Fluorescence lifetime imaging in scanning microscopes: acquisition speed, photon economy and lifetime resolution

In this paper a detailed discussion is presented of the factors that affect the fluorescence lifetime imaging performance of a scanning microscope equipped with a single photon counting based, two‐ to eight‐channel, time‐gated detection system. In particular we discuss the sensitivity, lifetime resolution, acquisition speed, and the shortest lifetimes that can be measured. Detection systems equipped with four to eight time‐gates are significantly more sensitive than the two time‐gate system. Only minor sensitivity differences were found between systems with four or more time‐gates. Experiments confirm that the lifetime resolution is dominated by photon statistics. The time response of the detector determines the shortest lifetimes that can be resolved; about 25 ps for fast MCP‐PMTs and 300–400 ps for other detectors. The maximum count rate of fast MCP‐PMTs, however, is 10–100 times lower than that of fast PMTs. Therefore, the acquisition speed with MCP‐PMT based systems is limited. With a fast PMT operated close to its maximum count rate we were able to record a fluorescence lifetime image of a beating myocyte in less than one second.     

Recent research on stimulated emission depletion microscopy for reducing photobleaching

Stimulated emission depletion (STED) microscopy is a useful tool in investigation for super‐resolution realm. By silencing the peripheral fluorophores of the excited spot, leaving only the very centre zone vigorous for fluorescence, the effective point spread function (PSF) could be immensely squeezed and subcellular structures, such as organelles, become discernable. Nevertheless, because of the low cross‐section of stimulated emission and the short fluorescence lifetime, the depletion power density has to be extremely higher than the excitation power density and molecules are exposed in high risk of photobleaching. The existence of photobleaching greatly limits the research of STED in achieving higher resolution and more delicate imaging quality, as well as long‐term and dynamic observation. Since the first experimental implementation of STED microscopy, researchers have lift out variety of methods and techniques to alleviate the problem. This paper would present some researches via conventional methods which have been explored and utilised relatively thoroughly, such as fast scanning, time‐gating, two‐photon excitation (TPE), triplet relaxation (T‐Rex) and background suppression. Alternatively, several up‐to‐date techniques, especially adaptive illumination, would also be unveiled for discussion in this paper. The contrast and discussion of these modalities would play an important role in ameliorating the research of STED microscopy.     

Calibration of a wide-field frequency-domain fluorescence lifetime microscopy system using light emitting diodes as light sources

High brightness light emitting diodes are an inexpensive and versatile light source for wide‐field frequency‐domain fluorescence lifetime imaging microscopy. In this paper a full calibration of an LED based fluorescence lifetime imaging microscopy system is presented for the first time. A radio‐frequency generator was used for simultaneous modulation of light emitting diode (LED) intensity and the gain of an intensified charge coupled device (CCD) camera. A homodyne detection scheme was employed to measure the demodulation and phase shift of the emitted fluorescence, from which phase and modulation lifetimes were determined at each image pixel. The system was characterized both in terms of its sensitivity to measure short lifetimes (500 ps to 4 ns), and its capability to distinguish image features with small lifetime differences. Calibration measurements were performed in quenched solutions containing Rhodamine 6G dye and the results compared to several independent measurements performed with other measurement methodologies, including time correlated single photon counting, time gated detection, and acousto optical modulator (AOM) based modulation of excitation sources. Results are presented from measurements and simulations. The effects of limited signal‐to‐noise ratios, baseline drifts and calibration errors are discussed in detail. The implications of limited modulation bandwidth of high brightness, large area LED devices (～40 MHz for devices used here) are presented. The results show that phase lifetime measurements are robust down to sub ns levels, whereas modulation lifetimes are prone to errors even at large signal‐to‐noise ratios. Strategies for optimizing measurement fidelity are discussed. Application of the fluorescence lifetime imaging microscopy system is illustrated with examples from studies of molecular mixing in microfluidic devices and targeted drug delivery research.     

