In situ dark field microscopy for on-line monitoring of yeast cultures

A new-type in situ probe has been developed to acquire dark field images of yeast in bioreactors. It has been derived from an in situ bright field microscope that is able to measure cell density in bioreactors during fermentation processes. The illumination part of the probe has been replaced with a dark field device, in which an aspheric condenser is used, so that high contrast dark field images can be obtained. The technique of second imaging is implemented to improve the sharpness of the images by means of a relay lens. This new in situ probe is expected to enable the evaluation of the cell viability without staining owing to modern image processing.     

Phytoluminography: Imaging Plants by Delayed Light Emission

It is demonstrated that photographic images of plants can be produced in the absence of external illumination using an image intensifier. The image is produced by the weak delayed light emission (afterglow) from photosynthetically active chloroplasts. We propose the use of such “phytoluminographs’ for the study and diagnosis at an early stage of disturbances due to parasites, mineral deficiency, herbicides, frost etc.     

Auto-align - multi-modality fluorescence microscopy image co-registration

Multi-modality microscopes incorporate multiple microscopy techniques into one module, imaging through a common objective lens. Simultaneous or consecutive image acquisition of a single specimen, using multiple techniques, increases the amount of measurable information available. In order to benefit from each modality, it is necessary to accurately co-register data sets. Intrinsic differences in the image formation process employed by each modality result in images which possess different characteristics. In addition, as a result of using different measurement devices, images often differ in size and can suffer relative geometrical deformations including rotation, scale and translation, making registration a complex problem. Current methods generally rely on manual input and are therefore subject to human error. Here, we present an automated image registration tool for fluorescence microscopy. We show that it successfully registers images obtained via total internal reflection fluorescence (TIRF), or epi-fluorescence, and confocal microscopy. Furthermore, we provide several other applications including channel merging following image acquisition through an emission beam splitter, and lateral stage drift correction. We also discuss areas of membrane trafficking which could benefit from application of Auto-Align. Auto-Align is an essential item in the advanced microscopist's toolbox which can create a synergy of single or multi-modality image data.     

The unusual visual system of the Strepsiptera: external eye and neuropils

Adult males of the insect order Strepsiptera are characterized by an unusual visual system that may use design principles from compound as well as simple eyes. The lenses of this eye are unusually large and focus images onto extended retinae. The light-gathering ability of the lens is sufficient to resolve multiple points of an image in each optical unit. We regard each unit as an independent image-forming eye that contributes an inverted partial image. Each partial image is re-inverted by optic chiasmata between the retinae and the lamina, where the complete image could be assembled from the neighboring units. The lamina, medulla and lobula are present, but their organization into cartridges is not clearly discernable. Fluorescent fills, whole-tissue stains, and synaptotagmin immunohistochemistry show that the optic neuropils nevertheless are densely packed, and that several parallel channels within the medulla underlie each of the lenses. The size and shape of the rhabdoms, as well as a relatively slow flicker-fusion frequency could suggest that these eyes evolved through a nocturnal life stage.Abbreviations O object size - U object distance - I image size - f focal length - A lens aperture - D lens diameter - interommatidial angle - S light sensitivity of optical system     

Biofilm thickness measurements by light microscopy

Light microscopy has been used to measure biofilm thickness. The vertical displacement of the sample required to focus from the biofilm-liquid interface to the biofilm-substratum interface is measured by the stage micrometer. Biofilm thickness is proportional, but not equal, to the measured vertical displacement. An expression for the proportionality constant, k_f, in terms of refractive indices is determined from a geometric analysis of the light path. k_f can be estimated as the ratio of the refractive index of the film to the refractive index of the media interfacing the film between the objective lens and the sample. The thickness of any transparent film may be determined by light microscopy when the refractive index of the film is known.     

