Phase Contrast Microscopy Images Research Articles

Segmentation of phase contrast microscopy images based on multi-scale local Basic Image Features histograms

Phase contrast microscopy (PCM) is routinely used for the inspection of adherent cell cultures in all fields of biology and biomedicine. Key decisions for experimental protocols are often taken by an operator based on typically qualitative observations. However, automated processing and analysis of PCM images remain challenging due to the low contrast between foreground objects (cells) and background as well as various imaging artefacts. We propose a trainable pixel-wise segmentation approach whereby image structures and symmetries are encoded in the form of multi-scale Basic Image Features local histograms, and classification of them is learned by random decision trees. This approach was validated for segmentation of cell versus background, and discrimination between two different cell types. Performance close to that of state-of-the-art specialised algorithms was achieved despite the general nature of the method. The low processing time ( < 4 s per 1280 × 960 pixel images) is suitable for batch processing of experimental data as well as for interactive segmentation applications.

Mechanisms of the formation of morphological features of micropipes in bulk crystals of silicon carbide

New morphological features of dislocation micropipes in silicon carbide single crystals have been investigated experimentally and theoretically. It has been shown that the cylindrical shape of micropipes is unstable, and the cross-sectional sizes of the micropipes change along their axes. The experimental results have been obtained by measuring X-ray phase-contrast microscopy images of micropipes in highly coherent synchrotron radiation. The cross-sectional sizes of the micropipes have been determined using computer simulation of their images. A theoretical model of the transformation of dislocations into micropipes due to nonequilibrium processes of pipe diffusion and coagulation of vacancies on dislocations parallel to the crystal growth axis has been proposed.

Segmentation and Tracking of Lymphocytes Based on Modified Active Contour Models in Phase Contrast Microscopy Images.

The paper proposes an improved active contour model for segmenting and tracking accurate boundaries of the single lymphocyte in phase-contrast microscopic images. Active contour models have been widely used in object segmentation and tracking. However, current external-force-inspired methods are weak at handling low-contrast edges and suffer from initialization sensitivity. In order to segment low-contrast boundaries, we combine the region information of the object, extracted by morphology gray-scale reconstruction, and the edge information, extracted by the Laplacian of Gaussian filter, to obtain an improved feature map to compute the external force field for the evolution of active contours. To alleviate initial location sensitivity, we set the initial contour close to the real boundaries by performing morphological image processing. The proposed method was tested on live lymphocyte images acquired through the phase-contrast microscope from the blood samples of mice, and comparative experimental results showed the advantages of the proposed method in terms of the accuracy and the speed. Tracking experiments showed that the proposed method can accurately segment and track lymphocyte boundaries in microscopic images over time even in the presence of low-contrast edges, which will provide a good prerequisite for the quantitative analysis of lymphocyte morphology and motility.

Cell Segmentation in Phase Contrast Microscopy by Constrained Optimization

Utilization of automatic cell segmentation process is difficult to identify in a cell due to halo and shade-off distortions when observing the phase contrast microscopy images. Therefore, it is an important step to restore artifact-free images made ready for segmentation process. The main focus of this paper is to define a gradient projection algorithm to restore images based on the minimization problem of quadratic objective function with non-negative constraints. The proposed algorithm converges to a global minimum solution independent on initialization. The experimental result shows that the proposed algorithm can restore artifact-free images, which could produce high quality segmentation results using a simple thresholding method.

PREPARATION OF LOW TEMPERATURE RESISTANT AND HIGH ELECTRICAL INSULATION CHLOROPRENE RUBBER–BUTADIENE RUBBER BLENDS

ABSTRACT To satisfy some special demands of many applications in the fields of aerospace and the electronic industry, low temperature resistant and high electrical insulation chloroprene rubber (CR) was prepared by blending pristine CR with different weight ratios of butadiene rubber (BR). The low temperature resistance, electrical insulation properties, and mechanical properties of CR/BR blends were investigated. With increasing BR content, the low temperature resistance and electrical insulation properties were improved, whereas the tensile strength and elongation at break decreased. For the CR/BR (65/35) blend, filled with SiO2, the brittleness temperature (Tb) was reduced to −61 °C and the high electrical insulation properties were obtained without sacrificing mechanical properties too much. The tan δ plots of CR/BR blends, investigated by dynamic mechanical analysis, also revealed that BR could reduce glass transition temperature (Tg) and improve low temperature resistance of CR. The phase contrast microscope images of CR/BR blends demonstrated that the phase structure of the blends changed with increasing BR content. Furthermore, the fracture surfaces of CR/BR blends, observed by scanning electron microscopy, showed that the compatibility of CR/BR blends was poor although the CR/BR blends were homogeneous in macrostructure.

