39,542 research outputs found
Complete Photoionization Experiments via Ultrafast Coherent Control with Polarization Multiplexing II: Numerics & Analysis Methodologies
The feasibility of complete photoionization experiments, in which the full
set of photoionization matrix elements are determined, using multiphoton
ionization schemes with polarization-shaped pulses has recently been
demonstrated [Hockett et. al., Phys. Rev. Lett. 112, 223001 (2014)]. Here we
extend on our previous work to discuss further details of the numerics and
analysis methodology utilised, and compare the results directly to new
tomographic photoelectron measurements, which provide a more sensitive test of
the validity of the results. In so doing we discuss in detail the physics of
the photoionziation process, and suggest various avenues and prospects for this
coherent multiplexing methodology
Open source bioimage informatics for cell biology
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the acquisition, visualization, analysis and dissemination of these datasets. These tools collectively make up a new subfield of computational biology called bioimage informatics, which is facilitated by open source approaches. We discuss why open source tools for image informatics in cell biology are needed, some of the key general attributes of what make an open source imaging application successful, and point to opportunities for further operability that should greatly accelerate future cell biology discovery
Phase-Retrieved Tomography enables imaging of a Tumor Spheroid in Mesoscopy Regime
Optical tomographic imaging of biological specimen bases its reliability on
the combination of both accurate experimental measures and advanced
computational techniques. In general, due to high scattering and absorption in
most of the tissues, multi view geometries are required to reduce diffuse halo
and blurring in the reconstructions. Scanning processes are used to acquire the
data but they inevitably introduces perturbation, negating the assumption of
aligned measures. Here we propose an innovative, registration free, imaging
protocol implemented to image a human tumor spheroid at mesoscopic regime. The
technique relies on the calculation of autocorrelation sinogram and object
autocorrelation, finalizing the tomographic reconstruction via a three
dimensional Gerchberg Saxton algorithm that retrieves the missing phase
information. Our method is conceptually simple and focuses on single image
acquisition, regardless of the specimen position in the camera plane. We
demonstrate increased deep resolution abilities, not achievable with the
current approaches, rendering the data alignment process obsolete.Comment: 21 pages, 5 figure
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Global morphogenetic flow is accurately predicted by the spatial distribution of myosin motors.
During embryogenesis tissue layers undergo morphogenetic flow rearranging and folding into specific shapes. While developmental biology has identified key genes and local cellular processes, global coordination of tissue remodeling at the organ scale remains unclear. Here, we combine in toto light-sheet microscopy of the Drosophila embryo with quantitative analysis and physical modeling to relate cellular flow with the patterns of force generation during the gastrulation process. We find that the complex spatio-temporal flow pattern can be predicted from the measured meso-scale myosin density and anisotropy using a simple, effective viscous model of the tissue, achieving close to 90% accuracy with one time dependent and two constant parameters. Our analysis uncovers the importance of a) spatial modulation of myosin distribution on the scale of the embryo and b) the non-locality of its effect due to mechanical interaction of cells, demonstrating the need for the global perspective in the study of morphogenetic flow
Phase Retrieval with Application to Optical Imaging
This review article provides a contemporary overview of phase retrieval in
optical imaging, linking the relevant optical physics to the information
processing methods and algorithms. Its purpose is to describe the current state
of the art in this area, identify challenges, and suggest vision and areas
where signal processing methods can have a large impact on optical imaging and
on the world of imaging at large, with applications in a variety of fields
ranging from biology and chemistry to physics and engineering
Single-shot compressed ultrafast photography: a review
Compressed ultrafast photography (CUP) is a burgeoning single-shot computational imaging technique that provides an imaging speed as high as 10 trillion frames per second and a sequence depth of up to a few hundred frames. This technique synergizes compressed sensing and the streak camera technique to capture nonrepeatable ultrafast transient events with a single shot. With recent unprecedented technical developments and extensions of this methodology, it has been widely used in ultrafast optical imaging and metrology, ultrafast electron diffraction and microscopy, and information security protection. We review the basic principles of CUP, its recent advances in data acquisition and image reconstruction, its fusions with other modalities, and its unique applications in multiple research fields
Prospects for Theranostics in Neurosurgical Imaging: Empowering Confocal Laser Endomicroscopy Diagnostics via Deep Learning
Confocal laser endomicroscopy (CLE) is an advanced optical fluorescence
imaging technology that has the potential to increase intraoperative precision,
extend resection, and tailor surgery for malignant invasive brain tumors
because of its subcellular dimension resolution. Despite its promising
diagnostic potential, interpreting the gray tone fluorescence images can be
difficult for untrained users. In this review, we provide a detailed
description of bioinformatical analysis methodology of CLE images that begins
to assist the neurosurgeon and pathologist to rapidly connect on-the-fly
intraoperative imaging, pathology, and surgical observation into a
conclusionary system within the concept of theranostics. We present an overview
and discuss deep learning models for automatic detection of the diagnostic CLE
images and discuss various training regimes and ensemble modeling effect on the
power of deep learning predictive models. Two major approaches reviewed in this
paper include the models that can automatically classify CLE images into
diagnostic/nondiagnostic, glioma/nonglioma, tumor/injury/normal categories and
models that can localize histological features on the CLE images using weakly
supervised methods. We also briefly review advances in the deep learning
approaches used for CLE image analysis in other organs. Significant advances in
speed and precision of automated diagnostic frame selection would augment the
diagnostic potential of CLE, improve operative workflow and integration into
brain tumor surgery. Such technology and bioinformatics analytics lend
themselves to improved precision, personalization, and theranostics in brain
tumor treatment.Comment: See the final version published in Frontiers in Oncology here:
https://www.frontiersin.org/articles/10.3389/fonc.2018.00240/ful
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