Edge extraction by active defocusing.

A novel edge extraction method that employs an active defocusing technique is presented. The method is based on the principle that a Laplacian-of-Gaussian (LOG) operation can be approximated by a Difference-of-Gaussian (DOG) operation. While such an operation is usually done in digital image processing, it can also be very effective conducted in a combination of optical techniques and digital processing. In this edge extraction method, a focused image of an object in a scene is first acquired. The image of the scene is then slightly defocused by changing the focal length of the camera. A real time subtraction operation is applied to subtract the defocused image from the previously acquired image. It produces a residual image that emphasizes abrupt intensity variations. An objective evaluation, called an edge index, is performed on the resulting image. The amount of defocusing is carefully adjusted according to this measurement so that a desired edge image is generated. Boundaries of objects can then be obtained by further enhancement of the edge image. Since this edge detection method is an optical-based process aided by digital processing, it is fast and relatively inexpensive.     

Aberrations of chick eyes during normal growth and lens induction of myopia

Understanding the control of eye growth may lead to the prevention of nearsightedness (myopia). Chicks develop refractive errors in response to defocusing lenses by changing the rate of eye elongation. Changes in optical image quality and the optical signal in lens compensation are not understood. Monochromatic ocular aberrations were measured in 16 chicks that unilaterally developed myopia in response to unilateral goggles with −15D lenses and in 6 chicks developing naturally. There is no significant difference in higher-order root mean square aberrations (RMSA) between control eyes of the goggled birds and eyes of naturally developing chicks. Higher-order RMSA for a constant pupil size exponentially decreases in the chick eye with age more slowly than defocus. In the presence of a defocusing lens, the exponential decrease begins after day 2. In goggled eyes, asymmetric aberrations initially increase significantly, followed by an exponential decrease. Higher-order RMSA is significantly higher in goggled eyes than in controls. Equivalent blur, a new measure of image quality that accounts for increasing pupil size with age, exponentially decreases with age. In goggled eyes, this decrease also occurs after day 2. The fine optical structure, reflected in higher-order aberrations, may be important in understanding normal development and the development of myopia.     

A novel three-dimensional hybrid framework based on fishbone-like copper halide inorganic units

A novel inorganic-organic hybrid cuprous chloride, , has been hydrothermally synthesized and structurally characterized by the elemental analyses, IR spectrum, TG analysis and the single crystal X-ray diffraction. The structure of 1 exhibits a three-dimensional network built up from unusual fishbone-like copper(I) chloride ribbons bridged by linear isonicotinato ligands. Its luminescent property was also investigated.     

Quantitative Optical Microscopy: Measurement of Cellular Biophysical Features with a Standard Optical Microscope

We describe the use of a standard optical microscope to perform quantitative measurements of mass, volume, and density on cellular specimens through a combination of bright field and differential interference contrast imagery. Two primary approaches are presented: noninterferometric quantitative phase microscopy (NIQPM), to perform measurements of total cell mass and subcellular density distribution, and Hilbert transform differential interference contrast microscopy (HTDIC) to determine volume. NIQPM is based on a simplified model of wave propagation, termed the paraxial approximation, with three underlying assumptions: low numerical aperture (NA) illumination, weak scattering, and weak absorption of light by the specimen. Fortunately, unstained cellular specimens satisfy these assumptions and low NA illumination is easily achieved on commercial microscopes. HTDIC is used to obtain volumetric information from through-focus DIC imagery under high NA illumination conditions. High NA illumination enables enhanced sectioning of the specimen along the optical axis. Hilbert transform processing on the DIC image stacks greatly enhances edge detection algorithms for localization of the specimen borders in three dimensions by separating the gray values of the specimen intensity from those of the background. The primary advantages of NIQPM and HTDIC lay in their technological accessibility using “off-the-shelf” microscopes. There are two basic limitations of these methods: slow z-stack acquisition time on commercial scopes currently abrogates the investigation of phenomena faster than 1 frame/minute, and secondly, diffraction effects restrict the utility of NIQPM and HTDIC to objects from 0.2 up to 10 (NIQPM) and 20 (HTDIC) μm in diameter, respectively. Hence, the specimen and its associated time dynamics of interest must meet certain size and temporal constraints to enable the use of these methods. Excitingly, most fixed cellular specimens are readily investigated with these methods.     