Using flow cytometry to detect haemic neoplasia in mussels (Mytilus trossulus) from the Pacific Coast of Southern British Columbia, Canada

Flow cytometry was investigated as an alternative to visual haemocytology for potentially higher-throughput and less subjective detection of neoplasia in Mytilus trossulus. In contrast to previous studies of ploidy in the Mytilus spp. complex, distinct tetra- and pentaploidal neoplastic cells were rare and a wide range of aneuploidy peaks from 1.4n to 5.5n were detected for late-stage leukemic animals. There was no correlation between aneuploidy and the number of diseased cells for early and intermediate disease stages. Formation of aneuploidy and neoplasia progression might not be simultaneous, and DNA content analysis using flow cytometry was only useful for detecting late stages of the disease.

Meniscus formation in a capillary and the role of contact line friction

We studied spontaneous formation of an internal meniscus by dipping glass capillaries of 25 μm to 350 μm radii into low volatile hexadecane and tributyl phosphate. X-ray phase contrast and high speed optical microscopy imaging were employed. We showed that the meniscus completes its formation when the liquid column is still shorter than the capillary radius. After that, the meniscus travels about ten capillary radii at a constant velocity. We demonstrated that the experimental observations can be explained by introducing a friction force linearly proportional to the meniscus velocity with a friction coefficient depending on the air/liquid/solid triplet. It was demonstrated that the friction coefficient does not depend on the capillary radius. Numerical solution of the force balance equation revealed four different uptake regimes that can be specified in a phase portrait. This phase portrait was found to be in good agreement with the experimental results and can be used as a guide for the design of thin porous absorbers.

Interactive Cell Segmentation based on Phase Contrast Optics

Cell segmentation in phase contrast microscopy images lays a crucial foundation for numerous subsequent computer-aided cell image analysis, but it encounters many unsolved challenges due to image qualities and artifacts caused by phase contrast optics. Addressing the unsolved challenges, the authors propose an interactive cell segmentation scheme over phase retardation features. After partitioning the images into phase homogeneous atoms, human annotations are propagated to unlabeled atoms over an affinity graph that is learned based on discrimination analysis. Then, an active query strategy is proposed for which the most informative unlabeled atom is selected for annotation, which is also propagated to the other unlabeled atoms. Cell segmentation converges to quality results after several rounds of interactions involving both the user's intentions and characteristics of image features. Experimental results demonstrate that cells with different optical properties are well segmented via the proposed approach.

Cell-sensitive microscopy imaging for cell image segmentation.

We propose a novel cell segmentation approach by estimating a cell-sensitive camera response function based on variously exposed phase contrast microscopy images on the same cell dish. Using the cell-sensitive microscopy imaging, cells' original irradiance signals are restored from all exposures and the irradiance signals on non-cell background regions are restored as a uniform constant (i.e., the imaging system is sensitive to cells only but insensitive to non-cell background). Cell segmentation is then performed on the restored irradiance signals by simple thresholding. The experimental results validate that high quality cell segmentation can be achieved by our approach.

Primary ciliary dyskinesia assessment by means of optical flow analysis of phase-contrast microscopy images

Primary ciliary dyskinesia implies cilia with defective or total absence of motility, which may result in sinusitis, chronic bronchitis, bronchiectasis and male infertility. Diagnosis can be difficult and is based on an abnormal ciliary beat frequency (CBF) and beat pattern. In this paper, we present a method to determine CBF of isolated cells through the analysis of phase-contrast microscopy images, estimating cilia motion by means of an optical flow algorithm. After having analyzed 28 image sequences (14 with a normal beat pattern and 14 with a dyskinetic pattern), the normal group presented a CBF of 5.2±1.6Hz, while the dyskinetic patients presented a 1.9±0.9Hz CBF. The cutoff value to classify a dyskinetic specimen was set to 3.45Hz (sensitivity 0.86, specificity 0.93). The presented methodology has provided excellent results to objectively diagnose PCD.

Evaluation of alpha and gamma aluminum oxide nanoparticle accumulation, toxicity, and depuration in Artemia salina larvae.

