Showing papers in "Journal of Microscopy in 2002"

Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object

Abstract: We demonstrate simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object. Subject to the assumptions explicitly stated in the derivation, the algorithm solves the twin-image problem of in-line holography and is capable of analysing data obtained using X-ray microscopy, electron microscopy, neutron microscopy or visible-light microscopy, especially as they relate to defocus and point projection methods. Our simple, robust, non-iterative and computationally efficient method is applied to data obtained using an X-ray phase contrast ultramicroscope.

New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope.

Abstract: We first obtain a frequency-space equation of diffraction tomography for the electric field vector, within the first-order Born approximation, using a simplified formalism resulting from using three-dimensional spatial frequencies and replacing outgoing waves by linear combinations of homogeneous plane waves. A coherent optical diffraction tomographic microscope is then described, in which a sample is successively illuminated by a series of plane waves having different directions, each scattered wave is recorded by phase-shifting interferometry, and the object is then reconstructed from these recorded waves. The measurement process in this device is analysed taking into account the illuminating wave, the wave scattered by the sample, the reference wave, and the phase relations between these waves. This analysis yields appropriate equations that take into account the characteristics of the reference wave and compensate random phase shifts. It makes it possible to obtain a high-resolution three-dimensional frequency representation in full conformity with theory. The experimentally obtained representations show index and absorptivity with a resolution limit of about a quarter of a wavelength, and have a depth of field of about 40 microm.

Freeze substitution of high-pressure frozen samples: the visibility of biological membranes is improved when the substitution medium contains water.

Abstract: Biological membranes are often poorly visible with the electron microscope after high-pressure freezing and freeze-substitution. The water content of the sample and of the substitution medium is one factor among others that strongly influences membrane visibility. In order to investigate this effect, high-pressure frozen yeast cells, rat-pancreas tissue and arthropod tissue were freeze-substituted with and without adding water to the substitution medium. The visibility of the biological membranes was generally improved if the substitution medium contained 1-5% water. The effect was especially pronounced in yeast cells, where membrane visibility was poor after freeze-substitution with water-free medium but good after addition of 5% water to the substitution medium.

Automatic fluorescent tag detection in 3D with super‐resolution: application to the analysis of chromosome movement

Abstract: In this paper, we describe an algorithmic framework for the automatic detection of diffraction-limited fluorescent spots in 3D optical images at a separation below the Rayleigh limit, i.e. with super-resolution. We demonstrate the potential of super-resolution detection by tracking fluorescently tagged chromosomes during mitosis in budding yeast. Our biological objective is to identify and analyse the proteins responsible for the generation of tensile force during chromosome segregation. Dynamic measurements in living cells are made possible by green fluorescent protein (GFP)-tagging chromosomes and spindle pole bodies to generate cells carrying four fluorescent spots, and observe the motion of the spots over time using 3D-fluorescence microscopy. The central problem in spot detection arises with the partial or complete overlap of spots when tagged objects are separated by distances below the resolution of the optics. To detect multiple spots under these conditions, a set of candidate mixture models is built, and the best candidate is selected from the set based on chi2-statistics of the residuals in least-square fits of the models to the image data. Even with images having a signal-to-noise ratio (SNR) as low as 5-10, we are able to increase the resolution two-fold below the Rayleigh limit. In images with a SNR of 5-10, the accuracy with which isolated tags can be localized is less than 5 nm. For two tags separated by less than the Rayleigh limit, the localization accuracy is found to be between 10 and 20 nm, depending on the effective point-to-point distance. This indicates the intimate relationship between resolution and localization accuracy.