Concepts in imaging and microscopy. Exploring biological structure and function with confocal microscopy

Confocal microscopy is providing new and exciting opportunities for imaging cell structure and physiology in thick biological specimens, in three dimensions, and in time. The utility of confocal microscopy relies on its fundamental capacity to reject out-of-focus light, thus providing sharp, high-contrast images of cells and subcellular structures within thick samples. Computer controlled focusing and image-capturing features allow for the collection of through-focus series of optical sections that may be used to reconstruct a volume of tissue, yielding information on the 3-D structure and relationships of cells. Tissues and cells may also be imaged in two or three spatial dimensions over time. The resultant digital data, which encode the image, are highly amenable to processing, manipulation and quantitative analyses. In conjunction with a growing variety of vital fluorescent probes, confocal microscopy is yielding new information about the spatiotemporal dynamics of cell morphology and physiology in living tissues and organisms. Here we use mammalian brain tissue to illustrate some of the ways in which multidimensional confocal fluorescence imaging can enhance studies of biological structure and function.     

Effect of focus on cell detection and recognition by the Cell Analyzer

The effect of defocusing on the quality of signals from live cells detected by an automated image cytometry device, the Cell Analyzer, was examined. The influence of these effects on the ability of this device to automatically locate cells plated into a tissue culture flask was then determined by measuring the performance of cell detection and recognition procedures as a function of focus setting. Acceptable limits for deviation from the optimal focus setting (as determined by microscope objective position) were found to be similar for both these procedures, ranging from 40 microns below to 25 microns above the optimal focus position. These limits were asymmetrical about ideal focus due to a pronounced asymmetry in the effects of positive and negative defocusing on the cell signal.     

Superficial Macromolecular Arrays on the Cell Wall of Spirillum putridiconchylium

Electron microscopy of the cell envelope of Spirillum putridiconchylium, using negatively stained, thin-sectioned, and replicated freeze-etched preparations, showed two superficial wall layers forming a complex macromolecular pattern on the external surface. The outer structured layer was a linear array of particles overlying an inner tetragonal array of larger subunits. They were associated in a very regular fashion, and the complex was bonded to the outer, pitted surface of the lipopolysaccharide tripartite layer of the cell wall. The relationship of the components of the two structured layers was resolved with the aid of optical diffraction, combined with image filtering and reconstruction and linear and rotary integration techniques. The outer structural layer consisted of spherical 1.5-nm units set in double lines determined by the size and arrangement of 6- by 3-nm inner structural layer subunits, which bore one outer structural layer unit on each outer corner. The total effect of this arrangement was a double-ridged linear structure that was evident in surface replicas and negatively stained fragments of the whole wall. The packing of these units was not square but skewed by 2 degrees off the perpendicular so that the "unit array" described by optical diffraction and linear integration appeared to be a deformed tetragon. The verity of the model was checked by using a photographically reduced image to produce an optical diffraction pattern for comparison with that of the actual layers. The correspondence was nearly perfect.     

Cryo-electron microscopy reveals macromolecular organization within biological liquid cyrstals seen in the polarizing microscope

A method is described for examining water dispersible biopolymers in the frozen, hydrated state by electron microscopy using the filamentous bacterial viruses Pf1 and fd as examples. The technique reveals liquid-crystalline textures that correlate well with polarizing microscopy of magnetically oriented specimens. At higher magnification the packing of the virus particle is revealed to a spatial resolution of better than 30 Å, thus linking directly with data from X-ray diffraction and optical microscopy. Electron diffraction confirms that the structure is preserved to high resolution (4 Å). The technique permits a detailed understanding of the processes involved in the orientation of these samples in a strong magnetic field and clarifies the long-range bi-axial properties of some fibres as seen by X-ray diffraction and optical microscopy.     

MICROTUBULE SURFACE LATTICE AND SUBUNIT STRUCTURE AND OBSERVATIONS ON REASSEMBLY

Neuronal microtubules have been reassembled from brain tissue homogenates and purified. In reassembly from purified preparations, one of the first structures formed was a flat sheet, consisting of up to 13 longitudinal filaments, which was identified as an incomplete microtubule wall. Electron micrographs of these flat sheets and intact microtubules were analyzed by optical diffraction, and the surface lattice on which the subunits are arranged was determined to be a 13 filament, 3-start helix. A similar, and probably identical, lattice was found for outer-doublet microtubules. Finally, a 2-D image of the structure and arrangement of the microtubule subunits was obtained by processing selected images with a computer filtering and averaging system. The 40 x 50 Å morphological subunit, which has previously been seen only as a globular particle and identified as the 55,000-dalton tubulin monomer, is seen in this higher resolution reconstructed image to be elongated, and split symmetrically by a longitudinal cleft into two lobes.     