In this study, Artemia salina (crustacean filter feeders) larvae were used as a test model to investigate the toxicity of aluminum oxide nanoparticles (Al2O3 NPs) on marine microorganisms. The uptake, toxicity, and elimination of α-Al2O3 (50 nm and 3.5 μm) and γ-Al2O3 (5 nm and 0.4 μm) NPs were studied. Twenty-four and ninety-six hour exposures of different concentrations of Al2O3 NPs to Artemia larvae were conducted in a seawater medium. When suspended in water, Al2O3 NPs aggregated substantially with the sizes ranging from 6.3 nm to >0.3 µm for spherical NPs and from 250 to 756 nm for rod-shaped NPs. The phase contrast microscope images showed that NPs deposited inside the guts as aggregates. Inductively coupled plasma mass spectrometry analysis showed that large particles (3.5 μm α-Al2O3) were not taken up by Artemia, whereas fine NPs (0.4 μm γ-Al2O3) and ultra-fine NPs (5 nm γ-Al2O3 and 50 nm α-Al2O3) accumulated substantially. Differences in toxicity were detected as changing with NP size and morphology. The malondialdehyde levels indicated that smaller γ-Al2O3 (5 nm) NPs were more toxic than larger γ-Al2O3 (0.4 µm) particulates in 96 h. The highest mortality was measured as 34% in 96 h for γ-Al2O3 NPs (5 nm) at 100 mg/L (LC50 > 100 mg/L). γ-Al2O3 NPs were more toxic than α-Al2O3 NPs at all conditions.

Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images

The quantitative determination of key adherent cell culture characteristics such as confluency, morphology, and cell density is necessary for the evaluation of experimental outcomes and to provide a suitable basis for the establishment of robust cell culture protocols. Automated processing of images acquired using phase contrast microscopy (PCM), an imaging modality widely used for the visual inspection of adherent cell cultures, could enable the non-invasive determination of these characteristics. We present an image-processing approach that accurately detects cellular objects in PCM images through a combination of local contrast thresholding and post hoc correction of halo artifacts. The method was thoroughly validated using a variety of cell lines, microscope models and imaging conditions, demonstrating consistently high segmentation performance in all cases and very short processing times (<1 s per 1,208 × 960 pixels image). Based on the high segmentation performance, it was possible to precisely determine culture confluency, cell density, and the morphology of cellular objects, demonstrating the wide applicability of our algorithm for typical microscopy image processing pipelines. Furthermore, PCM image segmentation was used to facilitate the interpretation and analysis of fluorescence microscopy data, enabling the determination of temporal and spatial expression patterns of a fluorescent reporter. We created a software toolbox (PHANTAST) that bundles all the algorithms and provides an easy to use graphical user interface. Source-code for MATLAB and ImageJ is freely available under a permissive open-source license. Biotechnol. Bioeng. 2014;111: 504–517. © 2013 Wiley Periodicals, Inc.

Selection and Tuning of a Fast and Simple Phase-Contrast Microscopy Image Segmentation Algorithm for Measuring Myoblast Growth Kinetics in an Automated Manner

Acquiring and processing phase-contrast microscopy images in wide-field long-term live-cell imaging and high-throughput screening applications is still a challenge as the methodology and algorithms used must be fast, simple to use and tune, and as minimally intrusive as possible. In this paper, we developed a simple and fast algorithm to compute the cell-covered surface (degree of confluence) in phase-contrast microscopy images. This segmentation algorithm is based on a range filter of a specified size, a minimum range threshold, and a minimum object size threshold. These parameters were adjusted in order to maximize the F-measure function on a calibration set of 200 hand-segmented images, and its performance was compared with other algorithms proposed in the literature. A set of one million images from 37 myoblast cell cultures under different conditions were processed to obtain their cell-covered surface against time. The data were used to fit exponential and logistic models, and the analysis showed a linear relationship between the kinetic parameters and passage number and highlighted the effect of culture medium quality on cell growth kinetics. This algorithm could be used for real-time monitoring of cell cultures and for high-throughput screening experiments upon adequate tuning.

A Novel Framework for Cellular Tracking and Mitosis Detection in Dense Phase Contrast Microscopy Images

The aim of this paper is to detail the development of a novel tracking framework that is able to extract the cell motility indicators and to determine the cellular division (mitosis) events in large time-lapse phase-contrast image sequences. To address the challenges induced by nonstructured (random) motion, cellular agglomeration, and cellular mitosis, the process of automatic (unsupervised) cell tracking is carried out in a sequential manner, where the interframe cell association is achieved by assessing the variation in the local cellular structures in consecutive frames of the image sequence. In our study, a strong emphasis has been placed on the robust use of the topological information in the cellular tracking process and in the development of targeted pattern recognition techniques that were designed to redress the problems caused by segmentation errors, and to precisely identify mitosis using a backward (reversed) tracking strategy. The proposed algorithm has been evaluated on dense phase-contrast cellular data and the experimental results indicate that the proposed algorithm is able to accurately track epithelial and endothelial cells in time-lapse image sequences that are characterized by low contrast and high level of noise. Our algorithm achieved 86.10% overall tracking accuracy and 90.12% mitosis detection accuracy.