Two-photon fluorescence absorption and emission spectra of dyes relevant for cell imaging

Abstract: Summary Two-photon absorption and emission spectra for fluorophores relevant in cell imaging were measured using a 45 fs Ti:sapphire laser, a continuously tuneable optical parametric amplifier for the excitation range 580 ‐1150 nm and an optical multichannel analyser. The measurements included DNA stains, fluorescent dyes coupled to antibodies as well as organelle trackers, e.g. Alexa and Bodipy dyes, Cy2, Cy3, DAPI, Hoechst 33342, propidium iodide, FITC and rhodamine. In accordance with the two-photon excitation theory, the majority of the investigated fluorochromes did not reveal significant discrepancies between the two-photon and the one-photon emission spectra. However, a blue-shift of the absorption maxima ranging from a few nanometres up to considerably differing courses of the spectrum was found for most fluorochromes. The potential of non-linear laser scanning fluorescence microscopy is demonstrated here by visualizing multiple intracellular structures in living cells. Combined with 3D reconstruction techniques, this approach gives a deeper insight into the spatial relationships of subcellular organelles.

Fluorescence lifetime imaging in scanning microscopes: Acquisition speed, photon economy and lifetime resolution

Abstract: In this paper a detailed discussion is presented of the factors that affect the fluorescence lifetime imaging performance of a scanning microscope equipped with a single photon counting based, two- to eight-channel, time-gated detection system. In particular we discuss the sensitivity, lifetime resolution, acquisition speed, and the shortest lifetimes that can be measured. Detection systems equipped with four to eight time-gates are significantly more sensitive than the two time-gate system. Only minor sensitivity differences were found between systems with four or more time-gates. Experiments confirm that the lifetime resolution is dominated by photon statistics. The time response of the detector determines the shortest lifetimes that can be resolved; about 25 ps for fast MCP-PMTs and 300-400 ps for other detectors. The maximum count rate of fast MCP-PMTs, however, is 10-100 times lower than that of fast PMTs. Therefore, the acquisition speed with MCP-PMT based systems is limited. With a fast PMT operated close to its maximum count rate we were able to record a fluorescence lifetime image of a beating myocyte in less than one second.

The smooth fractionator.

Abstract: Summary A modification of the general fractionator sampling technique called the smooth fractionator is presented. It may be used in almost every situation in which sampling is performed from distinct items that are uniquely defined, often they are physically separated items or clusters like pieces, blocks, slabs, sections, etc. To each item is associated a ‘guesstimate’ or an associated variable with a more-or-less close – and possibly biased − relationship to the content of the item. The smooth fractionator is systematic sampling among the items arranged according to the guesstimates in a unique, symmetric sequence with one peak and minimal jumps. The smooth fractionator is both very simple to implement and so efficient that it should probably always be used unless the natural sequence of the sampling items is equally smooth. So far, there is no theory for the prediction of the efficiency of smooth fractionator designs in general, and their properties are therefore illustrated with a range of real and simulated examples. At the cost of a slightly more elaborate sampling scheme, it is, however, always possible to obtain an unbiased estimate of the real precision and of some of the variance components. The only real practical problem for always obtaining a high precision with the smooth fractionator is specimen inhomogeneity, but that is detectable at almost no extra cost. With careful designs and for sample sizes of about 10, the sampling variation for the primary, smooth fractionator sampling step may in practice often be small enough to be ignored.

Quantitative phase‐amplitude microscopy I: optical microscopy

Abstract: In this paper, the application of a new optical microscopy method (quantitative phase-amplitude microscopy) to biological imaging is explored, and the issue of resolution and image quality is examined. The paper begins by presenting a theoretical analysis of the method using the optical transfer function formalism of Streibl (1985). The effect of coherence on the formation of the phase image is explored, and it is shown that the resolution of the method is not compromised over that of a conventional bright-field image. It is shown that the signal-to-noise ratio of the phase recovery, however, does depend on the degree of coherence in the illumination. Streibl (1985) notes that partially coherent image formation is a non-linear process because of the intermingling of amplitude and phase information. The work presented here shows that the quantitative phase-amplitude microscopy method acts to linearize the image formation process, and that the phase and amplitude information is properly described using a transfer function analysis. The theoretical conclusions are tested experimentally using an optical microscope and the theoretical deductions are confirmed. Samples for microscopy influence both the phase and amplitude of the light wave and it is demonstrated that the new phase recovery method can separate the amplitude and phase information, something not possible using traditional phase microscopy. In the case of a coherent wave, knowledge of the phase and amplitude constitutes complete information that can be used to emulate other forms of microscopy. This capacity is demonstrated by recovering the phase of a sample and using the data to emulate a differential interference contrast image.