Scanning-less wide-field single-photon counting device for fluorescence intensity, lifetime and time-resolved anisotropy imaging microscopy

A scanning‐less single‐photon counting system for FLIM and fluorescence anisotropy wide‐field imaging is described and characterized in this paper. The two polarizations of the fluorescence are divided by a Glan prism and acquired at the same time by the Q_A detector. Fluorescence decay profiles can be reconstructed for any desired area up to each pixel and used to calculate time‐resolved fluorescence anisotropy decays.     

A 3D aligning method for stimulated emission depletion microscopy using fluorescence lifetime distribution

Optimal resolution by stimulated emission depletion (STED) microscopy requires precise alignment of the donut‐shaped depletion focus to the excitation focus. In this article, we demonstrate that fluorescence lifetime distribution can be implemented to align the STED system. Different from the traditional aligning methods in which a scattering imaging module is often equipped, the lifetime‐based method is free from probable mismatches between the scattering mode and the fluorescent mode, drift errors caused by separate imaging and complex fitting methods. Based on this method, a spatial resolution of 38 nm by time‐gated detection has been achieved. Microsc. Res. Tech. 77:935–940, 2014. © 2014 Wiley Periodicals, Inc.     

A protocol for registration and correction of multicolour STED superresolution images

Multicolour fluorescence imaging by STimulated Emission Depletion (STED) superresolution microscopy with doughnut‐shaped STED laser beams based on different wavelengths for each colour channel requires precise image registration. This is especially important when STED imaging is used for co‐localisation studies of two or more native proteins in biological specimens to analyse nanometric subcellular spatial arrangements. We developed a robust postprocessing image registration protocol, with the aim to verify and ultimately optimise multicolour STED image quality. Importantly, this protocol will support any subsequent quantitative localisation analysis at nanometric scales. Henceforth, using an approach that registers each colour channel present during STED imaging individually, this protocol reliably corrects for optical aberrations and inadvertent sample drift. To achieve the latter goal, the protocol combines the experimental sample information, from corresponding STED and confocal images using the same optical beam path and setup, with that of an independent calibration sample. As a result, image registration is based on a strategy that maximises the cross‐correlation between sequentially acquired images of the experimental sample, which are strategically combined by the protocol. We demonstrate the general applicability of the image registration protocol by co‐staining of the ryanodine receptor calcium release channel in primary mouse cardiomyocytes. To validate this new approach, we identify user‐friendly criteria, which – if fulfilled – support optimal image registration. In summary, we introduce a new method for image registration and rationally based postprocessing steps through a highly standardised protocol for multicolour STED imaging, which directly supports the reproducibility of protein co‐localisation analyses. Although the reference protocol is discussed exemplarily for two‐colour STED imaging, it can be readily expanded to three or more colours and STED channels.     

A comparison study of detecting gold nanorods in living cells with confocal reflectance microscopy and two‐photon fluorescence microscopy

Two‐photon fluorescence microscopy and confocal reflectance microscopy were compared to detect intracellular gold nanorods in rat basophilic leukaemia cells. The two‐photon photoluminescence images of gold nanorods were acquired by an 800 nm fs laser with the power of milliwatts. The advantages of the obtained two‐photon photoluminescence images are high spatial resolution and reduced background. However, a remarkable photothermal effect on cells was seen after 30 times continuous scanning of the femto‐second laser, potentially affecting the subcellular localization pattern of the nanorods. In the case of confocal reflectance microscopy the images of gold nanorods can be obtained with the power of light source as low as microwatts, thus avoiding the photothermal effect, but the resolution of such images is reduced. We have noted that confocal reflectance images of cellular gold nanorods achieved with 50 μW 800 nm fs have a relatively poor resolution, whereas the 50 μW 488 nm CW laser can acquire reasonably satisfactory 3D reflectance images with improved resolution because of its shorter wavelength. Therefore, confocal reflectance microscopy may also be a suitable means to image intracellular gold nanorods with the advantage of reduced photothermal effect.     