Combining hyperspectral imaging and chemometrics to assess and interpret the effects of environmental stressors on zebrafish eye images at tissue level

Changes on an organism by the exposure to environmental stressors may be characterized by hyperspectral images (HSI), which preserve the morphology of biological samples, and suitable chemometric tools. The approach proposed allows assessing and interpreting the effect of contaminant exposure on heterogeneous biological samples monitored by HSI at specific tissue levels. In this work, the model example used consists of the study of the effect of the exposure of chlorpyrifos‐oxon on zebrafish tissues. To assess this effect, unmixing of the biological sample images followed by tissue‐specific classification models based on the unmixed spectral signatures is proposed. Unmixing and classification are performed by multivariate curve resolution‐alternating least squares (MCR‐ALS) and partial least squares‐discriminant analysis (PLS‐DA), respectively. Crucial aspects of the approach are: (1) the simultaneous MCR‐ALS analysis of all images from 1 population to take into account biological variability and provide reliable tissue spectral signatures, and (2) the use of resolved spectral signatures from control and exposed populations obtained from resampling of pixel subsets analyzed by MCR‐ALS multiset analysis as information for the tissue‐specific PLS‐DA classification models. Classification results diagnose the presence of a significant effect and identify the spectral regions at a tissue level responsible for the biological change.      

Use of an image restoration process to improve spatial resolution in bioluminescence imaging

To improve spatial resolution in in vivo bioluminescence imaging, a photon scattering correction, image restoration method was tested. The chosen algorithm was tested on in vivo bioluminescent images acquired on three representative tumor models: subcutaneous, pulmonary, and disseminated peritoneal. Tumor size was chosen as a quantitative criterion, such that the tumor reference measurements (determined photographically or by computed tomography) were compared to those derived from bioluminescent images, before and after restoration. This technique allowed a significant reduction to be achieved in the relative error between reference measurements and dimensions derived from bioluminescent images. In addition, improved delineation of the tumor foci was achieved. The restoration method allows spatial resolution in bioluminescence imaging to be improved, with interesting perspectives in terms of staging and quantitation in experimental oncology.     

Using Flatbed Scanners to Collect High-resolution Time-lapsed Images of the Arabidopsis Root Gravitropic Response

Research efforts in biology increasingly require use of methodologies that enable high-volume collection of high-resolution data. A challenge laboratories can face is the development and attainment of these methods. Observation of phenotypes in a process of interest is a typical objective of research labs studying gene function and this is often achieved through image capture. A particular process that is amenable to observation using imaging approaches is the corrective growth of a seedling root that has been displaced from alignment with the gravity vector. Imaging platforms used to measure the root gravitropic response can be expensive, relatively low in throughput, and/or labor intensive. These issues have been addressed by developing a high-throughput image capture method using inexpensive, yet high-resolution, flatbed scanners. Using this method, images can be captured every few minutes at 4,800 dpi. The current setup enables collection of 216 individual responses per day. The image data collected is of ample quality for image analysis applications.     

A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.     

An automatic 2D-3D image matching method for reproducing spatial knee joint positions using single or dual fluoroscopic images

Fluoroscopic image technique, using either a single image or dual images, has been widely applied to measure in vivo human knee joint kinematics. However, few studies have compared the advantages of using single and dual fluoroscopic images. Furthermore, due to the size limitation of the image intensifiers, it is possible that only a portion of the knee joint could be captured by the fluoroscopy during dynamic knee joint motion. In this paper, we presented a systematic evaluation of an automatic 2D-3D image matching method in reproducing spatial knee joint positions using either single or dual fluoroscopic image techniques. The data indicated that for the femur and tibia, their spatial positions could be determined with an accuracy and precision less than 0.2?mm in translation and less than 0.4° in orientation when dual fluoroscopic images were used. Using single fluoroscopic images, the method could produce satisfactory accuracy in joint positions in the imaging plane (in average up to 0.5?mm in translation and 1.3° in rotation), but large variations along the out-plane direction (in average up to 4.0?mm in translation and 2.2° in rotation). The precision of using single fluoroscopic images to determine the actual knee positions was worse than its accuracy obtained. The data also indicated that when using dual fluoroscopic image technique, if the knee joint outlines in one image were incomplete by 80%, the algorithm could still reproduce the joint positions with high precisions.     

Optical evaluation of red blood cell geometry using micropipette aspiration.