Adaptive correction of depth-induced aberrations in multiphoton scanning microscopy using a deformable mirror

Abstract: Summary We demonstrate adaptive aberration correction for depthinduced spherical aberration in a multiphoton scanning microscope with a micromachined deformable mirror. Correction was made using a genetic learning algorithm with two-photon fluorescence intensity feedback to determine the desired shape for an adaptive mirror. For a 40 × /0.6 NA long working distance objective, the axial scanning range was increased from 150 mm to 600 mm.

Nanosecond fluorescence resonance energy transfer‐fluorescence lifetime imaging microscopy to localize the protein interactions in a single living cell

Abstract: Visualizing and quantifying protein-protein interactions is a recent trend in biomedical imaging. The current advances in fluorescence microscopy, coupled with the development of new fluorescent probes such as green fluorescent proteins, allow fluorescence resonance energy transfer (FRET) to be used to study protein interactions in living specimens. Intensity-based FRET microscopy is limited by spectral bleed-through and fluorophore concentration. Fluorescence lifetime imaging (FLIM) microscopy and lifetime measurements are independent of change in fluorophore concentration or excitation intensity, and the combination of FRET and FLIM provides high spatial (nanometre) and temporal (nanoseconds) resolution. Because only the donor fluorophore lifetime is measured, spectral bleed-through is not an issue in FRET-FLIM imaging. In this paper we describe the development of a nanosecond FRET-FLIM microscopy instrumentation to acquire the time-resolved images of donor in the presence and the absence of the acceptor. Software was developed to process the acquired images for single and double exponential decays. Measurement of donor lifetime in two different conditions allowed us to calculate accurately the distance between the interacting proteins. We used this approach to quantify the dimerization of the transcription factor CAATT/enhancer binding protein alpha in living pituitary cells. The one- and two-component analysis of the donor molecule lifetime in the presence of acceptor demonstrates the distance distribution between interacting proteins.

Stereological length estimation using spherical probes

Abstract: Lineal structures in biological tissue support a wide variety of physiological functions, including membrane stabilization, vascular perfusion, and cell-to-cell communication. In 1953, Smith and Guttman demonstrated a stereological method to estimate the total length density (Lv) of linear objects based on random intersections with a two-dimensional sampling probe. Several methods have been developed to ensure the required isotropy of object-probe intersections, including isotropic-uniform-random (IUR) sections, vertical-uniform-random (VUR) slices, and isotropic virtual planes. The disadvantages of these methods are the requirements for inconvenient section orientations (IUR, VUR) or complex counting rules at multiple focal planes (isotropic virtual planes). To overcome these limitations we report a convenient and straightforward approach to estimate Lv and total length, L, for linear objects on tissue sections cut at any arbitrary orientation. The approach presented here uses spherical probes that are inherently isotropic, combined with unbiased fractionator sampling, to demonstrate total L estimation for thin nerve fibres in dorsal hippocampus of the mouse brain.

Autofluorescence of living cells

Abstract: We have investigated the autofluorescence of viable mammalian cells (DU-145 and V79) with a confocal laser scanning microscope equipped with a UV laser. Our aim was to investigate the autofluorescence dependence on different treatments in mitochondria and lysosomes by using different reagents and to improve the confocal laser scanning microscope image quality by deconvolution. The following conclusions were drawn from the results: (1) not all of the autofluorescence comes from mitochondria; (2) one can significantly affect the signal which comes from the mitochondria; (3) the other organelles involved are probably lysosomes; (4) it is harder to affect the autofluorescence signal from the lysosomes than that from the mitochondria, and (5) deconvoluted autofluorescence images provide better information than undeconvoluted ones.

