Depth-dependent resolution quantification in 3D fluorescence microscopy

A method is presented to quantify resolution as a function of depth in features of morphologically complex 3D samples. Applying the method to the brain of Drosophila, resolution is measured at increasing depth throughout the central brain region. The results quantify improvements in image quality when using two-photon microscopy compared to confocal. It is also demonstrated how resolution improvements through tuning a single parameter, laser power, can be measured objectively. Since the metric is interpretable as the average resolution within a feature, it is suitable for comparing results across optical systems, and can be used to inform the design of biological experiments requiring resolution of structures at a specific scale.Comment: 8 pages, 3 figure

A method for assessing the spatiotemporal resolution of Structured Illumination Microscopy (SIM)

A method is proposed for assessing the temporal resolution of Structured Illumination Microscopy (SIM), by tracking the amplitude of different spatial frequency components over time, and comparing them to a temporally-oscillating ground-truth. This method is used to gain insight into the performance limits of SIM, along with alternative reconstruction techniques (termed 'rolling SIM') that claim to improve temporal resolution. Results show that the temporal resolution of SIM varies considerably between low and high spatial frequencies, and that, despite being used in several high profile papers and commercial microscope software, rolling SIM provides no increase in temporal resolution over conventional SIM.Comment: 8 pages, 6 figures and 3 supplemental figure

Parallel super-resolution imaging

Massive parallelization of scanning-based super-resolution imaging allows fast imaging of large fields of view

Objective, comparative assessment of the penetration depth of temporal-focusing microscopy for imaging various organs

Temporal focusing is a technique for performing axially resolved widefield multiphoton microscopy with a large field of view. Despite significant advantages over conventional point-scanning multiphoton microscopy in terms of imaging speed, the need to collect the whole image simultaneously means that it is expected to achieve a lower penetration depth in common biological samples compared to point-scanning. We assess the penetration depth using a rigorous objective criterion based on the modulation transfer function, comparing it to point-scanning multiphoton microscopy. Measurements are performed in a variety of mouse organs in order to provide practical guidance as to the achievable penetration depth for both imaging techniques. It is found that two-photon scanning microscopy has approximately twice the penetration depth of temporal-focusing microscopy, and that penetration depth is organ-specific; the heart has the lowest penetration depth, followed by the liver, lungs, and kidneys, then the spleen, and finally white adipose tissue.National Institutes of Health (U.S.) (NIH-5-P41-EB015871-27)National Institutes of Health (U.S.) (DP3-DK101024 01)National Institutes of Health (U.S.) (1-U01-NS090438-01)National Institutes of Health (U.S.) (1-R01-EY017656 -0,6A1)National Institutes of Health (U.S.) (1-R01-HL121386-01A1)National Institutes of Health (U.S.) (NIH 5U54 CA151884-04)National Institutes of Health (U.S.) (9-P41-EB015871-26A1

High-Throughput Nonlinear Optical Microscopy

High-resolution microscopy methods based on different nonlinear optical (NLO) contrast mechanisms are finding numerous applications in biology and medicine. While the basic implementations of these microscopy methods are relatively mature, an important direction of continuing technological innovation lies in improving the throughput of these systems. Throughput improvement is expected to be important for studying fast kinetic processes, for enabling clinical diagnosis and treatment, and for extending the field of image informatics. This review will provide an overview of the fundamental limitations on NLO microscopy throughput. We will further cover several important classes of high-throughput NLO microscope designs with discussions on their strengths and weaknesses and their key biomedical applications. Finally, this review will close with a perspective of potential future technological improvements in this field.National Institutes of Health (U.S.) (9P41EB015871-26A1)National Institutes of Health (U.S.) (R01-EX017656)National Institutes of Health (U.S.) (5 R01 NS051320)National Institutes of Health (U.S.) (4R44EB012415-02)National Science Foundation (U.S.) (CBET-0939511)Singapore-MIT AllianceSkolkovo Institute of Science and TechnologySingapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology)Wellcome Trust (London, England) (Massachusetts Institute of Technology. Postdoctoral Fellowship 093831/Z/10/Z

Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element.