压缩传感用于极弱光计数成像

为解决灵敏度达到单光子水平的面阵探测器件其单位像素上灵敏度有限和测量数多等问题,研制了具有极高灵敏度的成像系统来实现欠采样的极弱光成像探测。该成像系统基于光子计数成像技术和压缩感知理论,利用数字微镜器件(DMD)完成随机空间光调制,通过单光子点探测器收集光子,以计数形式记录下光强值。然后,利用算法重建出极弱光照明下的图像。文中设计了相关实验,研究了测量数、光强极弱程度和测量时间对成像质量的影响。最后,引入了图像质量评价标准和系统信噪比,分析对比了实验数据。结果表明,当测量数高于信号总维度的19.5%时,系统能完美成像,信噪比可低至2.843 8dB,DMD单位像素上的平均光子数可低于1.106count/s,成像的关键在于信号的波动大于噪声的波动。该成像系统基本满足了极弱光成像探测在光强、灵敏度和采样数等方面的要求。     

Determination of particle number and brightness using a laser scanning confocal microscope operating in the analog mode

We describe a method to obtain the brightness and number of molecules at each pixel of an image stack obtained with a laser scanning microscope. The method is based on intensity fluctuations due to the diffusion of molecules in a pixel. For a detector operating in the analog mode, the variance must be proportional to the intensity. Once this constant has been calibrated, we use the ratio between the variance and the intensity to derive the particle brightness. Then, from the ratio of the intensity to the brightness we obtain the average number of particles in the pixel. We show that the method works with molecules in solution and that the results are comparable to those obtained with fluctuation correlation spectroscopy. We compare the results obtained with the detector operating in the analog and photon counting mode. Although the dynamic range of the detector operating in the photon counting mode is superior, the performance of the analog detector is acceptable under common experimental conditions. Since most commercial laser scanning microscopes operate in the analog mode, the calculation of brightness and number of particles can be applied to data obtained with these instruments, provided that the variance is proportional to the intensity. We demonstrate that the recovered brightness of mEGFP, independent of concentration, is similar whether measured in solution or in two different cell types. Furthermore, we distinguish between mobile and immobile components, and introduce a method to correct for slow variations in intensity.     

Fast scanning STED and two-photon fluorescence excitation microscopy with continuous wave beam

In this paper we report stimulated emission depletion (STED) and two-photon excitation (2PE) fluorescence microscopy with continuous wave (CW) laser beam using a new generation laser scanning confocal microscope equipped for STED-CW (TCS STED-CW, Leica Microsystems, Mannheim, Germany). We show the possibility to achieve CW-2PE with the very same beam used for STED-CW. This feature extends the performance of the microscope allowing multimodal imaging (CW-2PE, STED-CW, confocal).     

A software tool for tomographic axial superresolution in STED microscopy

A method for generating three‐dimensional tomograms from multiple three‐dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three‐dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three‐to‐four‐fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual‐information histogram similarity metric. Fusion of the projections into a single view is based on Richardson‐Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal‐to‐noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open‐source license.     

A simple and practical method to acquire geometrically correct images with resonant scanning-based line scanning in a custom-built video-rate laser scanning microscope

Most currently available confocal or two-photon laser scanning microscopes (LSMs) allow acquisition rates of the order of 1–5 images s⁻¹, which is too slow to fully resolve dynamic changes in intracellular messenger concentration in living cells or tissues. Several technologies exist to obtain faster imaging rates, either in the video-rate range (30 images s⁻¹) or beyond, but the most versatile technology available today is based on resonant scanners for horizontal line scanning. These scanning devices have several advantages over designs based on acousto-optical deflectors or Nipkow discs, but a drawback is that the scanning pattern is not a linear but rather a sinusoidal function of time. This puts additional constraints on the hardware necessary to read-in the image data flow, one of which is the generation of a pixel clock that varies in frequency with the position of the pixel on the scanned line. We describe a practical solution to obtain a variable pixel clock add-on that is easy to build and is easy to integrate into a custom-built LSM based on resonant scanning technology. In addition, we discuss some important hardware and software design aspects that simplify the construction of a resonant scanning-based LSM for high-speed, high-resolution imaging. Finally, we demonstrate that the microscope can be used to resolve calcium puffs triggered by photolytically increasing the intracellular concentration of inositol trisphosphate.     

