Artefacts in restored images due to intensity loss in three-dimensional fluorescence microscopy

Bleach correction ImageJ plugin for compensating the photobleaching of time-lapse sequences

During the capturing of the time-lapse sequence of fluorescently labeled samples, fluorescence intensity exhibits decays. This phenomenon is known as 'photobleaching' and is a widely known problem in imaging in life sciences. The photobleaching can be attenuated by tuning the imaging set-up, but when such adjustments only partially work, the image sequence can be corrected for the loss of intensity in order to precisely segment the target structure or to quantify true intensity dynamics. We implemented an ImageJ plugin that allows the user to compensate for the photobleaching to estimate the non-bleaching condition with choice of three different algorithms: simple ratio, exponential fitting, and histogram matching methods. The histogram matching method is a novel algorithm for photobleaching correction. This article presents details and characteristics of each algorithm based on application to actual image sequences.

Isolating specific cell and tissue compartments from 3D images for quantitative regional distribution analysis using novel computer algorithms

BACKGROUND

Isolating specific cellular and tissue compartments from 3D image stacks for quantitative distribution analysis is crucial for understanding cellular and tissue physiology under normal and pathological conditions. Current approaches are limited because they are designed to map the distributions of synapses onto the dendrites of stained neurons and/or require specific proprietary software packages for their implementation.

NEW METHOD

To overcome these obstacles, we developed algorithms to Grow and Shrink Volumes of Interest (GSVI) to isolate specific cellular and tissue compartments from 3D image stacks for quantitative analysis and incorporated these algorithms into a user-friendly computer program that is open source and downloadable at no cost.

RESULTS

The GSVI algorithm was used to isolate perivascular regions in the cortex of live animals and cell membrane regions of stained spinal motoneurons in histological sections. We tracked the real-time, intravital biodistribution of injected fluorophores with sub-cellular resolution from the vascular lumen to the perivascular and parenchymal space following a vascular microlesion, and mapped the precise distributions of membrane-associated KCC2 and gephyrin immunolabeling in dendritic and somatic regions of spinal motoneurons.

COMPARISON WITH EXISTING METHODS

Compared to existing approaches, the GSVI approach is specifically designed for isolating perivascular regions and membrane-associated regions for quantitative analysis, is user-friendly, and free.

CONCLUSIONS

The GSVI algorithm is useful to quantify regional differences of stained biomarkers (e.g., cell membrane-associated channels) in relation to cell functions, and the effects of therapeutic strategies on the redistributions of biomolecules, drugs, and cells in diseased or injured tissues.

Bleaching-corrected fluorescence microspectroscopy with nanometer peak position resolution

Fluorescence microspectroscopy (FMS) with environmentally sensitive dyes provides information about local molecular surroundings at microscopic spatial resolution. Until recently, only probes exhibiting large spectral shifts due to local changes have been used. For filter-based experimental systems, where signal at different wavelengths is acquired sequentially, photostability has been required in addition. Herein, we systematically analyzed our spectral fitting models and bleaching correction algorithms which mitigate both limitations. We showed that careful analysis of data acquired by stochastic wavelength sampling enables nanometer spectral peak position resolution even for highly photosensitive fluorophores. To demonstrate how small spectral shifts and changes in bleaching rates can be exploited, we analyzed vesicles in different lipid phases. Our findings suggest that a wide range of dyes, commonly used in bulk spectrofluorimetry but largely avoided in microspectroscopy due to the above-mentioned restrictions, can be efficiently applied also in FMS.

Analysis of cholesterol trafficking with fluorescent probes

Cholesterol plays an important role in determining the biophysical properties of biological membranes, and its concentration is tightly controlled by homeostatic processes. The intracellular transport of cholesterol among organelles is a key part of the homeostatic mechanism, but sterol transport processes are not well understood. Fluorescence microscopy is a valuable tool for studying intracellular transport processes, but this method can be challenging for lipid molecules because addition of a fluorophore may alter the properties of the molecule greatly. We discuss the use of fluorescent molecules that can bind to cholesterol to reveal its distribution in cells. We also discuss the use of intrinsically fluorescent sterols that closely mimic cholesterol, as well as some minimally modified fluorophore-labeled sterols. Methods for imaging these sterols by conventional fluorescence microscopy and by multiphoton microscopy are described. Some label-free methods for imaging cholesterol itself are also discussed briefly.

