Three-dimensional imaging by deconvolution microscopy

Deconvolution is a computational method used to reduce out-of-focus fluorescence in three-dimensional (3D) microscope images. It can be applied in principle to any type of microscope image but has most often been used to improve images from conventional fluorescence microscopes. Compared to other forms of 3D light microscopy, like confocal microscopy, the advantage of deconvolution microscopy is that it can be accomplished at very low light levels, thus enabling multiple focal-plane imaging of light-sensitive living specimens over long time periods. Here we discuss the principles of deconvolution microscopy, describe different computational approaches for deconvolution, and discuss interpretation of deconvolved images with a particular emphasis on what artifacts may arise.     

Image restoration for confocal microscopy: improving the limits of deconvolution, with application to the visualization of the mammalian hearing organ

Deconvolution algorithms have proven very effective in conventional (wide-field) fluorescence microscopy. Their application to confocal microscopy is hampered, in biological experiments, by the presence of important levels of noise in the images and by the lack of a precise knowledge of the point spread function (PSF) of the system. We investigate the application of wavelet-based processing tools to deal with these problems, in particular wavelet denoising methods, which turn out to be very effective in application to three-dimensional confocal images. When used in combination with more classical deconvolution algorithms, these methods provide a robust and efficient restoration scheme allowing one to deal with difficult imaging conditions. To make our approach applicable in practical situations, we measured the PSF of a Biorad-MRC1024 confocal microscope under a large set of imaging conditions, including in situ acquisitions. As a specific biological application, we present several examples of restorations of three-dimensional confocal images acquired inside an intact preparation of the hearing organ. We also provide a quantitative assessment of the gain in quality achieved by wavelet-aided restorations over classical deconvolution schemes, based on a set of numerical experiments that we performed with test images.     

Deconvolution of confocal images of dihydropyridine and ryanodine receptors in developing cardiomyocytes.

Colocalization of dihydropyridine (DHPR) and ryanodine (RyR) receptors, a key determinant of Ca(2+)-induced Ca2+ release, was previously estimated in 3-, 6-, 10-, and 20-day-old rabbit ventricular myocytes by immunocytochemistry and confocal microscopy. We now report on the effects of deconvolution (using a maximum-likelihood estimation algorithm) on the calculation of colocalization indexes. Clusters of DHPR and RyR can be accurately represented as point sources of fluorescence, which enables a model of their relative distributions to be constructed using images of point spread functions to simulate their fluorescence inside a cell. This model was used to investigate the effects of deconvolution on colocalization as a function of separation distance. Deconvolution resulted in significant improvements in both axial and transverse resolutions, producing significant increases in clarity. Comparisons of intensity profiles (full-width half-maximum) pre- and postdeconvolution showed decreased dispersion of the fluorescent signal and a corresponding decrease in false colocalization as determined by fluorescence modeling. This hypothesis was extended to physiological data previously collected. The number of colocalized voxels was quantified after deconvolution, and the degree of colocalization of DHPR with RyR decreased significantly after deconvolution in all age groups: 3 days (62 +/- 2% before deconvolution, 43 +/- 3 after deconvolution) to 20 days old (79 +/- 1% before deconvolution, 63 +/- 2% after deconvolution). The data demonstrate that confocal images should be deconvolved before any quantitative analysis, such as colocalization index determination, to minimize the detrimental effects of out-of-focus light in coincident voxels.     

图像反卷积复原技术在玉米45S rDNA转录图式研究中的运用

由于成像焦平面外杂光的干扰,宽场荧光显微镜所得的图像往往较模糊,使其不适合用来观察植物细胞核内的精细结构。该实验讨论了反卷积软件中对图像复原结果有较大影响的几个重要参数的设置。经过合适的图像反卷积复原,由宽场荧光显微镜获取的玉米45S rRNA原位杂交信号图像得以清楚显示。对所得杂交图像的分析表明:玉米45S rDNA转录往往先发生在核仁外围,且随着核仁转录活性的提高逐渐向核仁内部扩散,并最终与5S rRNA一起,在核仁内部的空洞结构中形成成熟rRNA。研究结果显示,反卷积复原可有效提高宽场荧光显微镜所得二维图像的分辨率,从而使宽场荧光显微镜在植物细胞核内精细结构研究中发挥更多的作用。     

A workingperson's guide to deconvolution in light microscopy.

