A Parallel Distributed-Memory Particle Method Enables Acquisition-Rate Segmentation of Large Fluorescence Microscopy Images

Modern fluorescence microscopy modalities, such as light-sheet microscopy, are capable of acquiring large three-dimensional images at high data rate. This creates a bottleneck in computational processing and analysis of the acquired images, as the rate of acquisition outpaces the speed of processing. Moreover, images can be so large that they do not fit the main memory of a single computer. We address both issues by developing a distributed parallel algorithm for segmentation of large fluorescence microscopy images. The method is based on the versatile Discrete Region Competition algorithm, which has previously proven useful in microscopy image segmentation. The present distributed implementation decomposes the input image into smaller sub-images that are distributed across multiple computers. Using network communication, the computers orchestrate the collectively solving of the global segmentation problem. This not only enables segmentation of large images (we test images of up to 10¹⁰ pixels), but also accelerates segmentation to match the time scale of image acquisition. Such acquisition-rate image segmentation is a prerequisite for the smart microscopes of the future and enables online data compression and interactive experiments.     

Integrated and correlative high-throughput and super-resolution microscopy

We have developed a method to perform microscopic temporal and spacial multi-scale experiments by imaging cellular phenotypes of interest on complementary fluorescence microscopy systems. In a low-resolution fast data acquisition screen for phenotypic cellular responses induced by small interfering RNA (siRNA), cells in spots of siRNA cell arrays showing characteristic alterations have been selected automatically by feature space analysis. These objects were imaged on a second super-resolution dSTORM microscope (direct stochastic optical reconstruction microscopy). The coordinate transfer was based on fixed cells as reference points without the use of additional fiducial markers. This procedure is suitable to combine any kind of fluorescence microscopy technique, in order to gain further insights on the observed specimen at multiple temporal or special scales.     

Nanoscale Imaging of Caveolin-1 Membrane Domains In Vivo

Light microscopy enables noninvasive imaging of fluorescent species in biological specimens, but resolution is generally limited by diffraction to ~200–250 nm. Many biological processes occur on smaller length scales, highlighting the importance of techniques that can image below the diffraction limit and provide valuable single-molecule information. In recent years, imaging techniques have been developed which can achieve resolution below the diffraction limit. Utilizing one such technique, fluorescence photoactivation localization microscopy (FPALM), we demonstrated its ability to construct super-resolution images from single molecules in a living zebrafish embryo, expanding the realm of previous super-resolution imaging to a living vertebrate organism. We imaged caveolin-1 in vivo, in living zebrafish embryos. Our results demonstrate the successful image acquisition of super-resolution images in a living vertebrate organism, opening several opportunities to answer more dynamic biological questions in vivo at the previously inaccessible nanoscale.     

Comparison of real-time PCR and microscopy to evaluate sclerotial colonisation by a biocontrol fungus

The biocontrol agent Trichoderma harzianum colonises sclerotia of the plant pathogenic fungus Sclerotinia sclerotiorum. Plating of sclerotia typically has been used to determine the incidence of mycoparasitism, but does not quantify the extent to which individual sclerotia are colonised. We developed a specific PCR primer/probe set for the green fluorescent protein (GFP)-transformant T. harzianum ThzID1-M3, which exhibited high precision and reproducibility. Quantitative real-time PCR was evaluated along with epifluorescence microscopy and image analysis to investigate dynamics of colonisation of sclerotia in non-sterile soil. Amounts of ThzID1-M3 DNA and S. sclerotiorum DNA from entire individual sclerotia were quantified using real-time PCR. Epifluorescence micrographs were captured from sclerotial thin-section samples, and GFP fluorescence from these was quantified using computer image analysis in order to estimate colonisation on a per-sclerotium basis. As determined by either method, ThzID1-M3 colonised sclerotia in soil, and both methods quantified colonisation dynamics over time. In a separate experiment, colonisation of sclerotia on agar plates was observed using confocal laser scanning microscopy to view the GFP-fluorescing hyphae of ThzID1-M3. This method, while highly labour-intensive, provided high spatial resolution of colonisation dynamics. Thus, each method has advantages: microscopy combined with image analysis can provide useful information on the spatial and temporal dynamics of colonisation, while real-time PCR can provide a more precise assessment of the extent of sclerotial colonisation over time and can more easily be used to sample entire sclerotia.     