Quantitative X-ray Projection Microscopy: Phase-Contrast and Multi-spectral imaging

Abstract: Summary We outline a new approach to X-ray projection microscopy in a scanning electron microscope (SEM), which exploits phase contrast to boost the quality and information content of images. These developments have been made possible by the combination of a high-brightness field-emission gun (FEG)-based SEM, direct detection CCD technology and new phase retrieval algorithms. Using this approach we have been able to obtain spatial resolution of < 0.2 µm and have demonstrated novel features such as: (i) phase-contrast enhanced visibility of high spatial frequency image features (e.g. edges and boundaries) over a wide energy range; (ii) energy-resolved imaging to simultaneously produce multiple quasi-monochromatic images using broad-band polychromatic illumination; (iii) easy implementation of microtomography; (iv) rapid and robust phase/amplitude-retrieval algorithms to enable new real-time and quantitative modes of microscopic imaging. These algorithms can also be applied successfully to recover object–plane information from intermediate-field images, unlocking the potentially greater contrast and resolution of the intermediate-field regime. Widespread applications are envisaged for fields such as materials science, biological and biomedical research and microelectronics device inspection. Some illustrative examples are presented. The quantitative methods described here are also very relevant to projection microscopy using other sources of radiation, such as visible light and electrons.

Extracting twins from orientation imaging microscopy scan data.

Abstract: Automated electron backscatter diffraction or orientation imaging microscopy (OIM) provides spatially specific measurements of crystallographic orientation. These measurements are typically collected on regular grids. By inspecting the misorientation between neighbouring measurements on the grid, potential twin boundaries can be identified. If the misorientation is within some given tolerance of a specified twin misorientation, the boundary separating the two measurements may be identified as a potential twin boundary. In addition, for a coherent twin, the twinning planes must be coincident with the grain boundary plane. As OIM scans are inherently two-dimensional, the scan data provide only limited information on the boundary plane. Thus, it is not possible to ascertain definitively whether the twinning planes are coincident with the boundary plane. Nonetheless, the alignment of the surface traces of the twinning planes with the trace of the boundary provides a partial indication of coincidence. An automated approach has been developed that allows data concerning both twin criterion to be extracted from OIM scans. Application of the methodology to deformed zirconium suggests that the twinning planes remain coherent during deformation. The methodology was also used to improve grain size distributions measured by OIM. These results more closely match those obtained by conventional metallography.

High-resolution scanning electron microscopy of immunogold-labelled cells by the use of thin plasma coating of osmium.

Abstract: Summary The feasibility of plasma coating of a thin osmium layer for high-resolution immuno-scanning electron microscopy of cell surfaces was tested, using Drosophila embryonic motor neurones as a model system. The neuro-muscular preparations were fixed with formaldehyde and labelled with a neurone-specific antibody and 10 or 5 nm colloidal gold-conjugated secondary antibodies. The specimens were post-fixed with osmium tetroxide and freeze-dried. Then they were coated with a 1–2 nm thick layer of osmium using a hollow cathode plasma coater. The thin and continuous coating of amorphous osmium gave good signals of gold particles and fine surface structures of neurites in backscattered electron images simultaneously. This method makes it possible to visualize the antigen distribution and the three-dimensionally complex surface structures of cellular processes with a resolution of several nanometres.

Generalized approach for accelerated maximum likelihood based image restoration applied to three-dimensional fluorescence microscopy.

Abstract: For deconvolution applications in three-dimensional microscopy we derived and implemented a generic, accelerated maximum likelihood image restoration algorithm. A conjugate gradient iteration scheme was used considering either Gaussian or Poisson noise models. Poisson models are better suited to low intensity fluorescent image data; typically, they show smaller restoration errors and smoother results. For the regularization, we modified the standard Tikhonov method. However, the generic design of the algorithm allows for more regularization approaches. The Hessian matrix of the restoration functional was used to determine the step size. We compared restoration error and convergence behaviour between the classical line-search and the Hessian matrix method. Under typical working conditions, the restoration error did not increase over that of the line-search and the speed of convergence did not significantly decrease allowing for a twofold increase in processing speed. To determine the regularization parameter, we modified the generalized cross-validation method. Tests that were done on both simulated and experimental fluorescence wide-field data show reliable results.