Optimal multiresolution blending of confocal microscope images

Typical mosaicing schemes assume that to-be-combined images are equally informative; thus, the images are processed in a similar manner. However, the new imaging technique for confocal fluorescence images has revealed a problem when two asymmetrically informative biological images are stitched during microscope image mosaicing. The latter process is widely used in biological studies to generate a higher resolution image by combining multiple images taken at different times and angles. To resolve the earlier problem, we propose a multiresolution optimization approach that evaluates the blending coefficients based on the relative importance of the overlapping regions of the to-be-combined image pair. The blending coefficients are the optimal solution obtained by a quadratic programming algorithm with constraints that are enforced by the biological requirements. We demonstrate the efficacy of the proposed approach on several confocal microscope fluorescence images and compare the results with those derived by other methods.

Potential of ultraviolet wide-field imaging and multiphoton microscopy for analysis of dehydroergosterol in cellular membranes

Dehydroergosterol (DHE) is an intrinsically fluorescent sterol with absorption/emission in the ultraviolet (UV) region and biophysical properties similar to those of cholesterol. We compared the potential of UV-sensitive low-light-level wide-field (UV-WF) imaging with that of multiphoton (MP) excitation microscopy to monitor DHE in living cells. Significantly reduced photobleaching in MP microscopy of DHE enabled us to acquire three-dimensional z-stacks of DHE-stained cells and to obtain high-resolution maps of DHE in surface ruffles, nanotubes, and the apical membrane of epithelial cells. We found that the lateral resolution of MP microscopy is ∼1.5-fold higher than that of UV-WF deconvolution microscopy, allowing for improved spatiotemporal analysis of plasma membrane sterol distribution. Surface intensity patterns of DHE with a diameter of 0.2 μm persisting over several minutes could be resolved by MP time-lapse microscopy. Diffusion coefficients of 0.25-μm-diameter endocytic vesicles containing DHE were determined by MP spatiotemporal image correlation spectroscopy. The requirement of extremely high laser power for visualization of DHE by MP microscopy made this method less potent for multicolor applications with organelle markers like green fluorescent protein-tagged proteins. The signal-to-noise ratio obtainable by UV-WF imaging could be significantly improved by pixelwise bleach rate fitting and calculation of an amplitude image from the decay model and by frame averaging after pixelwise bleaching correction of the image stacks. We conclude that UV-WF imaging and MP microscopy of DHE provide complementary information regarding membrane distribution and intracellular targeting of sterols.

High-resolution local imaging of temperature in dielectrophoretic platforms

The use of dielectrophoretic forces is crucially tied to the knowledge of Joule heating within a fluid, since the use of planar microelectrodes creates a temperature gradient within which the particle of interest is manipulated. Mapping temperature with sufficient spatial resolution within a dielectrophoretic trap is recognized to be of high importance. Herein, we demonstrate local temperature measurements in the vicinity of a trapped micrometer-size particle using confocal fluorescence spectroscopy. Such measurements are shown to provide a novel calibration tool for screening temperature-mediated processes with high resolution.

Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls

The vast majority of microscopic data in biology of the cell nucleus is currently collected using fluorescence microscopy, and most of these data are subsequently subjected to quantitative analysis. The analysis process unites a number of steps, from image acquisition to statistics, and at each of these steps decisions must be made that may crucially affect the conclusions of the whole study. This often presents a really serious problem because the researcher is typically a biologist, while the decisions to be taken require expertise in the fields of physics, computer image analysis, and statistics. The researcher has to choose between multiple options for data collection, numerous programs for preprocessing and processing of images, and a number of statistical approaches. Written for biologists, this article discusses some of the typical problems and errors that should be avoided. The article was prepared by a team uniting expertise in biology, microscopy, image analysis, and statistics. It considers the options a researcher has at the stages of data acquisition (choice of the microscope and acquisition settings), preprocessing (filtering, intensity normalization, deconvolution), image processing (radial distribution, clustering, co-localization, shape and orientation of objects), and statistical analysis.