Diffusion Measurements inside Biofilms by Image-Based Fluorescence Recovery after Photobleaching (FRAP) Analysis with a Commercial Confocal Laser Scanning Microscope

Research about the reactional and structural dynamics of biofilms at the molecular level has made great strides, owing to efficient fluorescence imaging methods in terms of spatial resolution and fast acquisition time but also to noninvasive conditions of observation consistent with in situ biofilm studies. In addition to conventional fluorescence intensity imaging, the fluorescence recovery after photobleaching (FRAP) module can now be routinely implemented on commercial confocal laser scanning microscopes (CLSMs). This method allows measuring of local diffusion coefficients in biofilms and could become an alternative to fluorescence correlation spectroscopy (FCS). We present here an image-based FRAP protocol to improve the accuracy of FRAP measurements inside “live” biofilms and the corresponding analysis. An original kymogram representation allows control of the absence of perturbing bacterial movement during image acquisition. FRAP data analysis takes into account molecular diffusion during the bleach phase and uses the image information to extract molecular diffusion coefficients. The fluorescence spatial intensity profile analysis used here for the first time with biofilms is supported both by our own mathematical model and by a previously published one. This approach was validated to FRAP experiments on fluorescent-dextran diffusion inside Lactoccocus lactis and Stenotrophomonas maltophilia biofilms, and the results were compared to previously published FCS measurements.Biofilms are spatially organized populations of microorganisms associated with surfaces in any natural or man-made environment and embedded in a highly hydrated matrix made up of extracellular polymeric substances (EPS). This intercellular matrix constitutes the true interface between the cells and their environment. Convergent evidences suggest a permanent reorganization of the matrix as an adaptive response of the microbial community toward a changing environment (2, 12, 14). In response to external changes, bacteria may metabolize and/or produce a variety of organic exopolymers (polysaccharides, DNA, proteins, etc.) with different physicochemical properties. These EPS may act as a defensive barrier against aggressive environmental parameters (e.g., antimicrobials or predation by bacteriophages, protists, or phagocytes) (6, 8). A deeper understanding of the interrelations between the structure, the reactivity, and the variability of the extracellular polymeric matrix fastening together surface-associated bacteria is of major importance in the comprehension of the biofilm mode of life. For this purpose, the use of specific microelectrodes or ex situ analysis following extraction of polymers has been reported (7, 21). However, these approaches are invasive and poorly resolutive and do not allow dynamic observations of biofilms over time. In recent years, it has been shown that analysis of EPS properties could be greatly improved by using optical-microscopy methods that allow noninvasive in situ observations.Confocal laser scanning microscopy (CLSM), in conjunction with the use of fluorescence reporters, allows direct visualization of the three-dimensional structure of spatiotemporal biofilm and its evolution under environmental stress (e.g., antimicrobials, phages, and protists). Using time lapse imaging, it is possible to track over time the mobility of free molecules in such spatially organized biosystems (16, 19). However, only average diffusion coefficients over the macrostructure are obtained, and the method is not appropriate for fast molecular diffusion. In contrast, fluorescence correlation spectroscopy (FCS) is now a well-established method of characterization of the local and fast diffusion of fluorescently labeled molecules through the depth of a biofilm (4, 10, 11). Early on, FCS was explored by means of homemade equipment by those with specialized knowledge (9, 17). Now the method can be adapted to CLSM but requires dedicated and expensive experimental setup.To access a local resolution similar to that of FCS diffusion processes in conjunction with CLSM convenience, fluorescence recovery after photobleaching (FRAP) appears to be a good technique when the fluorophore concentration is too high for correlation measurements and sufficient for imaging. The basic principle of FRAP is to photobleach a small, spatially confined area by high-intensity laser pulses and then to observe the recovery of fluorescence inside the photobleached area as a function of time. The method has hardly ever been applied to measurements in biofilms (5, 13), and the results present some limitations. In the first approach (13), due to the low-frequency image acquisition of the CLSM setup, a very large biofilm area (800 μm²) was photobleached, leading to average diffusion coefficients over the macrostructure, including water channels and clusters. In contrast, Bryers and Drummond (5) determined local diffusion coefficients in biofilm (with a photobleached surface of ∼80 μm²), using the Axelrod mathematical model (1), which precludes any molecular diffusion during the photobleaching time and is not well adapted for very common mobile molecules (e.g., fluorophores and antibacterial molecules).We present and analyze here an image-based FRAP protocol that can be readily applied by anyone familiar with a CLSM to improve the accuracy of FRAP measurements of the molecular diffusion inside bacterial biofilms. This protocol includes (i) image acquisition of photobleached areas acquired with a commercial CLSM at high frequency, allowing bleach zones smaller than 1 μm²; (ii) an original FRAP analysis used for the first time for measurements in biofilms that takes into account molecular diffusion during the bleach phase, which is based on fluorescence intensity profiles (18) to extract molecular diffusion coefficients; and (iii) a comparison of these results with those obtained by numerical calculation of fluorescence recovery curves, using our own analytical model and the one proposed by Braga et al. (3). This approach was validated by experiments with fluorescent-dextran diffusion inside regular Lactoccocus lactis biofilms and mucoid Stenotrophomonas maltophilia biofilms, and the results were compared to FCS data previously published. However, the proposed protocol may not lead to correct estimation of molecular diffusion coefficients if no consideration of bacterial movements is taken. Indeed, such cellular dynamics may invalidate FRAP analysis and thus indicate a need for using an appropriate visualization tool like kymogram representation. Kymograms are two-dimensional graphs of fluorescence intensity measured along a line (here a straight line drawn on the full width of the images) for each image of a time lapse acquisition. It can thus be used to show fluorescence intensity fluctuations over time along a chosen trajectory and to characterize the motion of structures present in the sample (bacteria in the present study) (15). We show for the first time that kymogram representation is a powerful tool to determine the global trends of biofilm dynamics.     