Gated‐sted microscopy with subnanosecond pulsed fiber laser for reducing photobleaching

The spatial resolution of a stimulated emission depletion (STED) microscope is theoretically unlimited and practically determined by the signal‐to‐noise ratio. Typically, an increase of the STED beam's power leads to an improvement of the effective resolution. However, this improvement may vanish because an increased STED beam's power is often accompanied by an increased photobleaching, which worsen the effective resolution by reducing the signal strength. A way to lower the photobleaching in pulsed STED (P‐STED) implementations is to reduce the peak intensity lengthening the pulses duration (for a given average STED beam's power). This also leads to a reduction of the fluorophores quenching, thus a reduction of the effective resolution, but the time‐gated detection was proved to be successful in recovering these reductions. Here we demonstrated that a subnanosecond fiber laser beam (pulse width ∼600 ps) reduces the photobleaching with respect to a traditional stretched hundreds picosecond (∼200 ps) beam provided by a Ti:Sapphire laser, without any effective spatial resolution lost.     

Measurement of nanosecond time-resolved fluorescence with a directly gated interline CCD camera

CCD cameras coupled optically to gated image intensifiers have been used for fast time‐resolved measurements for some years. Image intensifiers have disadvantages, however, and for some applications it would be better if the image sensor could be gated directly at high speed. Control of the ‘charge drain’ function on an interline‐transfer CCD allows the sensor to be switched rapidly from an insensitive state. The temporal and spatial properties of the charge drain are explored in the present paper and it is shown that nanosecond time resolution with acceptable spatial uniformity can be achieved for a small commercial sensor. A fluorescence lifetime imaging system is demonstrated, based on a repetitively pulsed laser excitation source synchronized to the CCD control circuitry via a programmable delay unit.     

Counting dendritic spines in brain tissue slices by image correlation spectroscopy analysis

Growth of new micrometre sized projections called dendritic spines in neurones has been linked to the encoding of long‐term memories in vertebrates. Numerous studies have been carried out at both the light and electron microscopy level to quantify dendritic spine densities in brain tissue in laboratory animals. Currently, such efforts using light microscopy have relied on manual counting of spines in confocal or two‐photon optical slice images of tissue containing fluorescently labelled spines. This manual approach can be slow and tedious, especially for samples with high spine densities. We introduce an alternative way of performing spine counting that uses an applied image intensity threshold followed by spatial image correlation spectroscopy (ICS) analysis. We investigated the effect of particle sizes above the diffraction limit on the autocorrelation analysis as well as the influence of background fluorescence. Our results show that, for well labelled cerebellar tissue samples imaged with a signal‐to‐noise ratio of 5 or greater, ICS‐based spine counts can be conducted with the same 15–20% precision as manual counting, but much more rapidly.     

Fluorescence lifetime imaging--techniques and applications

Fluorescence lifetime imaging (FLIM) uses the fact that the fluorescence lifetime of a fluorophore depends on its molecular environment but not on its concentration. Molecular effects in a sample can therefore be investigated independently of the variable, and usually unknown concentration of the fluorophore. There is a variety of technical solutions of lifetime imaging in microscopy. The technical part of this paper focuses on time‐domain FLIM by multidimensional time‐correlated single photon counting, time‐domain FLIM by gated image intensifiers, frequency‐domain FLIM by gain‐modulated image intensifiers, and frequency‐domain FLIM by gain‐modulated photomultipliers. The application part describes the most frequent FLIM applications: Measurement of molecular environment parameters, protein‐interaction measurements by Förster resonance energy transfer (FRET), and measurements of the metabolic state of cells and tissue via their autofluorescence. Measurements of local environment parameters are based on lifetime changes induced by fluorescence quenching or conformation changes of the fluorophores. The advantage over intensity‐based measurements is that no special ratiometric fluorophores are needed. Therefore, a much wider selection of fluorescence markers can be used, and a wider range of cell parameters is accessible. FLIM‐FRET measures the change in the decay function of the FRET donor on interaction with an acceptor. FLIM‐based FRET measurement does not have to cope with problems like donor bleedthrough or directly excited acceptor fluorescence. This relaxes the requirements to the absorption and emission spectra of the donors and acceptors used. Moreover, FLIM‐FRET measurements are able to distinguish interacting and noninteracting fractions of the donor, and thus obtain independent information about distances and interacting and noninteracting protein fractions. This is information not accessible by steady‐state FRET techniques. Autofluorescence FLIM exploits changes in the decay parameters of endogenous fluorophores with the metabolic state of the cells or the tissue. By resolving changes in the binding, conformation, and composition of biologically relevant compounds FLIM delivers information not accessible by steady‐state fluorescence techniques.     

