Prashant Prabhat

High Accuracy 3D Quantum Dot Tracking with Multifocal Plane Microscopy for the Study of Fast Intracellular Dynamics in Live Cells

Single particle tracking in three dimensions in a live cell environment holds the promise of revealing important new biological insights. However, conventional microscopy-based imaging techniques are not well suited for fast three-dimensional (3D) tracking of single particles in cells. Previously we developed an imaging modality multifocal plane microscopy (MUM) to image fast intracellular dynamics in three dimensions in live cells. Here, we introduce an algorithm, the MUM localization algorithm (MUMLA), to determine the 3D position of a point source that is imaged using MUM. We validate MUMLA through simulated and experimental data and show that the 3D position of quantum dots can be determined over a wide spatial range. We demonstrate that MUMLA indeed provides the best possible accuracy with which the 3D position can be determined. Our analysis shows that MUM overcomes the poor depth discrimination of the conventional microscope, and thereby paves the way for high accuracy tracking of nanoparticles in a live cell environment. Here, using MUM and MUMLA we report for the first time the full 3D trajectories of QD-labeled antibody molecules undergoing endocytosis in live cells from the plasma membrane to the sorting endosome deep inside the cell.

Elucidation of intracellular recycling pathways leading to exocytosis of the Fc receptor, FcRn, by using multifocal plane microscopy.

The intracellular events on the recycling pathway that lead from sorting endosomes to exocytosis at the plasma membrane are central to cellular function. However, despite intensive study, these processes are poorly characterized in spatial and dynamic terms. The primary reason for this is that, to date, it has not been possible to visualize rapidly moving intracellular compartments in three dimensions in cells. Here, we use a recently developed imaging setup in which multiple planes can be simultaneously imaged within the cell in conjunction with visualization of the plasma membrane plane by using total internal reflection fluorescence microscopy. This has allowed us to track and characterize intracellular events on the recycling pathway that lead to exocytosis of the MHC Class I-related receptor, FcRn. We observe both direct delivery of tubular and vesicular transport containers (TCs) from sorting endosomes to exocytic sites at the plasma membrane, and indirect pathways in which TCs that are not in proximity to sorting endosomes undergo exocytosis. TCs can also interact with different sorting endosomes before exocytosis. Our data provide insight into the intracellular events that precede exocytic fusion.

Improved single particle localization accuracy with dual objective multifocal plane microscopy

In single particle imaging applications, the number of photons detected from the fluorescent label plays a crucial role in the quantitative analysis of the acquired data. For example, in tracking experiments the localization accuracy of the labeled entity can be improved by collecting more photons from the labeled entity. Here, we report the development of dual objective multifocal plane microscopy (dMUM) for single particle studies. The new microscope configuration uses two opposing objective lenses, where one of the objectives is in an inverted position and the other objective is in an upright position. We show that dMUM has a higher photon collection efficiency when compared to standard microscopes. We demonstrate that fluorescent labels can be localized with better accuracy in 2D and 3D when imaged through dMUM than when imaged through a standard microscope. Analytical tools are introduced to estimate the nanoprobe location from dMUM images and to characterize the accuracy with which they can be determined.

Simultaneous imaging of several focal planes in fluorescence microscopy for the study of cellular dynamics in 3D

Fluorescence microscopy of live cells is an important tool to investigate cellular tracking pathways. The existing microscope design is very well suited to image fast moving vesicles, tubules and organelles in one focal plane. More problematic is the imaging of cellular components that move between different focal planes. This is due to the fact that tracking of such cellular components requires that the focal plane of the microscope be changed. This has to be done with a focusing device, which is relatively slow. More importantly, only one focal plane can be imaged at a time. Therefore, while the cell is imaged at one focal plane, important events could be missed at other focal planes. To overcome these shortcomings, we present a modification of the classical microscope design with which two or more focal planes can be imaged simultaneously. In this design, the emission light collected by a single stationary objective lens is split into multiple channels. Light in each channel is focused on a CCD camera by a tube lens. By ensuring that the camera position with respect to the tube lens focal plane position is not the same in any two channels, distinct planes within the specimen can be simultaneously imaged. Here we discuss the implementation of a configuration with which four focal planes can be imaged simultaneously.