Cell segmentation in phase contrast microscopy images via semi-supervised classification over optics-related features

Phase-contrast microscopy is one of the most common and convenient imaging modalities to observe long-term multi-cellular processes, which generates images by the interference of lights passing through transparent specimens and background medium with different retarded phases. Despite many years of study, computer-aided phase contrast microscopy analysis on cell behavior is challenged by image qualities and artifacts caused by phase contrast optics. Addressing the unsolved challenges, the authors propose (1) a phase contrast microscopy image restoration method that produces phase retardation features, which are intrinsic features of phase contrast microscopy, and (2) a semi-supervised learning based algorithm for cell segmentation, which is a fundamental task for various cell behavior analysis. Specifically, the image formation process of phase contrast microscopy images is first computationally modeled with a dictionary of diffraction patterns; as a result, each pixel of a phase contrast microscopy image is represented by a linear combination of the bases, which we call phase retardation features. Images are then partitioned into phase-homogeneous atoms by clustering neighboring pixels with similar phase retardation features. Consequently, cell segmentation is performed via a semi-supervised classification technique over the phase-homogeneous atoms. Experiments demonstrate that the proposed approach produces quality segmentation of individual cells and outperforms previous approaches.

The differential stress response of adapted chromite mine isolates Bacillus subtilis and Escherichia coli and its impact on bioremediation potential

In the current study, indigenous bacterial isolates Bacillus subtilis VITSUKMW1 and Escherichia coli VITSUKMW3 from a chromite mine were adapted to 100mgL(-1) of Cr(VI). The phase contrast and scanning electron microscopic images showed increase in the length of adapted E. coli cells and chain formation in case of adapted B. subtilis. The presence of chromium on the surface of the bacteria was confirmed by energy dispersive X-ray spectroscopy (EDX), which was also supported by the conspicuous Cr-O peaks in FTIR spectra. The transmission electron microscopic (TEM) images of adapted E. coli and B. subtilis showed the presence of intact cells with Cr accumulated inside the bacteria. The TEM-EDX confirmed the internalization of Cr(VI) in the adapted cells. The specific growth rate and Cr(VI) reduction capacity was significantly higher in adapted B. subtilis compared to that of adapted E. coli. To study the possible role of Cr(VI) toxicity affecting the Cr(VI) reduction capacity, the definite assays for the released reactive oxygen species (ROS) and ROS scavenging enzymes (SOD and GSH) were carried out. The decreased ROS production as well as SOD and GSH release observed in adapted B. subtilis compared to the adapted E. coli corroborated well with its higher specific growth rate and increased Cr(VI) reduction capacity.

A novel dynamic layer-by-layer assembled nano-scale biointerface: functionality tests with platelet adhesion and aggregate morphology influenced by adenosine diphosphate

An improved biointerface was developed, dynamic layer-by-layer self-assembly surface (d-LbL), and utilized as a biologically-active substrate for platelet adhesion and aggregation. Possible clinical applications for this research include improved anti-coagulation surfaces. This work demonstrated the functionality of d-LbL biointerfaces in the presence of platelet-rich-plasma (PRP) with the addition of 20 μM adenosine diphosphate (ADP), a thrombus activator. The surface morphology of the experimental control, plain PRP, was compared to PRP containing additional ADP (PRP + ADP) and resulted in an expected increase of platelet adhesions along the fibrinogen d-LbL substrate. The d-LbL process was used to coat glass slides with fibrinogen, Poly (sodium 4-styrene-sulfonate), and Poly (diallydimethlyammonium chloride). Slides were exposed to PRP under flow and static conditions with and without 20 μM of ADP. Fluorescence microscopy (FM), phase contrast microscopy (PCM), atomic force microscopy (AFM), and field emission-scanning electron microscopy (FE-SEM) were used to evaluate platelet adhesions under the influence of varied shear conditions. PCM images illustrated differences between the standard LbL and d-LbL substrates. FM images provided percent surface coverage values. For high-shear conditions, percent surface coverage values increased when using ADP whereas plain PRP exposure displayed no significant increase. AFM scans also displayed higher mean peak height values and unique surface characteristics for PRP + ADP as opposed to plain PRP. FE-SEM images revealed platelet adhesions along the biointerface and unique characteristics of the d-LbL surface. In conclusion, PRP + ADP was more effective at increasing platelet aggregation, especially under high shear conditions, providing further validation of the improved biointerface.

