
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Sintorn, Ida-Maria, 1976-, et al.
(författare)
Factors influencing high quality low voltage TEM imaging of biological routinely stained specimen
2013
Ingår i: Proceedings, part I. ; , s. 321-322
Konferensbidrag (populärvet., debatt m.m.) abstract
Low-voltage TEM imaging requires sufficient electron transmittance. One advantage of low-voltage TEM is the increased electron scattering resulting in higher contrast. Principally this implies that negative stain contrast agents may not be needed which would be beneficial since they inherently reduce the electron transmittance. However, negative stains are not only used to increase the contrast when imaging biological specimens. They also help in fixation and protect the specimen from dehydration. Hence, a requirement to acquire high quality images of biological specimen using a low-voltage TEM is fixation/staining while maintaining enough electron transmittance. This identifies and a few factors that can be investigated in order to acquire images of biological specimens using low-voltage TEM: supporting film, choice (molecular weight) of stain and thickness of stain layer. Here we have focused on the first factor, the supporting film. More specifically, we have focused on the thickness of amorphous carbon films since such supports tend to have negligible influence of the specimen, and the negative stains generally distribute evenly (which to our experience is not the case when using very thin graphene grids). We here present a small study where the influence of the thickness of the carbon supporting film on electron transmittance has been investigated. The electron transmittance for two thicknesses of carbon films (EMS grids >30 nm and KC S6 grids <10 nm) has been measured at a range of energies, from 5 keV to 100 keV in an LVEM 5 (5keV), and a Tecnai Spirit BioTwin (20 to 100keV). The transmittance was derived as the ratio of the mean intensity values of images acquired with and without the grids inserted into the electron beam. How the transmittance for the two carbon film thicknesses varies for different electron voltages is shown in Figure 1. To illustrate how the final low-voltage TEM image quality is influenced by the carbon film thickness, thick and thin carbon film grids containing BK virus-like particles stained with 2% UAc were prepared and imaged at 20 keV in a Tecnai Spirit BioTwin microscope at magnifications ranging from 6000 to 87000. Example images of the EMS and KS C6 grids are shown in Figure 2 together with their corresponding histograms. In conclusion: reducing the carbon layer thickness from ~30 nm to <10 nm results in a significant increase in electron transmittance showing the following benefits: – Improved image quality– Reduced risk for dehydration effects– Rapid and reproducible preparation procedures– Conventional nsTEM procedures can be utilized– Reduced chromatic aberration originating from the non-elastic scattering of the incident beam in the sample This work was carried out jointly by the Centre for Image Analysis at Uppsala University and Swedish University of Agricultural Sciences, Vironova AB, and Delong Instruments, as part of the Eurostars miniTEM project, in which a low-voltage TEM with built in automated acquisition and analysis functionally is being developed.
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