Excitation-scanning hyperspectral imaging microscope

Abstract. Hyperspectral imaging is a versatile tool that has recently been applied to a variety of biomedical applications, notably live-cell and whole-tissue signaling. Traditional hyperspectral imaging approaches filter the fluorescence emission over a broad wavelength range while exciting at a single band. However, these emission-scanning approaches have shown reduced sensitivity due to light attenuation from spectral filtering. Consequently, emission scanning has limited applicability for time-sensitive studies and photosensitive applications. In this work, we have developed an excitation-scanning hyperspectral imaging microscope that overcomes these limitations by providing high transmission with short acquisition times. This is achieved by filtering the fluorescence excitation rather than the emission. We tested the efficacy of the excitation-scanning microscope in a side-by-side comparison with emission scanning for detection of green fluorescent protein (GFP)-expressing endothelial cells in highly autofluorescent lung tissue. Excitation scanning provided higher signal-to-noise characteristics, as well as shorter acquisition times (300  ms/wavelength band with excitation scanning versus 3  s/wavelength band with emission scanning). Excitation scanning also provided higher delineation of nuclear and cell borders, and increased identification of GFP regions in highly autofluorescent tissue. These results demonstrate excitation scanning has utility in a wide range of time-dependent and photosensitive applications.

Thin-film tunable filters for hyperspectral fluorescence microscopy

Abstract. Hyperspectral imaging is a powerful tool that acquires data from many spectral bands, forming a contiguous spectrum. Hyperspectral imaging was originally developed for remote sensing applications; however, hyperspectral techniques have since been applied to biological fluorescence imaging applications, such as fluorescence microscopy and small animal fluorescence imaging. The spectral filtering method largely determines the sensitivity and specificity of any hyperspectral imaging system. There are several types of spectral filtering hardware available for microscopy systems, most commonly acousto-optic tunable filters (AOTFs) and liquid crystal tunable filters (LCTFs). These filtering technologies have advantages and disadvantages. Here, we present a novel tunable filter for hyperspectral imaging—the thin-film tunable filter (TFTF). The TFTF presents several advantages over AOTFs and LCTFs, most notably, a high percentage transmission and a high out-of-band optical density (OD). We present a comparison of a TFTF-based hyperspectral microscopy system and a commercially available AOTF-based system. We have characterized the light transmission, wavelength calibration, and OD of both systems, and have then evaluated the capability of each system for discriminating between green fluorescent protein and highly autofluorescent lung tissue. Our results suggest that TFTFs are an alternative approach for hyperspectral filtering that offers improved transmission and out-of-band blocking. These characteristics make TFTFs well suited for other biomedical imaging devices, such as ophthalmoscopes or endoscopes.

Tunable thin-film optical filters for hyperspectral microscopy

Hyperspectral imaging was originally developed for use in remote sensing applications. More recently, it has been applied to biological imaging systems, such as fluorescence microscopes. The ability to distinguish molecules based on spectral differences has been especially advantageous for identifying fluorophores in highly autofluorescent tissues. A key component of hyperspectral imaging systems is wavelength filtering. Each filtering technology used for hyperspectral imaging has corresponding advantages and disadvantages. Recently, a new optical filtering technology has been developed that uses multi-layered thin-film optical filters that can be rotated, with respect to incident light, to control the center wavelength of the pass-band. Compared to the majority of tunable filter technologies, these filters have superior optical performance including greater than 90% transmission, steep spectral edges and high out-of-band blocking. Hence, tunable thin-film optical filters present optical characteristics that may make them well-suited for many biological spectral imaging applications. An array of tunable thin-film filters was implemented on an inverted fluorescence microscope (TE 2000, Nikon Instruments) to cover the full visible wavelength range. Images of a previously published model, GFP-expressing endothelial cells in the lung, were acquired using a charge-coupled device camera (Rolera EM-C2, Q-Imaging). This model sample presents fluorescently-labeled cells in a highly autofluorescent environment. Linear unmixing of hyperspectral images indicates that thin-film tunable filters provide equivalent spectral discrimination to our previous acousto-optic tunable filter–based approach, with increased signal-to-noise characteristics. Hence, tunable multi-layered thin film optical filters may provide greatly improved spectral filtering characteristics and therefore enable wider acceptance of hyperspectral widefield microscopy.