Relative labelling index: a novel stereological approach to test for non‐random immunogold labelling of organelles and membranes on transmission electron microscopy thin sections

Abstract: Summary Simple and efficient protocols for quantifying immunogold labelling of antigens localized in different cellular compartments (organelles or membranes) and statistically evaluating resulting labelling distributions are presented. Two key questions are addressed: (a) is compartmental labelling within an experimental group (e.g. control or treated) consistent with a random distribution? and (b) do labelling patterns vary between groups (e.g. control vs. treated)? Protocols rely on random sampling of cells and compartments. Numbers of gold particles lying on specified organelle compartments provide an observed frequency distribution. By superimposing test-point lattices on cell profiles, design-based stereology is used to determine numbers of points lying on those same compartments. Random points hit compartments with probabilities determined by their relative sizes and so provide a convenient internal standard, namely, the expected distribution if labelling is purely random. By applying test-line lattices, and counting sites at which these intersect membrane traces, analogous procedures provide observed and expected labelling distributions for different classes of membranes. Dividing observed golds by expected golds provides a relative labelling index (RLI) for each compartment and, for random labelling, the predicted RLI = 1. In contrast to labelling densities of organelles (golds µm−2) or membranes (golds µm−1), RLI values are estimated without needing to know lattice constants (area per point or length per intersection) or specimen magnification. Gold distributions within a group are compared by chi-squared analysis to test if the observed distribution differs significantly from random and, if it is non-random, to identify compartments which are preferentially labelled (RLI > 1). Contingency table analysis allows labelling distributions in different groups of cells to be compared. Protocols are described and illustrated using worked specimen examples and real data.

Comparative evaluation of retrospective shading correction methods

Abstract: Because of the inherent imperfections of the image formation process, microscopical images are often corrupted by spurious intensity variations. This phenomenon, known as shading or intensity inhomogeneity, may have an adverse affect on automatic image processing, such as segmentation and registration. Shading correction methods may be prospective or retrospective. The former require an acquisition protocol tuned to shading correction, whereas the latter can be applied to any image, because they only use the information already present in an image. Nine retrospective shading correction methods were implemented, evaluated and compared on three sets of differently structured synthetic shaded and shading-free images and on three sets of real microscopical images acquired by different acquisition set-ups. The performance of a method was expressed quantitatively by the coefficient of joint variations between two different object classes. The results show that all methods, except the entropy minimization method, work well for certain images, but perform poorly for others. The entropy minimization method outperforms the other methods in terms of reduction of true intensity variations and preservation of intensity characteristics of shading-free images. The strength of the entropy minimization method is especially apparent when applied to images containing large-scale objects.

SMART – a program to measure SEM resolution and imaging performance

Abstract: It is important to be able to measure the parameters, such as spatial resolution, astigmastism, signal-to-noise ratio, and drift and instability, that characterize the performance of a scanning electron microscope. These quantities can be determined most reliably by a Fourier analysis of digital micrographs from the instrument, recorded under conditions of interest. A program designed to implement all of the necessary steps in an automated manner has been developed as a 'macro' for the popular, and freely available, NIH Image and SCION Image programs.

Nonlinear bio-photonic crystal effects revealed with multimodal nonlinear microscopy.

Abstract: Highly optically active nonlinear bio-photonic crystalline and semicrystalline structures in living cells were studied by a novel multimodal nonlinear microscopy. Numerous biological structures, including stacked membranes and aligned protein structures are highly organized on a nanoscale and have been found to exhibit strong optical activities through second-harmonic generation (SHG) interactions, behaving similarly to man-made nonlinear photonic crystals. The microscopic technology used in this study is based on a combination of different imaging modes including SHG, third-harmonic generation, and multiphoton-induced fluorescence. With no energy release during harmonic generation processes, the nonlinear-photonic-crystal-like SHG activity is useful for investigating the dynamics of structure-function relationships at subcellular levels and is ideal for studying living cells, as minimal or no preparation is required.