Fluorescent sterols as tools in membrane biophysics and cell biology

Cholesterol is an important constituent of cellular membranes playing a fundamental role in many biological processes. This sterol affects membrane permeability, lateral lipid organization, signal transduction and membrane trafficking. Intracellular sterol transport modes and pathways as well as the regulation of sterol metabolism and disposition in various tissues are areas of intense research. Progress is intimately linked to development and use of appropriate analogs, which closely mimic the properties of cholesterol while allowing to be detected by spectroscopic or microscopic methods. This review provides an overview of various fluorescent sterols used in membrane biophysics and cell biology including analogs of cholesterol and cholesteryl esters. Attention is paid to the natural fluorescent sterol dehydroergosterol (DHE). A survey of the many applications of DHE in biological research is presented. Special emphasis is on recent developments in fluorescence microscopy instrumentation to visualize DHE as an intrinsically fluorescent analog of cholesterol in living cells.

Discrimination between benign and malignant prostate tissue using chromatin texture analysis in 3-D by confocal laser scanning microscopy

BACKGROUND

Analysis of chromatin texture may improve both the diagnosis and the assessment of the prognosis of prostate cancer. Confocal laser scanning microscopy (CLSM) allows performing measurements in nuclei reconstructed in 3-D. The aim of this study was to evaluate the clinical usefulness of 3-D texture analysis of prostate tissue.

METHODS

Image stacks of eight prostate cancer sections were obtained by CLSM of both benign and malignant areas. Texture feature values were computed for individual nuclei. The discriminative power of the texture features was established by receiver operating characteristic (ROC) analysis and linear discriminant analysis (LDA).

RESULTS

Texture features were identified that could discriminate between benign and malignant nuclei. LDA correctly classified 89% of the nuclei of the pooled set of benign and malignant nuclei.

CONCLUSIONS

3-D nuclear texture features allow discrimination of most benign and malignant prostate nuclei. We estimate that the classification rates can be increased by improving the image quality.

Towards many colors in FISH on 3D-preserved interphase nuclei

The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process. We discuss (1) M-FISH (combinatorial labeling + deconvolution + wide-field microscopy); (2) multicolor labeling + SIM (structured illumination microscopy); (3) the standard approach to multicolor FISH + CLSM (confocal laser scanning microscopy; one fluorochrome - one color channel); (4) combinatorial labeling + CLSM; (5) non-combinatorial labeling + CLSM + linear unmixing. Two related issues, deconvolution of images acquired with CLSM and correction of data for chromatic Z-shift, are also discussed. All methods are illustrated with practical examples. Finally, several rules of thumb helping to choose an optimal labeling + microscopy combination for the planned experiment are suggested.

Methods for compensation of the light attenuation with depth of images captured by a confocal microscope

A confocal laser scanning microscope (CLSM) enables us to capture images from a biological specimen in different depths and obtain a series of precisely registered fluorescent images. However, images captured from deep layers of the specimen may be darker than images from the topmost layers because of light loss distortions. This effect causes difficulties in subsequent analysis of biological objects. We propose a solution using two approaches: either an online method working already during image acquisition or an offline method assisting as a postprocessing step. In the online method, the gain value of a photomultiplier tube of a CLSM is controlled according to the difference of mean image intensities between the reference and currently acquired image. The offline method consists of two stages. In the first stage, a standard histogram maintaining relative frequencies of gray levels and improving brightness and contrast is created from all images in the series. In the second stage, individual image histograms are warped according to this standard histogram. The methods were tested on real confocal image data captured from human placenta and rat skeletal muscle specimens. It was shown that both approaches diminish the light attenuation in images captured from deep layers of the specimen.

Improved visualization and quantitative analysis of fluorescent membrane sterol in polarized hepatic cells

Dehydroergosterol is a natural yeast sterol which has recently been employed for direct observation of intracellular sterol transport by UV microscopy. Here, methods are described for improved visualization and quantification of dehydroergosterol in the membranes of polarized HepG2 cells. Using a new online assay, it is shown that dehydroergosterol derived from a cyclodextrin complex inserted into the plasma membrane with a half time of t(1/2) approximately 34 s. Based on a detailed bleaching analysis of dehydroergosterol, slightly different bleaching rates for dehydroergosterol in the basolateral and canalicular membrane were found, indicating different fluorophore environments. Bleaching correction in concert with 3D imaging allows for detection of dehydroergosterol enrichment in microvilli of the canalicular membrane forming the biliary canaliculus. Evidence is provided that some dehydroergosterol accumulating in a subapical compartment or apical recycling compartment can rapidly (t(1/2) approximately 2 min) exchange in vesicles towards the biliary canaliculus while the majority of dehydroergosterol does not redistribute from this compartment. The rapidly exchanging pool resembles only a small portion of the total subapical compartment or apical recycling compartment-associated dehydroergosterol (about 15-30%). Kinetic modelling supports the theory that the subapical compartment or apical recycling compartment to biliary canaliculus transport pathway for sterol is unidirectional. This pathway might be important for rapid biliary transport of free sterol produced by hydrolysis of cholesteryl esters derived from high density lipoprotein.