Comparison of laser diffraction and image analysis for measurement of Streptomyces coelicolor cell clumps and pellets

Morphology is important in industrial processes involving filamentous organisms because it affects the mixing and mass transfer and can be linked to productivity. Image analysis provides detailed information about the morphology but, in practice, it is often laborious including both collection of high quality images and image processing. Laser diffraction is rapid and fully automatic and provides a volume-weighted distribution of the particle sizes. However, it is based on a number of assumptions that do not always apply to samples. We have evaluated laser diffraction to measure cell clumps and pellets of Streptomyces coelicolor compare to image analysis. Samples, taken five times during fed-batch cultivation, were analyzed by image analysis and laser diffraction. The volume-weighted size distribution was calculated for each sample. Laser diffraction and image analysis yielded similar size distributions, i.e. unimodal or bimodal distributions. Both techniques produced similar estimations of the population means, whereas the estimates of the standard deviations were generally higher using laser diffraction compared to image analysis. Therefore, laser diffraction measurements are high quality and the technique may be useful when rapid measurements of filamentous cell clumps and pellets are required.     

"Blind focusing": an objective method for avoiding errors of focus at the television texture analysis system (TAS).

The amount of light energy a particle absorbs does not depend upon correct focus. The change in the path of light rays brought about by defocusing causes absorbing areas to be registered as areas of higher transmittance than when in focus. Already wellknown in photometry, this effect is put to use by the "blind focus" method at the television texture analysis system (TAS, Leitz). Some chromophores within the object to be measured are compared to a preset value of transmittance, for example T = 0.40. Only the area representing the structures as dense or denser than the preset density are registered. If the structures are out of focus the size of the registered area is too low, since by defocusing, structures to be measured become pale and diffuse, the correct focus corresponds to the largest area to a preset value of transmittance.     

Effects of Thimerosal on Lipid Bilayers and Human Erythrocytes: An In Vitro Study

Thimerosal (THI, ethyl-mercury thiosalicylate) is added to vaccines as a preservative; as a consequence, infants may have been exposed to bolus doses of Hg that collectively added up to nominally 200 µg Hg during the first 6 months of life. While several studies report an association between THI-containing vaccines and neurological disorders, other studies do not support the causal relation between THI and autism. With the purpose to understand the molecular mechanisms of the toxic effect of THI it was assayed on human red cells and in bilayers built-up of dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylethanolamine (DMPE), classes of phospholipids found in the outer and inner monolayers of the human erythrocyte membrane, respectively. The capacity of THI to interact with DMPC and DMPE was determined by X-ray diffraction and differential scanning calorimetry, whereas intact human erythrocytes were observed by optical, defocusing and scanning electron microscopy. The experimental findings of this study demonstrated that THI interacted in a concentration-dependent manner with DMPC and DMPE bilayers, and in vitro interacted with erythrocytes inducing morphological changes. However, concentrations were considerable higher than those present in vaccines.     

Zero-loss energy filtering as improved imaging mode in cryoelectronmicroscopy of frozen-hydrated specimens

One of the remaining problems in attaining higher structural resolution with cryoelectronmicroscopy of frozen-hydrated specimens is the low contrast of micrographs taken close to the electron optical focus. By measuring electron energy loss spectra (EELS) of ice layers we show that a large fraction of incident electrons undergoes an inelastic electron-plasmon scattering process. Thus these electrons do not carry structural information of the protein but increase the background of the electron image and therefore reduce the contrast of the negative. Here we report the improvement in contrast gained by filtering out inelastically scattered electrons using an energy-filtered transmission electron microscope (EFTEM). This gain in contrast permits a dramatic decrease in defocusing values, resulting in improved structural resolution. In addition, the increased signal to noise ratio allows the recording of micrographs at a reduced electron dose. This should result in less damage to vitrified and unstained proteins and other beam-sensitive specimens.     

Analysis of three-dimensional cell imaging obtained with optical microscopy techniques based on defocusing

The properties of an optical microscope are analyzed and analytically evaluated with a simple and effective model in order to understand the true meaning, limitations, and real capabilities of a defocusing technique. Major emphasis is given to the applications related to microscopic objects of biological interest using fluorescence and absorption light microscopy. A procedure for three-dimensional viewing is analyzed and discussed.     

Analysis of three-dimensional cell imaging obtained with optical microscopy techniques based on defocusing

The properties of an optical microscope are analyzed and analytically evaluated with a simple and effective model in order to understand the true meaning, limitations, and real capabilities of a defocusing technique. Major emphasis is given to the applications related to microscopic objects of biological interest using fluorescence and absorption light microscopy. A procedure for three-dimensional viewing is analyzed and discussed.     