When Phase Contrast Fails: ChainTracer and NucTracer,Two ImageJ Methods for Semi-Automated Single Cell Analysis Using Membrane or DNA Staining

Within bacterial populations, genetically identical cells often behave differently. Single-cell measurement methods are required to observe this heterogeneity. Flow cytometry and fluorescence light microscopy are the primary methods to do this. However, flow cytometry requires reasonably strong fluorescence signals and is impractical when bacteria grow in cell chains. Therefore fluorescence light microscopy is often used to measure population heterogeneity in bacteria. Automatic microscopy image analysis programs typically use phase contrast images to identify cells. However, many bacteria divide by forming a cross-wall that is not detectable by phase contrast. We have developed ‘ChainTracer’, a method based on the ImageJ plugin ObjectJ. It can automatically identify individual cells stained by fluorescent membrane dyes, and measure fluorescence intensity, chain length, cell length, and cell diameter. As a complementary analysis method we developed ''NucTracer'', which uses DAPI stained nucleoids as a proxy for single cells. The latter method is especially useful when dealing with crowded images. The methods were tested with Bacillus subtilis and Lactococcus lactis cells expressing a GFP-reporter. In conclusion, ChainTracer and NucTracer are useful single cell measurement methods when bacterial cells are difficult to distinguish with phase contrast.     

Detection of Legionella species in potting mixes using fluorescent in situ hybridisation (FISH)

This study used Fluorescent in situ Hybridisation (FISH) with rRNA targeted oligonucleotide probes combined with scanning confocal laser microscopy to successfully detect Legionella spp. in commercially available potting mix. A range of techniques were explored to optimise the FISH method by reducing background fluorescence and preventing non-specific binding of probes. These techniques included the use of a blocking agent, UV light treatment, image subtraction of a nonsense probe and spectral unmixing of specific probes fluorescence and autofluorescence dependent on the specific emission spectra of probe fluorophores.Spectral unmixing was the best microscopy technique for reducing background fluorescence and non-specific binding of probes was not observed. The rapid turnaround time and increased sensitivity of the FISH provides as an alternative to traditional culture methods, which are tedious and often give varied results. FISH is also advantageous compared to PCR methods as it provides information on the structure of the microbial community the bacteria is situated in. This study demonstrates that FISH could provide an alternative method for Legionella detection and enumeration in environmental samples.     