Although red blood cell (RBC) geometry has been extensively studied by micropipette aspiration, the small size of RBC and pipettes vs. the optical resolution of light microscopy suggests the need to consider potential errors. The present study addressed such difficulties and investigated four specific problems: (1) use of exact equations to calculate RBC membrane area and volume; (2) calibration of the pipette internal diameter (PID); (3) correction for a noncylindrical pipette barrel; (4) diffraction distortion of the RBC image. The observed PID represents a cylinder lens enlargement that can be theoretically derived from the glass/buffer refractive index ratio (1.49/1.33 = 1.12). This enlargement was experimentally confirmed by: (1) studying pipettes bent to allow measurement through the barrel (horizontal) and at the orifice (vertical), with a resulting diameter ratio of 1.12 +/- 0.01; (2) and by replacing the surrounding buffer with immersion oil and hence abolishing the lens phenomenon (ratio = 1.12 +/- 0.02). In addition, use of aspirated oil droplets demonstrated a 3.2 +/- 0.2% error when the PID is focused at a sharp, maximum diameter. The average pipette cone angle was 1.49 +/- 0.09 degrees and varied considerably with pipette pulling procedures; calculated tongue geometry inside the pipette was affected by the noncylindrical pipette barrel. The RBC diffraction error, demonstrated by touching two aspirated cells held by opposing pipettes, was 0.091 +/- 0.002 microns. The PID, cone angle, and diffraction artifacts significantly (p < 0.001) affected calculated RBC geometry (average errors up to 5.4% for area and 9.6% for volume). Two new methods to calculate, rather than directly measure, the PID from images of a single RBC, during either osmotic or pressure manipulation, were evaluated; the osmotic method closely predicted the PID, whereas the pressure method markedly underestimated the PID. Our results thus confirm the need to consider the above-mentioned phenomena when determining RBC geometric parameters via micropipette aspiration.     

Femtosecond laser-based mutagenesis strategy for micronomicin production enhancement of Micromonospora sagamiensis ATCC 21826

In this work, a mutant MX3004 with improved micronomicin (MCR) production was derived from Micromonospora sagamiensis ATCC21826, which was treated with femtosecond laser under the optimized irradiation conditions of 75 mW and 180 s, with a maximum of positive mutation rate of 17.8 % and the mortality rate of 69.2 %. A novel high-throughput method was established using microplate reader by quantifying the concentration of MCR for efficient screening of positive mutant from large numbers of mutants. Consequently, MX3004 displayed the highest MCR production capacity of 126 U/ml and a stable heredity (ten generations). Moreover, under the optimal fermentation conditions in a 7.5 l fermenter, the MCR production of MX3004 reached the maximum of 263 U/ml, which was increased by 484 % compared with the parent strain. The results suggest that femtosecond laser is a suitable method for the MCR production improvement and the screening method has a great potential application for aminoglycoside antibiotic production.     

Fluorescence lifetime imaging.

We describe a new fluorescence imaging methodology in which the image contrast is derived from the fluorescence lifetime at each point in a two-dimensional image and not the local concentration and/or intensity of the fluorophore. In the present apparatus, lifetime images are created from a series of images obtained with a gain-modulated image intensifier. The frequency of gain modulation is at the light-modulation frequency (or a harmonic thereof), resulting in homodyne phase-sensitive images. These stationary phase-sensitive images are collected using a slow-scan CCD camera. A series of such images, obtained with various phase shifts of the gain-modulation signal, is used to determine the phase angle and/or modulation of the emission at each pixel, which is in essence the phase or modulation lifetime image. An advantage of this method is that pixel-to-pixel scanning is not required to obtain the images, as the information from all pixels is obtained at the same time. The method has been experimentally verified by creating lifetime images of standard fluorophores with known lifetimes, ranging from 1 to 10 ns. As an example of biochemical imaging we created life-time images of Yt-base when quenched by acrylamide, as a model for a fluorophore in distinct environments that affect its decay time. Additionally, we describe a faster imaging procedure that allows images in which a specific decay time is suppressed to be calculated, allowing rapid visualization of unique features and/or regions with distinct decay times. The concepts and methodologies of fluorescence lifetime imaging (FLIM) have numerous potential applications in the biosciences. Fluorescence lifetimes are known to be sensitive to numerous chemical and physical factors such as pH, oxygen, temperature, cations, polarity, and binding to macromolecules. Hence the FLIM method allows chemical or physical imaging of macroscopic and microscopic samples.     