Thefluorescence microscope is routinely used to study cellular structure in many biomedical research laboratories and is increasingly used as a quantitative assay system for cellular dynamics. One of the major causes of image degradation in the fluorescence microscope is blurring. Deconvolution algorithms use a model of the microscope imaging process to either subtract or reassign out-of-focus blur. A variety of algorithms are now commercially available, each with its own characteristic advantages and disadvantages. In this article, we review the imaging process in the fluorescence microscope and then discuss how the various deconvolution methods work. Finally, we provide a summary of practical tips for using deconvolution and discuss imaging artifacts and how to minimize them.     

外用红色诺卡氏菌细胞壁骨架效力测试实验方法的研究

摸索改进外用红色诺卡氏菌(Nocardia rubra)细胞壁骨架的两种效力测试方法,即流式细胞术-荧光微球法、流式细胞术-免疫双标法(荧光微球+荧光抗体),并与国家食品药品监督管理局原审批方法进行比较,经过统计学评估,评价两种方法的可行性.通过抽取小鼠免疫后获得的腹腔液注入到流式细胞仪,在发射光的荧光通路中,检测巨噬...     

Wide-field photon counting fluorescence lifetime imaging microscopy: application to photosynthesizing systems

Fluorescence lifetime imaging microscopy (FLIM) is a technique that visualizes the excited state kinetics of fluorescence molecules with the spatial resolution of a fluorescence microscope. We present a scanningless implementation of FLIM based on a time- and space-correlated single photon counting (TSCSPC) method employing a position-sensitive quadrant anode detector and wide-field illumination. The standard time-correlated photon counting approach leads to picosecond temporal resolution, making it possible to resolve complex fluorescence decays. This allows parallel acquisition of time-resolved images of biological samples under minimally invasive low-excitation conditions (<10mW/cm²). In this way unwanted photochemical reactions induced by high excitation intensities and distorting the decay kinetics are avoided. Comparably low excitation intensities are practically impossible to achieve with a conventional laser scanning microscope, where focusing of the excitation beam into a tight spot is required. Therefore, wide-field FLIM permits to study Photosystem II (PS II) in a way so far not possible with a laser scanning microscope. The potential of the wide-field TSCSPC method is demonstrated by presenting FLIM measurements of the fluorescence dynamics of photosynthetic systems in living cells of the chlorophyll d-containing cyanobacterium Acaryochloris marina.     

Image-adaptive deconvolution for three-dimensional deep biological imaging

Deconvolution algorithms are widely used in conventional fluorescence microscopy, but they remain difficult to apply to deep imaging systems such as confocal and two-photon microscopy, due to the practical difficulty of measuring the system's point spread function (PSF), especially in biological experiments. Since a separate PSF measurement performed under the design optical conditions of the microscope cannot reproduce the true experimental conditions prevailing in situ, the most natural approach to solve the problem is to extract the PSF from the images themselves. We investigate here the approach of cropping an approximate PSF directly from the images, by exploiting the presence of small structures within the samples under study. This approach turns out to be practical in many cases, allowing significantly better restorations than with a design PSF obtained by imaging fluorescent beads in gel. We demonstrate the advantages of this approach with a number of deconvolution experiments performed both on artificially blurred and noisy test images, and on real confocal images taken within an in vitro preparation of the mouse hearing organ.     

DeconvTest: Simulation framework for quantifying errors and selecting optimal parameters of image deconvolution

Deconvolution is an essential step of image processing that aims to compensate for the image blur caused by the microscope's point spread function. With many existing deconvolution methods, it is challenging to choose the method and its parameters most appropriate for particular image data at hand. To facilitate this task, we developed DeconvTest: an open‐source Python‐based framework for generating synthetic microscopy images, deconvolving them with different algorithms, and quantifying reconstruction errors. In contrast to existing software, DeconvTest combines all components required to analyze deconvolution performance in a systematic, high‐throughput and quantitative manner. We demonstrate the power of the framework by using it to identify the optimal deconvolution settings for synthetic and real image data. Based on this, we provide a guideline for (a) choosing optimal values of deconvolution parameters for image data at hand and (b) optimizing imaging conditions for best results in combination with subsequent image deconvolution.     