Comparison of the axial resolution of practical nipkow-disk confocal fluorescence microscopy with that of multifocal multiphoton microscopy: theory and experiment

Abstract: Summary We compare the axial sectioning capability of multifocal confocal and multifocal multiphoton microscopy in theory and in experiment, with particular emphasis on the background arising from the cross-talk between adjacent imaging channels. We demonstrate that a time-multiplexed non-linear excitation microscope exhibits significantly less background and therefore a superior axial resolution as compared to a multifocal single-photon confocal system. The background becomes irrelevant for thin (< 15 µm) and sparse fluorescent samples, in which case the confocal parallelized system exhibits similar or slightly better sectioning behaviour due to its shorter excitation wavelength. Theoretical and experimental axial responses of practically implemented microscopes are given.

Topographic contrast of partially wetting water droplets in environmental scanning electron microscopy.

Abstract: Partially wetting water droplets with sizes smaller than the capillary length acquire a distinct spherical cap shape controlled by the equilibrium contact angle, which is specific for different substrates and conditions. Images of such droplets in an environmental scanning electron microscope (ESEM) show strong topographic contrast. This contrast across the droplets can be analysed within a simple theoretical model, as the droplet sides are inclined smooth surfaces. Very small droplets have ESEM intensity profiles which deviate from this topographic model. Such deviations indicate that other sources of electron signal may be important for such droplets, and also demonstrate the limits of the analytical model. For droplets sufficiently large that they lie within the range of the topographic contrast model, values of contact angles on different substrates can be deduced. These are found to agree with independent direct measurements, as well as the results given in the literature. The possibilities of using this technique to analyse physical properties of different substrates are discussed.

Phase evolution in cholesterol/DPPC monolayers: atomic force microscopy and near field scanning optical microscopy studies.

Abstract: A combination of atomic force microscopy (AFM) and near field scanning optical microscopy has been used to study domain formation in dipalmitoylphosphatidylcholine (DPPC)/cholesterol monolayers with cholesterol concentrations ranging from 0 to 50%. The results show a clear evolution from a mixture of liquid expanded and liquid condensed phases for cholesterol concentrations < 10% to a mixture of liquid expanded and two cholesterol-containing phases at intermediate concentrations, and finally to a single homogeneous liquid ordered phase for 33% cholesterol. Mixtures of the various phases are clearly identified by height differences in AFM and in some cases by fluorescence imaging for samples containing 0.5% BODIPY dye, which localizes preferentially in the more fluid phase. Note that fluorescence imaging, at least with the dye used here, is unable to distinguish between the cholesterol-rich and cholesterol-poor phases detected at intermediate cholesterol concentrations. The combination of fluorescence and AFM imaging provides a more complete picture of the phase evolution for cholesterol/DPPC monolayers than could be obtained by either technique alone, and presents substantial advantages over conventional fluorescence microscopy in that submicrometre-sized domains can be readily detected.

Automated high-throughput electron tomography by pre-calibration of image shifts.

Abstract: Electron tomography is a versatile method for obtaining three-dimensional (3D) images with transmission electron microscopy. The technique is suitable to investigate cell organelles and tissue sections (100-500 nm thick) with 4-20 nm resolution. 3D reconstructions are obtained by processing a series of images acquired with the samples tilted over different angles. While tilting the sample, image shifts and defocus changes of several microm can occur. The current generation of automated acquisition software detects and corrects for these changes with a procedure that incorporates switching the electron optical magnification. We developed a novel method for data collection based on the measurement of shifts prior to data acquisition, which results in a five-fold increase in speed, enabling the acquisition of 151 images in less than 20 min. The method will enhance the quality of a tilt series by minimizing the amount of required focus-change compensation by aligning the optical axis to the tilt axis of the specimen stage. The alignment is achieved by invoking an amount of image shift as deduced from the mathematical model describing the effect of specimen tilt. As examples for application in biological and materials sciences 3D reconstructions of a mitochondrion and a zeolite crystal are presented.