An improved method for quantifying hematozoa by digital microscopy

Intensity of hematozoan infection is infrequently quantified because accurate calculations require visual counts of parasites relative to a large number of erythrocytes. Manual quantification of erythrocytes can be circumvented by using ImageJ software (developed by the National Institutes of Health) to count erythrocyte nuclei from digital images. Here we use the ratio of microscope erythrocyte counts to digital image erythrocyte counts (field:image ratio) to extrapolate erythrocyte counts from smaller digital images to the microscope's larger field of view. Field:image ratios were consistently calculated from 10 slides (resampling P = 0.049) and used to rapidly estimate intensity of infection within 50,000 or more erythrocytes. Intensity of hematozoan infection calculated from manual quantification of 2,000 erythrocytes was significantly lower (0.46 times) than intensity calculated from digital quantification of 50,000 erythrocytes (bootstrap P = 0.02). We contend that digital quantification of hematozoan infection offers a rapid and precise method to quantify infections of low to moderate intensity.     

Automated identification of Fos expression

The concentration of Fos, a protein encoded by the immediate-early gene c-fos, provides a measure of synaptic activity that may not parallel the electrical activity of neurons. Such a measure is important for the difficult problem of identifying dynamic properties of neuronal circuitries activated by a variety of stimuli and behaviours. We employ two-stage statistical pattern recognition to identify cellular nuclei that express Fos in two-dimensional sections of rat forebrain after administration of antipsychotic drugs. In stage one, we distinguish dark-stained candidate nuclei from image background by a thresholding algorithm and record size and shape measurements of these objects. In stage two, we compare performance of linear and quadratic discriminants, nearest-neighbour and artificial neural network classifiers that employ functions of these measurements to label candidate objects as either Fos nuclei, two touching Fos nuclei or irrelevant background material. New images of neighbouring brain tissue serve as test sets to assess generalizability of the best derived classification rule, as determined by lowest cross-validation misclassification rate. Three experts, two internal and one external, compare manual and automated results for accuracy assessment. Analyses of a subset of images on two separate occasions provide quantitative measures of inter- and intra-expert consistency. We conclude that our automated procedure yields results that compare favourably with those of the experts and thus has potential to remove much of the tedium, subjectivity and irreproducibility of current Fos identification methods in digital microscopy.     

Two genetically distinct methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum strain Marburg and delta H

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaebacteria. The reductase has been characterized in detail from Methanobacterium thermoautotrophicum strain Marburg and delta H, which grow on H2 and CO2 as energy source. During purification of the enzyme we have now discovered a second methyl-coenzyme M reductase (MCR II) in the two strains, which elutes at lower salt concentration from anion-exchange columns than the enzyme (MCR I) previously characterized. MCR II is similar to MCR I in that it is also composed of three different subunits alpha, beta, and gamma but distinct from MCR I in that the gamma subunit is 5 kDa smaller, as revealed by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The N-terminal amino acid sequences of the alpha, beta, and gamma subunits of MCR II and MCR I were found to be different in several amino acid positions. The respective sequences showed, however, strong similarities indicating that MCR II was not derived from MCR I by limited proteolysis. The relative amounts of MCR I and MCR II present in the cells were affected by the growth conditions. When the cultures were supplied with sufficient H2 and and CO2 and the cells grew exponentially, essentially only MCR II was found. When growth was limited by the gas supply, MCR I predominated.     

Estimating loop length from CryoEM images at medium resolutions

Background

De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results

We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2Å.

Conclusions

The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

     

Single-scan stereotactic tumor biopsy and brachytherapy

Stereotactic tumor biopsy and brachytherapy catheter implantation can be accomplished with targets derived from computed axial tomography and magnetic resonance scans. Computer manipulation of image data allows both diagnostic and therapeutic procedures to be carried out from a single set of scan slices. This eliminates the need for repeat scanning as part of the surgical procedure. Microcomputer technology is sufficiently advanced to handle the images and graphics necessary for stereotactic neurosurgery. A system based on the IBM PC/AT designed for this purpose uses readily available graphics software and custom-designed imaging programs. Direct loading of computed axial or magnetic resonance scan images from magnetic tape can be accomplished. Determination of points, contours and volumes in three-dimensional space allows intraoperative alignment of image data and patient landmarks within the stereotactic head frame using pattern recognition overlays. Three-axis scaling for magnification correction along with rotational and linear data transformations provide the basis for single-scan stereotaxis. Interactive computer graphics integrate image, patient and frame coordinates for target determination. This method eliminates the need to design and fabricate nonmagnetic or radiolucent scanner-compatible devices.