Super-resolution single-molecule localization microscopy, often referred to as PALM/STORM, works by ensuring that fewer than one fluorophore in a diffraction-limited volume is emitting at any one time, allowing the observer to infer that the emitter is located at the center of the point-spread function. This requires careful control over the incident light intensity in order to control the rate at which fluorophores are switched on; if too many fluorophores are activated, their point-spread functions overlap, which impedes efficient localization. If too few are activated, the imaging time is impractically long. There is therefore considerable recent interest in constructing so-called 'top-hat' illumination profiles that provide a uniform illumination over the whole field of view. We present the use of a single commercially-available low-cost refractive beamshaping element that can be retrofitted to almost any existing microscope; the illumination profile created by this element demonstrates a marked improvement in the power efficiency of dSTORM microscopy, as well as a significant reduction in the propensity for reconstruction artifacts, compared to conventional Gaussian illumination

NS2 is dispensable for efficient assembly of hepatitis C virus-like particles in a bipartite trans-encapsidation system.

Infectious hepatitis C virus (HCV) particle production in the genotype 2a JFH-1-based cell culture system involves non-structural proteins in addition to canonical virion components. NS2 has been proposed to act as a protein adaptor, co-ordinating the early stages of virion assembly. However, other studies have identified late-acting roles for this protein, making its precise involvement in infectious particle production unclear. Using a robust, bipartite trans-encapsidation system based upon baculovirus expression of HCV structural proteins, we have generated HCV-like particles (HCV-LP) in the absence of NS2 with overt similarity to wild-type virions. HCV-LP could transduce naive cells with trans-encapsidated subgenomic replicon RNAs and shared similar biochemical and biophysical properties with JFH-1 HCV. Both genotype 1b and JFH-1 intracellular HCV-LP were produced in the absence of NS2, whereas restoring NS2 to the JFH-1 system dramatically enhanced secreted infectivity, consistent with a late-acting role. Our system recapitulated authentic HCV particle assembly via trans-complementation of bicistronic, NS2-deleted, chimeric HCV, which is otherwise deficient in particle production. This closely resembled replicon-mediated NS2 trans-complementation, confirming that baculovirus expression of HCV proteins did not unduly affect particle production. Furthermore, this suggests that separation of structural protein expression from replicating HCV RNAs that are destined to be packaged alleviates an early stage requirement for NS2 during particle formation. This highlights our current lack of understanding of how NS2 mediates assembly, yet comparison of full-length and bipartite systems may provide further insight into this process

3D Super-Resolution Ultrasound with Adaptive Weight-Based Beamforming

Super-resolution ultrasound (SRUS) imaging through localising and tracking sparse microbubbles has been shown to reveal microvascular structure and flow beyond the wave diffraction limit. Most SRUS studies use standard delay and sum (DAS) beamforming, where large main lobe and significant side lobes make separation and localisation of densely distributed bubbles challenging, particularly in 3D due to the typically small aperture of matrix array probes. This study aims to improve 3D SRUS by implementing a low-cost 3D coherence beamformer based on channel signal variance, as well as two other adaptive weight-based coherence beamformers: nonlinear beamforming with p-th root compression and coherence factor. The 3D coherence beamformers, together with DAS, are compared in computer simulation, on a microflow phantom, and in vivo. Simulation results demonstrate that the adaptive weight-based beamformers can significantly narrow the main lobe and suppress the side lobes for modest computational cost. Significantly improved 3D SR images of microflow phantom and a rabbit kidney are obtained through the adaptive weight-based beamformers. The proposed variance-based beamformer performs best in simulations and experiments.Comment: Ultrasound localisation microscopy (ULM), super-resolution, contrast-enhanced ultrasound, 3D beamformin

Picture This! Reflecting on the Use of Posters as Expressions of PhD Research Projects

The presentation of posters at scientific conferences to visually represent research projects is a widespread international practice. The main purpose of this paper is to offer reflections relating to posters as visual representations of research studies conducted by PhD candidates. As the basis for our reflections, we consider the main purposes and intended learning outcomes linked to posters and reflect on some of the design and assessment issues associated with the multi-faceted purposes of posters in contexts such as postgraduate research conferences. Notably, the paper includes a set of illustrative vignettes written by a group of PhD students from the Faculty of Humanities at the University of Manchester who were required to design and exhibit posters at an annually held postgraduate research conference. This reflexive dialogue raises a series of issues for consideration by those who are actively involved with the design, presentation, observation and assessment of posters produced by PhD candidates.Exploring Visual Representation of Concepts in Learning and Teaching in Higher Educatio