In vivo resolution of multiexponential decays of multiple near-infrared molecular probes by fluorescence lifetime-gated whole-body time-resolved diffuse optical imaging

The biodistribution of two near-infrared fluorescent agents was assessed in vivo by time-resolved diffuse optical imaging. Bacteriochlorophyll a (BC) and cypate-glysine-arginine-aspartic acid-serine-proline-lysine-OH (Cyp-GRD) were administered separately or combined to mice with subcutaneous xenografts of human breast adenocarcinoma and slow-release estradiol pellets for improved tumor growth. The same excitation (780 nm) and emission (830 nm) wavelengths were used to image the distinct fluorescence lifetime distribution of the fluorescent molecular probes in the mouse cancer model. Fluorescence intensity and lifetime maps were reconstructed after raster-scanning whole-body regions of interest by time-correlated single-photon counting. Each captured temporal point-spread function (TPSF) was deconvolved using both a single and a multiexponental decay model to best determine the measured fluorescence lifetimes. The relative signal from each fluorophore was estimated for any region of interest included in the scanned area. Deconvolution of the individual TPSFs from whole-body fluorescence intensity scans provided corresponding lifetime images for comparing individual component biodistribution. In vivo fluorescence lifetimes were determined to be 0.8 ns (Cyp-GRD) and 2 ns (BC). This study demonstrates that the relative biodistribution of individual fluorophores with similar spectral characteristics can be compartmentalized by using the time-domain fluorescence lifetime gating method.     

Deconvolution of images from 3D printed cells in layers on a chip

Layer‐by‐layer cell printing is useful in mimicking layered tissue structures inside the human body and has great potential for being a promising tool in the field of tissue engineering, regenerative medicine, and drug discovery. However, imaging human cells cultured in multiple hydrogel layers in 3D‐printed tissue constructs is challenging as the cells are not in a single focal plane. Although confocal microscopy could be a potential solution for this issue, it compromises the throughput which is a key factor in rapidly screening drug efficacy and toxicity in pharmaceutical industries. With epifluorescence microscopy, the throughput can be maintained at a cost of blurred cell images from printed tissue constructs. To rapidly acquire in‐focus cell images from bioprinted tissues using an epifluorescence microscope, we created two layers of Hep3B human hepatoma cells by printing green and red fluorescently labeled Hep3B cells encapsulated in two alginate layers in a microwell chip. In‐focus fluorescent cell images were obtained in high throughput using an automated epifluorescence microscopy coupled with image analysis algorithms, including three deconvolution methods in combination with three kernel estimation methods, generating a total of nine deconvolution paths. As a result, a combination of Inter‐Level Intra‐Level Deconvolution (ILILD) algorithm and Richardson‐Lucy (RL) kernel estimation proved to be highly useful in bringing out‐of‐focus cell images into focus, thus rapidly yielding more sensitive and accurate fluorescence reading from the cells in different layers. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:445–454, 2018     

Three-dimensional tracking of single secretory granules in live PC12 cells

Deconvolution wide-field fluorescence microscopy and single-particle tracking were used to study the three-dimensional mobility of single secretory granules in live PC12 cells. Acridine orange-labeled granules were found to travel primarily in random and caged diffusion, whereas only a small fraction of granules traveled in directed fashion. High K(+) stimulation increased significantly the percentage of granules traveling in directed fashion. By dividing granules into the near-membrane group (within 1 microm from the plasma membrane) and cytosolic group, we have revealed significant differences between these two groups of granules in their mobility. The mobility of these two groups of granules is also differentially affected by disruption of F-actin, suggesting different mechanisms are involved in the motion of the two groups of granules. Our results demonstrate that combined deconvolution and single-particle tracking may find its application in three-dimensional tracking of long-term motion of granules and elucidating the underlying mechanisms.     