Nuclear magnetic resonance analysis of carotenoids from the burgundy plumage of the Pompadour Cotinga (Xipholena punicea)

Previous analysis of carotenoids extracted from the burgundy plumage of the Pompadour Cotinga (Xipholena punicea) revealed six novel keto-carotenoid pigments with methoxyl groups in the C3-position of one or both β-rings. High performance liquid chromatography (HPLC), mass spectrometry, chemical analysis and, in some instances ¹H NMR spectroscopy were employed to determine the structures of the molecules. Further analysis by NMR was precluded due to lack of material. The recent acquisition of multiple feathers from X. punicea specimens has made it possible to complete this work using correlated homonuclear spectroscopy (COSY), nuclear overhauser effect spectroscopy (NOESY) and ¹H NMR. These new data conclusively confirm the structures of the six methoxy-carotenoids suggested by the earlier work. In addition, the resonance positions of the protons from the novel 3-methoxy-4-keto-β-ring and 2,3-didehydro-3-methoxy-4-keto-β-ring moieties are reported here for the first time.     

Promising anti-growth effects of palladium(II) saccharinate complex of terpyridine by inducing apoptosis on transformed fibroblasts in vitro

Fibrosarcoma is one of the fatal cancer types and there is still not satisfactory success in its treatment despite new drugs. Therefore, the search for a new compound has been going on. It is currently known that some palladium-based anti-cancer compounds seem to have powerful apoptosis-inducing effects in cancer cells. For this purpose, a palladium(II)-saccharinate complex containing terpyridine which was synthesized by our research group was investigated in terms of its anti-tumor effects against mouse embryonic fibroblast NIH/3T3 (normal cell line) and rat embryonic fibroblast 5RP7 (H-ras transformed cell line) in vitro. The MTT and ATP viability assays were used to determine anti-growth/cytotoxic effects. Cytotoxic activity was confirmed by real time cytotoxicity analysis system. Flow cytometry analysis was further used to determine the mode of cell death (apoptosis/necrosis). Apoptosis was confirmed by triple-staining the cells with Hoechst 33342/PI/Calcein-AM triple and evaluated with fluorescence microscopy. It was found that the compound showed significant anti-growth activity by inducing apoptosis in a dose dependent manner. In conclusion, taking into account the cytotoxic activity of the compound at even relatively lower doses, in vivo experiments to elucidate its potential use for the treatment of fibrosarcoma are warranted.     

Amino acid analysis with o-phthalaldehyde detection: effects of reaction temperature and thiol on fluorescence yields.

Chromatographic separation of amino acids with fluorometric detection of the o-phthalaldehyde-thiol reaction product offers an analytical system of high sensitivity for most amino acids. The fluorescence yield for amino acids having a fully substituted carbon atom in the α-position with respect to the amino group can be substantially improved by increasing the temperature of the reaction with o-phthalaldehyde-thiol and by substituting either ethanethiol or methanethiol for the more commonly used β-mercaptoethanol. The analytical sensitivity for these α-branched amino acids is thus brought into line with that for the other primary amino acids. A comparison of chromatograms obtained at reaction temperatures of 25 and 100°C allows recognition of amino acids of this type in complex mixtures by the substantial increase in fluorescence yield at 100°C.     

Medium-Throughput Processing of Whole Mount In Situ Hybridisation Experiments into Gene Expression Domains

Understanding the function and evolution of developmental regulatory networks requires the characterisation and quantification of spatio-temporal gene expression patterns across a range of systems and species. However, most high-throughput methods to measure the dynamics of gene expression do not preserve the detailed spatial information needed in this context. For this reason, quantification methods based on image bioinformatics have become increasingly important over the past few years. Most available approaches in this field either focus on the detailed and accurate quantification of a small set of gene expression patterns, or attempt high-throughput analysis of spatial expression through binary pattern extraction and large-scale analysis of the resulting datasets. Here we present a robust, “medium-throughput” pipeline to process in situ hybridisation patterns from embryos of different species of flies. It bridges the gap between high-resolution, and high-throughput image processing methods, enabling us to quantify graded expression patterns along the antero-posterior axis of the embryo in an efficient and straightforward manner. Our method is based on a robust enzymatic (colorimetric) in situ hybridisation protocol and rapid data acquisition through wide-field microscopy. Data processing consists of image segmentation, profile extraction, and determination of expression domain boundary positions using a spline approximation. It results in sets of measured boundaries sorted by gene and developmental time point, which are analysed in terms of expression variability or spatio-temporal dynamics. Our method yields integrated time series of spatial gene expression, which can be used to reverse-engineer developmental gene regulatory networks across species. It is easily adaptable to other processes and species, enabling the in silico reconstitution of gene regulatory networks in a wide range of developmental contexts.     