Overcoming the depth discrimination barrier in widefield microscopes: 3D single molecule tracking with high axial accuracy

Current widefield microscopy techniques are well suited for imaging fast moving single molecules in two dimensions even within cells. However, the 3D imaging of single molecules poses several technical challenges. Foremost being that in the current microscope design only one focal plane can be imaged at any given point in time. Hence single molecule tracking in a 3D environment such as a cell is problematic since the molecule can easily move out of the focal plane that is currently being imaged. Focusing devices such as piezo nano-positioners could be used to overcome this shortcoming by sequentially scanning the sample at different planes. However, these devices are typically slow and therefore may not be suitable for 3D tracking of fast moving single molecules. Aside from this, widefield microscopes suffer from poor depth discrimination capability. Therefore, there exists significant uncertainty in determining the axial location of the single molecule, especially when the molecule is close to the plane of focus. To overcome the above limitations, we have developed a new microscopy technique called multifocal plane microscopy (MUM) that can simultaneously image distinct planes within the specimen. In contrast to standard microscopes, a MUM setup exhibits significantly improved depth discrimination capability, especially close to focus, which markedly improves the accuracy with which the axial position of the single molecule can be determined. Results are presented to illustrate the applicability of MUM for 3D single molecule tracking.

SearchLight: a freely available web-based quantitative spectral analysis tool(Conference Presentation)

In order to design a fluorescence experiment, typically the spectra of a fluorophore and of a filter set are overlaid on a single graph and the spectral overlap is evaluated intuitively. However, in a typical fluorescence imaging system the fluorophores and optical filters are not the only wavelength dependent variables - even the excitation light sources have been changing. For example, LED Light Engines may have a significantly different spectral response compared to the traditional metal-halide lamps. Therefore, for a more accurate assessment of fluorophore-to-filter-set compatibility, all sources of spectral variation should be taken into account simultaneously. Additionally, intuitive or qualitative evaluation of many spectra does not necessarily provide a realistic assessment of the system performance. “SearchLight” is a freely available web-based spectral plotting and analysis tool that can be used to address the need for accurate, quantitative spectral evaluation of fluorescence measurement systems. This tool is available at: http://searchlight.semrock.com/. Based on a detailed mathematical framework [1], SearchLight calculates signal, noise, and signal-to-noise ratio for multiple combinations of fluorophores, filter sets, light sources and detectors. SearchLight allows for qualitative and quantitative evaluation of the compatibility of filter sets with fluorophores, analysis of bleed-through, identification of optimized spectral edge locations for a set of filters under specific experimental conditions, and guidance regarding labeling protocols in multiplexing imaging assays. Entire SearchLight sessions can be shared with colleagues and collaborators and saved for future reference. [1] Anderson, N., Prabhat, P. and Erdogan, T., Spectral Modeling in Fluorescence Microscopy, http://www.semrock.com (2010).

Ion-beam sputtered (IBS) thin-film interference filters for nonlinear optical imaging

Nonlinear optical (NLO) microscopy is emerging as a powerful technique for the study of biological samples. By combining several different imaging modalities such as multiphoton (MP) fluorescence, second-harmonic and thirdharmonic generation (SHG and THG), and coherent Raman scattering techniques such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS), it is possible to combine the best practices of label and label-free imaging into a single platform capable of imaging structures within single cells and elucidating the health of biological tissue samples, even at the submicron level. Single-substrate, ion-beam-sputtered (IBS) thinfilm interference filters are a key enabling technology in laser-based optical microscopy and play a critical role in multimodal NLO imaging. In microscopy applications, optical filters are used to select and discriminate exactly which wavelengths of light are to be transmitted, reflected and suppressed. In this paper we discuss various important characteristics of hard-coated thin-film interference filters, such as high light throughput, steep edges, and high out-of-band blocking, all of which require careful consideration when designing and manufacturing optical filters for NLO imaging applications. To understand the true performance of hard-coated IBS filters, a simple CARS imaging experiment was performed. We found a 2.6 times increase in signal enhancement and 70% improvement in image contrast when compared to a commercially available filter commonly used in CARS microscopy applications.