Measuring and interpreting point spread functions to determine confocal microscope resolution and ensure quality control

This protocol outlines a procedure for collecting and analyzing point spread functions (PSFs). It describes how to prepare fluorescent microsphere samples, set up a confocal microscope to properly collect 3D confocal image data of the microspheres and perform PSF measurements. The analysis of the PSF is used to determine the resolution of the microscope and to identify any problems with the quality of the microscope's images. The PSF geometry is used as an indicator to identify problems with the objective lens, confocal laser scanning components and other relay optics. Identification of possible causes of PSF abnormalities and solutions to improve microscope performance are provided. The microsphere sample preparation requires 2-3 h plus an overnight drying period. The microscope setup requires 2 h (1 h for laser warm up), whereas collecting and analyzing the PSF images require an additional 2-3 h.     

活体细胞三维图像科学可视化方法的研究

科学可视化是指运用计算机图形学和图像处理技术,将科学计算过程中或者是计算结果的数据转换为图形或图像,在屏幕上显示出来并进行交互式处理的理论技术或方法。介绍了用反卷积荧光显微成像技术获得活体大鼠胰腺B细胞三维图像及对其进行科学可视化的主要过程和两种常用可视化算法,并运用这两种方法对所得到的三维图像进行处理以分析和研究细胞内分泌囊泡的空间分布。结果显示,当仅观察细胞三维图像的二维切片时,三维图像中的某些重要信息会被忽略,而使用科学可视化方法则可以从三维角度直观观察活体细胞内分泌囊泡的空间分布,并且可以观察到分泌囊泡的释放趋势和整体分布,从而为细胞生物学研究提供重要的信息。     

An automated analysis of highly complex flow cytometry-based proteomic data

The combination of color-coded microspheres as carriers and flow cytometry as a detection platform provides new opportunities for multiplexed measurement of biomolecules. Here, we developed a software tool capable of automated gating of color-coded microspheres, automatic extraction of statistics from all subsets and validation, normalization, and cross-sample analysis. The approach presented in this article enabled us to harness the power of high-content cellular proteomics. In size exclusion chromatography-resolved microsphere-based affinity proteomics (Size-MAP), antibody-coupled microspheres are used to measure biotinylated proteins that have been separated by size exclusion chromatography. The captured proteins are labeled with streptavidin phycoerythrin and detected by multicolor flow cytometry. When the results from multiple size exclusion chromatography fractions are combined, binding is detected as discrete reactivity peaks (entities). The information obtained might be approximated to a multiplexed western blot. We used a microsphere set with >1,000 subsets, presenting an approach to extract biologically relevant information. The R-project environment was used to sequentially recognize subsets in two-dimensional space and gate them. The aim was to extract the median streptavidin phycoerythrin fluorescence intensity for all 1,000+ microsphere subsets from a series of 96 measured samples. The resulting text files were subjected to algorithms that identified entities across the 24 fractions. Thus, the original 24 data points for each antibody were compressed to 1-4 integrated values representing the areas of individual antibody reactivity peaks. Finally, we provide experimental data on cellular protein changes induced by treatment of leukemia cells with imatinib mesylate. The approach presented here exemplifies how large-scale flow cytometry data analysis can be efficiently processed to employ flow cytometry as a high-content proteomics method.     

A duplexed microsphere-based fluorescent immunoassay

Microsphere-based immunoassays are described for the simultaneous measurement of the clinically important drugs digoxin and theophylline. Competitive immunoassays were performed using haptenized microspheres and antibodies labeled with horseradish peroxidase. Enzyme-catalyzed reporter deposition (CARD) resulted in immunofluorescence signal amplification. Two encoding dyes were used to differentiate analytical signals from microspheres containing assays for the two analytes. An epifluorescence microscope and a CCD camera interfaced with a computer were utilized to measure fluorescence signals of individual microspheres. The microspheres from a duplexed assay were mounted on microscope slides as well as inserted into wells etched into the distal ends of optical imaging fibers. Fluorescence images from both formats were captured. In the experiments using microscope slides, the immunoassays were successfully duplexed and only marginal interferences at high analyte concentrations were observed. Preliminary results suggest that simultaneous determination of the two analytes using a fiber-based sensor-array format is feasible, but requires further development before precise quantitative analyses are possible.     