细胞计数板在荧光显微镜观察B细胞吞噬现象的应用探讨

目的:基于细胞计数板建立一种简单、快速使用免疫荧光显微镜观察B淋巴细胞吞噬卡介苗(BCG)现象的新方法,对即将进行流式细胞检测的样品进行质控,提高流式细胞术检测吞噬率的稳定性,同时为流式细胞仪检测吞噬率提供镜下依据。方法:B细胞与FITC标记的BCG共培养24 h后,PE anti-human CD19抗体直接标记细胞膜,应用细胞计数板在荧光显微镜下观察B细胞吞噬现象,流式细胞仪检测吞噬率。结果:应用细胞计数板在荧光镜下可观察到B细胞与BCG的荧光标记及B细胞与BCG共标记现象,证实B细胞可吞噬BCG,流式细胞仪检测结果显示吞噬率为13.9%。结论:应用细胞计数板在荧光镜下可观察B细胞吞噬现象,且操作简便快速,能对流式细胞检测的样品进行质控,并提供镜下依据。     

Attachment of flagellum to the cell body is important to the kinetics of transferrin uptake by Trypanosoma cruzi

The flagellar pocket and the cytostome are surface domains of Trypanosoma cruzi epimastigote involved in acquisition of nutrients. The cytostome is physically connected to the flagellar complex. To investigate if this association plays a role in endocytosis in T. cruzi, the endocytic activity in wild type and gp72 null mutant (flagellum-cell body attachment region is absent) epimastigotes was compared. Both wild type and mutant cells were incubated with transferrin conjugated with Alexa 543 or gold particles over different time periods and thereafter qualitatively and quantitatively analyzed by flow cytometry and transmission electron microscopy. Flow cytometry analysis showed a reduction in transferrin uptake by null mutant after 30 min of incubation. In addition, at this time period, signals detected by fluorescence microscopy were slightly lower in null mutant cells. At lower incubation times, no differences between wild type and mutant epimastigotes could be observed. Quantitative data obtained by morphometric and flow cytometry analysis suggested that the speed of the endocytic process in the null mutant was similar to wild type cells, although null mutants were not able to bind cargo and therefore internalize as much as wild type epimastigotes. Our observations suggest that the physical association between cytostome and the flagellar complex plays a role in endocytosis efficiency by epimastigotes of T. cruzi.     

Extended-resolution imaging of the interaction of lipid droplets and mitochondria

Physical contacts between organelles play a pivotal role in intracellular trafficking of metabolites. Monitoring organelle interactions in living cells using fluorescence microscopy is a powerful approach to functionally assess these cellular processes. However, detailed target acquisition is typically limited due to light diffraction. Furthermore, subcellular compartments such as lipid droplets and mitochondria are highly dynamic and show significant subcellular movement. Thus, high-speed acquisition of these organelles with extended-resolution is appreciated. Here, we present an imaging informatics pipeline enabling spatial and time-resolved analysis of the dynamics and interactions of fluorescently labeled lipid droplets and mitochondria in a fibroblast cell line. The imaging concept is based on multispectral confocal laser scanning microscopy and includes high-speed resonant scanning for fast spatial acquisition of organelles. Extended-resolution is achieved by the recording of images at minimized pinhole size and by post-processing of generated data using a computational image restoration method. Computation of inter-organelle contacts is performed on basis of segmented spatial image data. We show limitations of the image restoration and segmentation part of the imaging informatics pipeline. Since both image processing methods are implemented in other related methodologies, our findings will help to identify artifacts and the false-interpretation of obtained morphometric data. As a proof-of-principle, we studied how lipid load and overexpression of PLIN5, considered to be involved in the tethering of LDs and mitochondria, affects organelle association.