42 research outputs found
BUbble Flow Field: a Simulation Framework for Evaluating Ultrasound Localization Microscopy Algorithms
Ultrasound contrast enhanced imaging has seen widespread uptake in research
and clinical diagnostic imaging. This includes applications such as vector flow
imaging, functional ultrasound and super-resolution Ultrasound Localization
Microscopy (ULM). All of these require testing and validation during
development of new algorithms with ground truth data. In this work we present a
comprehensive simulation platform BUbble Flow Field (BUFF) that generates
contrast enhanced ultrasound images in vascular tree geometries with realistic
flow characteristics and validation algorithms for ULM. BUFF allows complex
micro-vascular network generation of random and user-defined vascular networks.
Blood flow is simulated with a fast Computational Fluid Dynamics (CFD) solver
and allows arbitrary input and output positions and custom pressures. The
acoustic field simulation is combined with non-linear Microbubble (MB) dynamics
and simulates a range of point spread functions based on user-defined MB
characteristics. The validation combines both binary and quantitative metrics.
BFF's capacity to generate and validate user-defined networks is demonstrated
through its implementation in the Ultrasound Localisation and TRacking
Algorithms for Super Resolution (ULTRA-SR) Challenge at the International
Ultrasonics Symposium (IUS) 2022 of the Institute of Electrical and Electronics
Engineers (IEEE). The ability to produce ULM images, and the availability of a
ground truth in localisation and tracking enables objective and quantitative
evaluation of the large number of localisation and tracking algorithms
developed in the field. BUFF can also benefit deep learning based methods by
automatically generating datasets for training. BUFF is a fully comprehensive
simulation platform for testing and validation of novel ULM techniques and is
open source.Comment: 10 Pages, 9 Figure
Application of ultrafast gold luminescence to measuring the instrument response function for multispectral multiphoton fluorescence lifetime imaging
When performing multiphoton fluorescence lifetime imaging in multiple spectral emission channels, an instrument response function must be acquired in each channel if accurate measurements of complex fluorescence decays are to be performed. Although this can be achieved using the reference reconvolution technique, it is difficult to identify suitable fluorophores with a mono-exponential fluorescence decay across a broad emission spectrum. We present a solution to this problem by measuring the IRF using the ultrafast luminescence from gold nanorods. We show that ultrafast gold nanorod luminescence allows the IRF to be directly obtained in multiple spectral channels simultaneously across a wide spectral range. We validate this approach by presenting an analysis of multispectral autofluorescence FLIM data obtained from human skin ex vivo
FLIM FRET Technology for Drug Discovery: Automated Multiwell-Plate High-Content Analysis, Multiplexed Readouts and Application in Situ**
A fluorescence lifetime imaging (FLIM) technology platform intended to read out changes in Förster resonance energy transfer (FRET) efficiency is presented for the study of protein interactions across the drug-discovery pipeline. FLIM provides a robust, inherently ratiometric imaging modality for drug discovery that could allow the same sensor constructs to be translated from automated cell-based assays through small transparent organisms such as zebrafish to mammals. To this end, an automated FLIM multiwell-plate reader is described for high content analysis of fixed and live cells, tomographic FLIM in zebrafish and FLIM FRET of live cells via confocal endomicroscopy. For cell-based assays, an exemplar application reading out protein aggregation using FLIM FRET is presented, and the potential for multiple simultaneous FLIM (FRET) readouts in microscopy is illustrated
Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway
Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how Mug binds DNA is of significance when considering how Mug interacts with downstream enzymes in the base-excision repair pathway. We have demonstrated differential binding modes of Mug between its substrate and abasic DNA product using both band shift and fluorescence anisotropy assays. Mug binds its product cooperatively, and a stoichiometric analysis of DNA binding, catalytic activity and salt-dependence indicates that dimer formation is of functional significance in both catalytic activity and product binding. This is the first report of cooperativity in the uracil DNA glycosylase superfamily of enzymes, and forms the basis of product inhibition in Mug. It therefore provides a new perspective on abasic site protection and the findings are discussed in the context of downstream lesion processing and enzyme communication in the base excision repair pathway
Remodelling of Cortical Actin Where Lytic Granules Dock at Natural Killer Cell Immune Synapses Revealed by Super-Resolution Microscopy
Super-resolution 3D imaging reveals remodeling of the cortical actin meshwork at the natural killer cell immune synapse, which is likely to be important for secretion of lytic granules
Wide-field coherence-gated imaging techniques including photorefractive holography
EThOS - Electronic Theses Online ServiceGBUnited Kingdo
In Vivo Acoustic Super-Resolution and Super-Resolved Velocity Mapping Using Microbubbles
The structure of microvasculature cannot be resolved using standard clinical ultrasound (US) imaging frequencies due to the fundamental diffraction limit of US waves. In this work, we use a standard clinical US system to perform in vivo sub-diffraction imaging on a CD1, female mouse aged eight weeks by localizing isolated US signals from microbubbles flowing within the ear microvasculature, and compare our results to optical microscopy. Furthermore, we develop a new technique to map blood velocity at super-resolution by tracking individual bubbles through the vasculature. Resolution is improved from a measured lateral and axial resolution of 112 μm and 94 μm respectively in original US data, to super-resolved images of microvasculature where vessel features as fine as 19 μm are clearly visualized. Velocity maps clearly distinguish opposing flow direction and separated speed distributions in adjacent vessels, thereby enabling further differentiation between vessels otherwise not spatially separated in the image. This technique overcomes the diffraction limit to provide a noninvasive means of imaging the microvasculature at super-resolution, to depths of many centimeters. In the future, this method could noninvasively image pathological or therapeutic changes in the microvasculature at centimeter depths in vivo