Analysis of Fluorescence Decay by the Nonlinear Least Squares Method

Fluorescence decay deconvolution analysis to fit a multiexponential function by the nonlinear least squares method requires numerical calculation of a convolution integral. A linear approximation of the successive data of the instrument response function is proposed for the computation of the convolution integral. Deconvolution analysis of simulated fluorescence data were carried out to show that the linear approximation method is generally better when one of the lifetimes is comparable to the time interval between data.     

Determination of linear fluorescence intensities from flow cytometric data accumulated with logarithmic amplifiers

Logarithmic amplifiers are useful in accumulating flow cytometric data with a large dynamic range. However, quantitative comparison of fluorescence intensities for different samples or different subpopulations within a sample is simplified by the conversion of data from log space back to linear space. A method is described in which fluorescent polystyrene spheres of differing intensities are used to construct a calibration curve for the logarithmic intensity scale. This allows calculation of relative linear intensity for each channel of the logarithmically accumulated data and determination of linear fluorescence means and coefficients of variation for comparative purposes. Fluorescent spheres of appropriate intensity may also be used as internal standards to monitor instrument and/or stain stability for samples accumulated using logarithmic amplifiers.     

IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ, and TMT

Isobaric peptide labeling plays an important role in relative quantitative comparisons of proteomes. Isobaric labeling techniques utilize MS/MS spectra for relative quantification, which can be either based on the relative intensities of reporter ions in the low mass region (iTRAQ and TMT) or on the relative intensities of quantification signatures throughout the spectrum due to isobaric peptide termini labeling (IPTL). Due to the increased quantitative information found in MS/MS fragment spectra generated by the recently developed IPTL approach, new software was required to extract the quantitative information. IsobariQ was specifically developed for this purpose; however, support for the reporter ion techniques iTRAQ and TMT is also included. In addition, to address recently emphasized issues about heterogeneity of variance in proteomics data sets, IsobariQ employs the statistical software package R and variance stabilizing normalization (VSN) algorithms available therein. Finally, the functionality of IsobariQ is validated with data sets of experiments using 6-plex TMT and IPTL. Notably, protein substrates resulting from cleavage by proteases can be identified as shown for caspase targets in apoptosis.     

Novel, fluorescent, magnetic, polysaccharide-based microsphere for orientation, tracing, and anticoagulation: preparation and characterization

A fluorescent, magnetic composite poly(styrene-maleic anhydride) microsphere, suitable for conjugation with polysaccharide, was synthesized using magnetite/europium phthalate particles as seeds by copolymerization of styrene and maleic anhydride. The magnetite/europium phthalate particles were wrapped up by poly(ethylene glycol), which improved the affinity between the seed particles and the monomers. The composite microspheres obtained, with a diameter of 0.15-0.7 microm, contain 586-1013 microg of magnetite/g of microsphere and 0.5-16 mmol surface anhydride groups/g of microsphere. Heparin was conjugated with the reactive surface anhydride groups on the surface of the microspheres by covalent binding to obtain a fluorescent, magnetic, polysaccharide-based microsphere. The microspheres not only retain their bioactivities but also provide magnetic susceptibility and fluorescence. They can be used as a carrier with magnetic orientation and fluorescence tracer for potent drug targeting. The orientation, tracer, and anticoagulation of the fluorescence, magnetic, polysaccharide-based microspheres were studied. The anticoagulant activity of the microspheres and heparin binding capacity reached 54,212.8 U and 607.1 mg/g of dry microspheres. The activity recovery was 50.2%. The anticoagulant activity of the microspheres increases with the increase of the conjugated heparin on the surface of the microspheres and the decrease of the microsphere size. Furthermore, The fluorescent, magnetic, polysaccharide-based microspheres can be easily transported to a given position in a magnetic field and traced via their fluorescence.