Multi-field 3D scanning light microscopy of early embryogenesis.

Abstract: A computer-controlled microscopy system was devised to allow the observation of avian embryo development over an extended time period. Parallel experiments, as well as extended specimen volumes, can be recorded at cellular resolution using a three-dimensional scanning procedure. The resulting large set of data is processed automatically into registered, focal- and positional-drift corrected mosaic images, assembled as montages of adjacent microscopic fields. The configuration of the incubator and a sterile embryo chamber prevents condensation of the humidified culturing atmosphere in the optical path and is compatible with both differential interference contrast and epifluorescence optics. As a demonstration, recordings are presented showing the large-scale remodelling of the embryonic primordial vascular structure.

A dual path programmable array microscope (PAM): simultaneous acquisition of conjugate and non-conjugate images.

Abstract: A programmable array microscope (PAM) incorporates a spatial light modulator (SLM) placed in the primary image plane of a widefield microscope, where it is used to define patterns of illumination and/or detection. We describe the characteristics of a special type of PAM collecting two images simultaneously. The conjugate image (Ic) is formed by light originating from the object plane and returning along the optical path of the illumination light. The non-conjugate image (Inc) receives light from only those regions of the SLM that are not used for illuminating the sample. The dual-signal PAM provides much more time-efficient excitation than the confocal laser scanning microscope (CLSM) and greater utilization of the available emission light. It has superior noise characteristics in comparison to single-sided instruments. The axial responses of the system under a variety of conditions were measured and the behaviour of the novel Inc image characterized. As in systems in which only Ic images are collected (Nipkow-disc microscopes, and previously characterized PAMs), the axial response to thin fluorescent films showed a sharpening of the axial response as the unit cell of the repetitive patterns decreased in size. The dual-signal PAM can be adapted to a wide range of data analysis and collection strategies. We investigated systematically the effects of patterns and unit cell dimensions on the axial response. Sufficiently sparse patterns lead to an Ic image formed by the superposition of the many parallel beams, each of which is equivalent to the single scanning spot of a CLSM. The sectioning capabilities of the system, as given by its axial responses, were similar for a given scan pattern and for processed pseudorandom sequence (PRS) scans with the same size of the unit cell. For the PRS scans, optical sectioning was achieved by a subtraction of an Inc image or, alternatively, a scaled widefield image from the Ic image. Based on the comparative noise levels of the two methods, the non-conjugate subtraction was significantly superior. A point spread function for Ic and Inc was simulated and properties of the optical transfer functions (OTFs) were compared. Simulations of the OTF in non-conjugate imaging did not suffer from the missing cone problem, enabling a high quality deconvolution of the non-conjugate side alone. We also investigated the properties of images obtained by subjecting the Ic and Inc data to a combined maximum likelihood deconvolution.

Deconvolution improves colocalization analysis of multiple fluorochromes in 3D confocal data sets more than filtering techniques

Abstract: Background and noise impair image quality by affecting resolution and obscuring image detail in the low intensity range. Because background levels in unprocessed confocal images are frequently at about 30% maximum intensity, colocalization analysis, a typical segmentation process, is limited to high intensity signal and prone to noise-induced, false-positive events. This makes suppression or removal of background crucial for this kind of image analysis. This paper examines the effects of median filtering and deconvolution, two image-processing techniques enhancing the signal-to-noise ratio (SNR), on the results of colocalization analysis in confocal data sets of biological specimens. The data show that median filtering can improve the SNR by a factor of 2. The technique eliminates noise-induced colocalization events successfully. However, because filtering recovers voxel values from the local neighbourhood false-negative ('dissipation' of signal intensity below threshold value) as well as false-positive ('fusion' of noise with low intensity signal resulting in above threshold intensities), results can be generated. In addition, filtering involves the convolution of an image with a kernel, a procedure that inherently impairs resolution. Image restoration by deconvolution avoids both of these disadvantages. Such routines calculate a model of the object considering various parameters that impair image formation and are able to suppress background down to very low levels (< 10% maximum intensity, resulting in a SNR improved by a factor 3 as compared to raw images). This makes additional objects in the low intensity but high frequency range available to analysis. In addition, removal of noise and distortions induced by the optical system results in improved resolution, which is of critical importance in cases involving objects of near resolution size. The technique is, however, sensitive to overestimation of the background level. In conclusion, colocalization analysis will be improved by deconvolution more than by filtering. This applies especially to specimens characterized by small object size and/or low intensities.