Signal‐to‐noise ratio enhancement on SEM images using a cubic spline interpolation with Savitzky–Golay filters and weighted least squares error

A new technique based on cubic spline interpolation with Savitzky–Golay smoothing using weighted least squares error filter is enhanced for scanning electron microscope (SEM) images. A diversity of sample images is captured and the performance is found to be better when compared with the moving average and the standard median filters, with respect to eliminating noise. This technique can be implemented efficiently on real‐time SEM images, with all mandatory data for processing obtained from a single image. Noise in images, and particularly in SEM images, are undesirable. A new noise reduction technique, based on cubic spline interpolation with Savitzky–Golay and weighted least squares error method, is developed. We apply the combined technique to single image signal‐to‐noise ratio estimation and noise reduction for SEM imaging system. This autocorrelation‐based technique requires image details to be correlated over a few pixels, whereas the noise is assumed to be uncorrelated from pixel to pixel. The noise component is derived from the difference between the image autocorrelation at zero offset, and the estimation of the corresponding original autocorrelation. In the few test cases involving different images, the efficiency of the developed noise reduction filter is proved to be significantly better than those obtained from the other methods. Noise can be reduced efficiently with appropriate choice of scan rate from real‐time SEM images, without generating corruption or increasing scanning time.     

A real‐time image dynamic range compensation for scanning electron microscope imaging system

This paper presents the development and implementation of a real‐time dynamic range compensation system for scanning electron microscope (SEM) imaging applications. Compared with conventional automatic brightness contrast compensators that are based on the average image or pixel intensity level, the proposed system utilizes histogram‐profiling techniques to compensate continuously the dynamic range of the processed video signal. The algorithms are implemented in software with a frame grabber card forming the front‐end video capture element. The proposed technique yields better image compensation compared with conventional methods.     

An electron beam lithography and digital image acquisition system for scanning electron microscopes

A low‐cost microcontroller based control and data acquisition unit for digital image recording of scanning electron microscope (SEM) images and scanning electron microscope based electron beam lithography (EBL) is described. The developed microcontroller low‐level embedded software incorporates major time critical functions for image acquisition and electron beam lithography and makes the unit an intelligent module which communicates via USB with the main computer. The system allows recording of images with up to 4096 × 4096 pixel size, different scan modes, controllable dwell time, synchronization with main power frequency, and other user controllable functions. The electron beam can be arbitrary positioned with 12‐bit precision in both dimensions and this is used to extend the scanning electron microscope capabilities for electron beam lithography. Hardware and software details of the system are given to allow its easy duplication. Performance of the system is discussed and exemplary results are presented.     

Maximum pixel spectrum: a new tool for detecting and recovering rare, unanticipated features from spectrum image data cubes

A new software tool, the maximum pixel spectrum, detects rare events within a spectrum image data cube, such as that generated with electron‐excited energy‐dispersive X‐ray spectrometry in a scanning electron microscope. The maximum pixel spectrum is a member of a class of ‘derived spectra’ that are constructed from the spectrum image data cube. Similar to a conventional spectrum, a derived spectrum is a linear array of intensity vs. channel index that corresponds to photon energy. A derived spectrum has the principal characteristics of a real spectrum so that X‐ray peaks can be recognized. A common example of a derived spectrum is the summation spectrum, which is a linear array in which the summation of all pixels within each energy plane gives the intensity value for that channel. The summation spectrum is sensitive to the dominant features of the data cube. The maximum pixel spectrum is constructed by selecting the maximum pixel value within each X‐ray energy plane, ignoring the remaining pixels. Peaks corresponding to highly localized trace constituents or foreign contaminants, even those that are confined to one pixel of the image, can be seen at a glance when the maximum pixel spectrum is compared with the summation spectrum.