Fully automated intensity compensation for confocal microscopic images

One well-recognized problem in three-dimensional (3D) confocal microscopic images is that the intensities in deeper slices are generally weaker than those in shallower slices. The loss of intensity with depth hampers both qualitative observation and quantitative measurement of specimens. Two major types of methods exist to compensate for this intensity loss: the first is based on the geometrical optics inside the specimen, and the second applies an empirical parametric intensity decay function (IDF) of depth. A common feature shared by both methods is that they are parameter-dependent. However, for the optics-based method there are as yet no fully automated parameter-setting approaches; and for the IDF method the traditional profile-fitting approach cannot provide proper parameters if the presumed IDF model does not match the experimental intensity-depth profile of the 3D image. In this paper, we propose a novel maximum-entropy (ME) approach to fully automated parameter-setting. In principle the ME approach is suitable for any compensation method as long as it is parameter-dependent. The basic assumption is that without intensity loss an ideal 3D image should be generally homogeneous with respect to depth and this axial homogeneity can be represented by the entropy of a normalized intensity-depth profile. Experiments on real confocal images showed that such a profile was consistent with visual evaluation of axial intensity homogeneity and that the ME approach could provide proper parameters for both compensation methods mentioned above. Moreover, for the IDF method, experiments on both real and simulated data showed that the ME approach could provide more precise parameters than with traditional profile-fitting. The Appendix provides a proof that under certain conditions the global maximization of the profile-entropy is guaranteed.

A method for the blind correction of the effects of attenuation and shading in light micrographs based upon moderated histogram equalization

A means of correcting for the effects of attenuation and shading in multi-dimensional, digital, light micrographs, blindly, i.e. without the need for additional control sets of image data that record these effects, is described. The method, termed trans-elemental moderated histogram equalization (TEMHE), works with all three types of image that are collected in light microscopy: bright objects viewed against a dark background, bright and dark objects set against a grey background and darker objects set against a light background. In its most simple form TEMHE requires that the features of interest are distributed widely and evenly throughout the image data. If, however, the pattern of attenuation or shading is extracted, smoothed and the result used to correct the original set of image data, then the only restriction is that when different classes of feature are present the boundaries between them are not approximately parallel to the axes of one, or more, of the dimensions to be corrected. Moreover, when it is possible to formulate a simple model of the pattern of attenuation or shading this is no longer a constraint. The method does need to analyse a large number of elements of image data (pixels, voxels, etc.) to function correctly but it will correct shading in single frames of image data providing that they are quite large and the overall signal-to-noise ratio is relatively high.

Nascent RNA synthesis in the context of chromatin architecture

Based on the idea that chromatin domains provide physical barriers for large molecules and multi-enzyme complexes, including the components of the transcription machinery, it has been proposed that transcription should be confined to the surfaces of chromatin domains. As a consequence nascent RNA should accumulate in the interchromatin space, which is thought to provide a special nuclear compartment involved in transcription, as well as in the processing and export of RNA (Cremer et al. 1993, Cremer & Cremer 2001). To further address the relationships between chromatin organization and RNA synthesis, we investigated the localization of BrUTP-labelled nascent RNA in HeLa cells stably expressing green fluorescent protein (GFP)-tagged histone H2B, which highlights the chromatin structure. Our results showed that nascent RNA does not preferentially localize within the interchromatin space. The findings do not support the idea that the interchromatin space provides a nuclear compartment playing an essential role in nascent RNA synthesis. However, the results are in agreement with the emerging view that even condensed chromatin domains display a highly dynamic organization and are not a physical barrier for transcription factors.

Visualizing chromatin and chromosomes in living cells

The dynamic organization of eukaryotic genomes in cell nuclei recently came into the focus of research interest. The kinetics of genome dynamics can be addressed only by approaches involving live cell microscopy. Different methods are available to visualize chromatin, specific chromatin fractions, or individual chromosome territories within nuclei of living mammalian cells. Appropriate labeling procedures as well as cell chamber systems and important controls for live cell microscopy are described.