Image Quality Analysis of Eyes Undergoing LASER Refractive Surgery

Laser refractive surgery for myopia increases the eye’s higher-order wavefront aberrations (HOA’s). However, little is known about the impact of such optical degradation on post-operative image quality (IQ) of these eyes. This study determined the relation between HOA’s and IQ parameters (peak IQ, dioptric focus that maximized IQ and depth of focus) derived from psychophysical (logMAR acuity) and computational (logVSOTF) through-focus curves in 45 subjects (18 to 31yrs) before and 1-month after refractive surgery and in 40 age-matched emmetropic controls. Computationally derived peak IQ and its best focus were negatively correlated with the RMS deviation of all HOA’s (HORMS) (r≥-0.5; p<0.001 for all). Computational depth of focus was positively correlated with HORMS (r≥0.55; p<0.001 for all) and negatively correlated with peak IQ (r≥-0.8; p<0.001 for all). All IQ parameters related to logMAR acuity were poorly correlated with HORMS (r≤|0.16|; p>0.16 for all). Increase in HOA’s after refractive surgery is therefore associated with a decline in peak IQ and a persistence of this sub-standard IQ over a larger dioptric range, vis-à-vis, before surgery and in age-matched controls. This optical deterioration however does not appear to significantly alter psychophysical IQ, suggesting minimal impact of refractive surgery on the subject’s ability to resolve spatial details and their tolerance to blur.     

Regular structures in unit membranes. III. Further observations on the particulate component of the suckling rat ileum endocytic membrane complex

Further morphological observations on the particulate components decorating the lumenal surfaces of membranes of the endocytic complex of the epithelial cells of the suckling rat ileum are presented. The particles each measure approximately 7.5 nm across and give the appearance of the capital letter H in frontal view. They consist of the enzyme n-acetyl-beta-glucosaminidase (NAG). They are arranged in rows called "decorated strips" with the symmetrical lateral bars in register and spaced approximately 14.5 nm apart. Decorated strips lie side-by-side in the external (lumenal) surface of the membrane. They are parallel and sometimes spaced approximately 14.5 nm apart making an orthogonal lattice. The lateral spacing between the decorated strips under certain conditions is reduced and sometimes there is shear between the adjacent ones. Occasionally, shear is present within the decorated strips themselves, with slight displacement of the two sides of each H-shaped particle. A purified preparation of these membranes has been studied by electron microscopy using thin sectioning, negative stain, Markham translation and optical diffraction computer image reconstruction methods. The individual particles comprising the array can be seen in the membrane surface in profile view when dried in a pool of negative stain. They appear either triangular or diamond-shaped in such views. If triangular, they appear to consist of three domains at the corners of an equilateral triangle. One side of each triangular figure is parallel to the membrane surface but separated from it by a dense band of negative stain approximately 2 nm thick that runs along the surface of the membrane. Sometimes a fourth symmetrical domain is visible within this dense band, giving a diamond-shaped figure. This fourth domain connects the particle to the membrane. Thus, each H-shaped particle is a double structure, with each half in profile view appearing as a diamond figure of four symmetrical domains. Each H-shaped particle is believed to consist of either two or four molecules of NAG.     

Large‐depth‐of‐field full‐field optical angiography

A large‐depth‐of‐field full‐field optical angiography (LD‐FFOA) method is developed to expand the depth‐of‐field (DOF) using a contrast pyramid fusion algorithm (CPFA). The absorption intensity fluctuation modulation effect is utilized to obtain full‐field optical angiography (FFOA) images at different focus positions. The CPFA is used to process these FFOA images with different focuses. By selecting high‐contrast areas, the CPFA can highlight the characteristics and details of blood vessels to obtain LD‐FFOA images. In the optimal case of the proposed method, the DOF for FFOA is more than tripled using 10 differently focused FFOA images. Both the phantom and animal experimental results show that the LD‐FFOA resolves FFOA defocusing issues induced by surface and thickness inhomogeneities in biological samples. The proposed method can be potentially applied to practical biological experiments.      

Diffraction imaging of single particles and biomolecules

Theory predicts that with a very short and very intense X-ray pulse, the image of a single diffraction pattern may be recorded from a large macromolecule, a virus, or a nanocluster of proteins without the need for a crystal. A three-dimensional data set can be assembled from such images when many copies of the molecule are exposed to the beam one by one in random orientations. We outline a method for structure reconstruction from such a data set in which no independent information is available about the orientation of the images. The basic requirement for reconstruction and/or signal averaging is the ability to tell whether two noisy diffraction patterns represent the same view of the sample or two different views. With this knowledge, averaging techniques can be used to enhance the signal and extend the resolution in a redundant data set. Based on statistical properties of the diffraction pattern, we present an analytical solution to the classification problem. The solution connects the number of incident X-ray photons with the particle size and the achievable resolution. The results are surprising in that they show that classification can be done with less than one photon per pixel in the limiting resolution shell, assuming Poisson-type photon noise in the image. The results can also be used to provide criteria for improvements in other image classification procedures, e.g., those used in electron tomography or diffraction.