Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

An investigation into factors affecting electron density calibration for a megavoltage cone-beam CT system

There is a growing interest in the use of megavoltage cone-beam computed tomography (MV CBCT) data for radiotherapy treatment planning. To calculate accurate dose distributions, knowledge of the electron density (ED) of the tissues being irradiated is required. In the case of MV CBCT, it is necessary to determine a calibration-relating CT number to ED, utilizing the photon beam produced for MV CBCT. A number of different parameters can affect this calibration. This study was undertaken on the Siemens MV CBCT system, MVision, to evaluate the effect of the following parameters on the reconstructed CT pixel value to ED calibration: the number of monitor units (MUs) used (5, 8, 15 and 60 MUs), the image reconstruction filter (head and neck, and pelvis), reconstruction matrix size (256 by 256 and 512 by 512), and the addition of extra solid water surrounding the ED phantom. A Gammex electron density CT phantom containing EDs from 0.292 to 1.707 was imaged under each of these conditions. The linear relationship between MV CBCT pixel value and ED was demonstrated for all MU settings and over the range of EDs. Changes in MU number did not dramatically alter the MV CBCT ED calibration. The use of different reconstruction filters was found to affect the MV CBCT ED calibration, as was the addition of solid water surrounding the phantom. Dose distributions from treatment plans calculated with simulated image data from a 15 MU head and neck reconstruction filter MV CBCT image and a MV CBCT ED calibration curve from the image data parameters and a 15 MU pelvis reconstruction filter showed small and clinically insignificant differences. Thus, the use of a single MV CBCT ED calibration curve is unlikely to result in any clinical differences. However, to ensure minimal uncertainties in dose reporting, MV CBCT ED calibration measurements could be carried out using parameter-specific calibration measurements.

Infrared spectra of Mg-SiO smokes : comparison with analytical electron microscopy studies

An important component of current models for interstellar and circumstellar evolution is the infrared (IR)spectral data collected from stellar outflows around oxygen-rich stars and from the general interstellar medium [1]. IR spectra from these celestial bodies are usually interpreted as showing the general properties of sub-micron sized silicate grains [2]. Two major features at 10 and 20 microns are reasonably attributed to amorphous olivine or pyroxene (e.g. Mg2Si04 or MgSi03) on the basis of comparisons with natural standards and vapor condensed silicates [3-6]. In an attempt to define crystallisation rates for spectrally amorphous condensates, Nuth and Donn [5] annealed experimentally produced amorphous magnesium silicate smokes at 1000K. On analysing these smokes at various annealing times, Nuth and Donn [5] showed that changes in crystallinity measured by bulk X-ray diffraction occured at longer annealing times (days) than changes measured by IR spectra (a few hours). To better define the onset of crystallinity in these magnesium silicates, we have examined each annealed product using a JEOL 1OOCX analytical electron microscope (AEM). In addition, the development of chemical diversity with annealing has been monitored using energy dispersive spectroscopy of individual grains from areas <20nm in diameter. Furthermore, the crystallisation kinetics of these smokes under ambient, room temperature conditions have been examined using bulk and fourier transform infrared (FTIR)spectra.

Analytical electron microscopy of Mg-SiO smokes; a comparison with infrared and XRD studies

Experimentally obtained Mg.SiO smokes were studied by analytical electron microscopy using the same samples that had been previously characterized by repeated infrared spectroscopy. Analytical electron microscopy shows that unannealed smokes contain some degree of microcrystallinity which increases with increased annealing for up to 30 hr. An SiO2 polymorph (tridymite) and MgO may form contemporaneously as a result of growth of forsterite (Mg2SiO4) microcrystallites in the initially nonstoichiometric smokes. After 4 hr annealing, forsterite and tridymite react to enstatite (MgSiO3). We suggest that infrared spectroscopy and X-ray diffraction analysis should be complemented by detailed analytical electron microscopy to detect budding crystallinity in vapor phase condensates.

Electron petrography of fine-grained matrix in the Karoonda C4 carbonaceous chondrite

The study of matrices of rare Type 4 carbonaceous chondrites can reveal important information on parent body rnetamorp~ic processes and provide a comparison with processes on parent bodies of ordinary chc-idrites. Reflectance spectra (Tholen, 1984) from the two largest asteroids in the asteroid belt, Ceres and Pallas, suggest that they may be metamorphosed carbonaceous chondrites. These two asteroids constitute - onethird of the mass in the asteroid belt implying that type 4-6 carbonaceous chondrites are poorly represented in the meteorite collection and may be of considerable importance. The matrix of the C4 chondrite Karoonda has been investigated using a JEOL 2000FX analytical electron microscope (AEM) with an attached Tracor-Northem TN5500 energy dispersive spectrometer (EDS). In previous studies (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969), the petrography of the Karoonda matrix has been described as consisting largely of coarse-grained (50-200 urn in size) olivine and plagioclase (20-100 um in size), associated with micrometer sized magnetite and rare sulphides. AEM observations on matrix show that in addition to these large grains, there is a significant fraction (10 vol%) of interstitial fine grained phases « 5 urn). The mineralogy of these fine-grained phases differs in some respects from that of the coarser-grained matrix identified by optical and SEM techniques (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969). I~ particular crystals of two compositionally distinct pyroxenes « 2 urn in size) have been identified which have not been previously observed in Karoonda by other analytical techniques. Thin film microanalyses (Mackinnon et al., 1986) of these two pyroxenes indicate compositions consistent with augite and low-Ca pyroxene (- Fs27). Fine-grained anhedral olivine « 2 urn size) is the most abundant phase with composition -Fa29' This composition is essentially indistinguishable from that determined for coarser-grained matrix olivines using an electron microprobe (Scott and Taylor, 1985; Fitzgerald, 1979; Van Schmus, 1969). All olivines are associated with subhedral magnetites « 1 urn size) which contain significant Cr (- 2%) and Al (- 1%) as was also noted for larger sized Karoonda magnetites by Delaney et al. (1985). It has recently been suggested (Burgess et al., 1987) on the basis of sulphur release profiles for S-isotope analyses of Karoonda that CaS04 (anhydrite) may be present. However, no sulphate phase has, as yet, been identified in the matrix of Karoonda. Low magnification contrast images suggest that Karoonda may have a significant porosity within the fine-grained matrix fraction. Most crystals are anhedral and do not show evidence for significant compaction. Individual grains often show single point contact with other grains which result in abundant intergranular voids. These voids frequently contain epoxy which was used as part of the specimen preparation procedure due to the friable nature of the bulk sample.

Analytical electron microscopy of fine-grained phases in primitive interplanetary dust particles and carbonaceous chondrites

In order to describe the total mineralogical diversity within primitive extraterrestrial materials, individual interplanetary dust particles (IDPs) collected from the stratosphere as part of the JSC Cosmic Dust Curatorial Program were analyzed using a var ...