An integrated approach to the study of living cells by atomic force microscopy

Abstract: We describe a technique for studying living cells with the atomic force microscope (AFM) in tapping mode using a thermostated, controlled-environment culture system. We also describe the integration of the AFM with bright field, epifluorescence and surface interference microscopy, achieving the highest level of integration for the AFM thus far described. We succeeded in the continuous, longterm imaging of relatively flat but very fragile cytoplasmic regions of COS cells at a lateral resolution of about 70 nm and a vertical resolution of about 3 nm. In addition, we demonstrate the applicability of our technology for continuous force volume imaging of cultured vertebrate cells. The hybrid instrument we describe can be used to collect simultaneously a diverse variety of physical, chemical and morphological data on living vertebrate cells. The integration of light microscopy with AFM and steady-state culture methods for vertebrate cells represents a new approach for studies in cell biology and physiology.

Lamellar subcomponents of the cuticular cell membrane complex of mammalian keratin fibres show friction and hardness contrast by AFM.

Abstract: There is a substantial body of information indicating that 18-methyleicosanoic acid (18-MEA) is covalently linked to the outer surface of all mammalian keratin fibres and also forms the outer β-layer of the cuticular cell membrane complex (CCMC) which separates the cuticle cells from each other. Low cohesive forces are expected between the lipid-containing outer β-layer and the δ-layer of the CCMC, thus providing a weak point for cuticular delamination and presenting a fresh layer of 18-MEA to the newly exposed surface. We have used lateral force microscopy and force modulation atomic force microscopy (AFM) to examine human hair fibres in which the non-covalently linked fatty acids have been removed. Examination of the lateral force images of new cuticle surfaces revealed by the attrition of overlying cuticle layers showed three separate zones of clearly defined frictional contrast. These are thought to correspond with the δ-layer, the proteinaceous epicuticle and outer β-layers of the CCMC. The δ-layer was found to have a thickness of 16 nm (SD = 1 nm, n = 25), comparable to the 18.0 nm thickness measured from transverse crosssections of fibres with transmission electron microscopy. Force modulation AFM showed that the outer β-layer was softer than the epicuticle and the δ-layer. The frictional contrast was removed following treatment with methanolic KOH (0.1 mol dm−3) at 25 °C for 30 min, suggesting the hydrolysis of the thioester linkage and removal of 18-MEA from the surface.

Automated reconstruction of curvilinear fibres from 3D datasets acquired by X‐ray microtomography

Abstract: Summary The characterization of fibrous structures is important in both composites and textiles research for relating to the bulk properties of the material. However, the microscopic nature of the fibres and their high densities make them very difficult to characterize. Many techniques have been developed for the measurement and characterization of fibrous structures but they tend to be restricted to measurements on the sample surface or within physical cross-sections. X-ray microtomography can be used to non-destructively probe the internal structure of a range of fibrous materials, providing large amounts of 3D data. A technique has been developed for tracing fibres within 3D datasets acquired by X-ray microtomography and this has been applied to a glass fibre reinforced composite and also a non-woven textile sample. The 3D fibrous structures of both samples were successfully reconstructed and their fibre orientation distributions calculated. This technique enables novel characterizations, such as the through-thickness variation of fibre orientation in non-wovens.