Post-yield crack toughness behavior of polyamide-6/polypropylene grafted maleic anhydride/nanoclay ternary nanocomposites

The fracture properties of melt-mixed polyamide-6 (PA-6)/polypropylene grafted maleic anhydride (PP-g-MA)/nanoclay ternary nanocomposites were investigated following essential work of fracture (EWF) approach based on post-yield fracture mechanics principles. Fourier transform infrared (FTIR) spectroscopy studies revealed distinct interactions between optimized impact-modified PA-6 based blend matrix and nanoclay whereas the incorporation of nanoclay leading to enhanced lighter phase-contrast atomic force microscope (AFM) images have indicated enhanced hard-phase fractions. FTIR revealed tripartite interactions between amide functionality, maleic anhydride moiety and hydroxyl group of the three constituents of the nanocomposite. The validity of essential work of fracture (EWF) concept to these ternary nanocomposites has been demonstrated via self-similarity and Hill’s analysis. The EWF (we) showed an increase by ∼35% with the incorporation of 2wt.% of nanoclay followed by a continuous reduction up to ∼67% in 6wt.% of nanoclay loaded composite whereas non-EWF (βwp) increased almost consistently with the maximum up to ∼264% in the entire composition range. Thus linear increase in the resistance to crack propagation is attributed to nanoclay induced enhanced micro-fibrillation accompanied with the generation of fracture surface as revealed from scanning electron microscopy studies.

Label-free detection and dynamic monitoring of drug-induced intracellular vesicle formation enabled using a 2-dimensional matched filter

Analysis of vesicle formation and degradation is a central issue in autophagy research and microscopy imaging is revolutionizing the study of such dynamic events inside living cells. A limiting factor is the need for labeling techniques that are labor intensive, expensive, and not always completely reliable. To enable label-free analyses we introduced a generic computational algorithm, the label-free vesicle detector (LFVD), which relies on a matched filter designed to identify circular vesicles within cells using only phase-contrast microscopy images. First, the usefulness of the LFVD is illustrated by presenting successful detections of autophagy modulating drugs found by analyzing the human colorectal carcinoma cell line HCT116 exposed to each substance among 1266 pharmacologically active compounds. Some top hits were characterized with respect to their activity as autophagy modulators using independent in vitro labeling of acidic organelles, detection of LC3-II protein, and analysis of the autophagic flux. Selected detection results for 2 additional cell lines (DLD1 and RKO) demonstrate the generality of the method. In a second experiment, label-free monitoring of dose-dependent vesicle formation kinetics is demonstrated by recorded detection of vesicles over time at different drug concentrations. In conclusion, label-free detection and dynamic monitoring of vesicle formation during autophagy is enabled using the LFVD approach introduced.

Comparative evaluation of impact of Zn and ZnO nanoparticles on brine shrimp (Artemia salina) larvae: effects of particle size and solubility on toxicity.

Brine shrimp (Artemia salina) larvae were exposed to different sizes of zinc (Zn) and zinc oxide (ZnO) nanoparticles (NPs) to evaluate their toxicity in marine aquatic ecosystems. Acute exposure was conducted in seawater with 10, 50 and 100 mg L(-1) concentrations of the NPs for 24 h and 96 h. Phase contrast microscope images confirmed the accumulation of the NPs inside the guts. Artemia were unable to eliminate the ingested particles, which was thought to be due to the formation of massive particles in the guts. Although the suspensions of the NPs did not exhibit any significant acute toxicity within 24 h, mortalities increased remarkably in 96 h and escalated with increasing concentration of NP suspension to 42% for Zn NPs (40-60 nm) (LC50∼ 100 mg L(-1)) and to about 34% for ZnO NPs (10-30 nm) (LC50 > 100 mg L(-1)). The suspensions of Zn NPs were more toxic to Artemia than those of ZnO NPs under comparable regimes. This effect was attributed to higher Zn(2+) levels (ca. up to 8.9 mg L(-1)) released to the medium from Zn NPs in comparison to that measured in the suspensions of ZnO NPs (ca. 5.5 mg L(-1)). In addition, the size of the nanopowders appeared to contribute to the observed toxicities. Although the suspensions possessed aggregates of comparable sizes, smaller Zn NPs (40-60 nm) were relatively more toxic than larger Zn NPs (80-100 nm). Likewise, the suspensions of 10-30 nm ZnO NPs caused higher toxicity than those of 200 nm ZnO NPs. Lipid peroxidation levels were substantially higher in 96 h (p < 0.05), indicating that the toxic effects were due to the oxidative stress.