246 research outputs found
An extended quantitative model for super-resolution optical fluctuation imaging (SOFI)
Super-resolution optical fluctuation imaging (SOFI) provides super-resolution (SR) fluorescence imaging by analyzing fluctuations in the fluorophore emission. The technique has been used both to acquire quantitative SR images and to provide SR biosensing by monitoring changes in fluorophore blinking dynamics. Proper analysis of such data relies on a fully quantitative model of the imaging. However, previous SOFI imaging models made several assumptions that can not be realized in practice. In this work we address these limitations by developing and verifying a fully quantitative model that better approximates real-world imaging conditions. Our model shows that (i) SOFI images are free of bias, or can be made so, if the signal is stationary and fluorophores blink independently, (ii) allows a fully quantitative description of the link between SOFI imaging and probe dynamics, and (iii) paves the way for more advanced SOFI image reconstruction by offering a computationally fast way to calculate SOFI images for arbitrary probe, sample and instrumental properties
Homogeneous variational problems: a minicourse
A Finsler geometry may be understood as a homogeneous variational problem,
where the Finsler function is the Lagrangian. The extremals in Finsler geometry
are curves, but in more general variational problems we might consider extremal
submanifolds of dimension . In this minicourse we discuss these problems
from a geometric point of view.Comment: This paper is a written-up version of the major part of a minicourse
given at the sixth Bilateral Workshop on Differential Geometry and its
Applications, held in Ostrava in May 201
On symmetries of Chern-Simons and BF topological theories
We describe constructing solutions of the field equations of Chern-Simons and
topological BF theories in terms of deformation theory of locally constant
(flat) bundles. Maps of flat connections into one another (dressing
transformations) are considered. A method of calculating (nonlocal) dressing
symmetries in Chern-Simons and topological BF theories is formulated
High-speed multiplane structured illumination microscopy of living cells using an image-splitting prism
Symmetries of Helmholtz forms and globally variational dynamical forms
Invariance properties of classes in the variational sequence suggested to
Krupka et al. the idea that there should exist a close correspondence between
the notions of variationality of a differential form and invariance of its
exterior derivative. It was shown by them that the invariance of a closed
Helmholtz form of a dynamical form is equivalent with local variationality of
the Lie derivative of the dynamical form, so that the latter is locally the
Euler--Lagrange form of a Lagrangian. We show that the corresponding local
system of Euler--Lagrange forms is variationally equivalent to a global
Euler--Lagrange form.Comment: Presented at QTS7 - Quantum Theory and Symmetries VII, Prague
7-13/08/201
Adaptive density estimation for stationary processes
We propose an algorithm to estimate the common density of a stationary
process . We suppose that the process is either or
-mixing. We provide a model selection procedure based on a generalization
of Mallows' and we prove oracle inequalities for the selected estimator
under a few prior assumptions on the collection of models and on the mixing
coefficients. We prove that our estimator is adaptive over a class of Besov
spaces, namely, we prove that it achieves the same rates of convergence as in
the i.i.d framework
Constraint algorithm for k-presymplectic Hamiltonian systems. Application to singular field theories
The k-symplectic formulation of field theories is especially simple, since
only tangent and cotangent bundles are needed in its description. Its defining
elements show a close relationship with those in the symplectic formulation of
mechanics. It will be shown that this relationship also stands in the
presymplectic case. In a natural way, one can mimick the presymplectic
constraint algorithm to obtain a constraint algorithm that can be applied to
-presymplectic field theory, and more particularly to the Lagrangian and
Hamiltonian formulations of field theories defined by a singular Lagrangian, as
well as to the unified Lagrangian-Hamiltonian formalism (Skinner--Rusk
formalism) for k-presymplectic field theory. Two examples of application of the
algorithm are also analyzed.Comment: 22 p
A Study of Concurrency Bugs and Advanced Development Support for Actor-based Programs
The actor model is an attractive foundation for developing concurrent
applications because actors are isolated concurrent entities that communicate
through asynchronous messages and do not share state. Thereby, they avoid
concurrency bugs such as data races, but are not immune to concurrency bugs in
general. This study taxonomizes concurrency bugs in actor-based programs
reported in literature. Furthermore, it analyzes the bugs to identify the
patterns causing them as well as their observable behavior. Based on this
taxonomy, we further analyze the literature and find that current approaches to
static analysis and testing focus on communication deadlocks and message
protocol violations. However, they do not provide solutions to identify
livelocks and behavioral deadlocks. The insights obtained in this study can be
used to improve debugging support for actor-based programs with new debugging
techniques to identify the root cause of complex concurrency bugs.Comment: - Submitted for review - Removed section 6 "Research Roadmap for
Debuggers", its content was summarized in the Future Work section - Added
references for section 1, section 3, section 4.3 and section 5.1 - Updated
citation
Unambiguous Formalism for Higher-Order Lagrangian Field Theories
The aim of this paper is to propose an unambiguous intrinsic formalism for
higher-order field theories which avoids the arbitrariness in the
generalization of the conventional description of field theories, which implies
the existence of different Cartan forms and Legendre transformations. We
propose a differential-geometric setting for the dynamics of a higher-order
field theory, based on the Skinner and Rusk formalism for mechanics. This
approach incorporates aspects of both, the Lagrangian and the Hamiltonian
description, since the field equations are formulated using the Lagrangian on a
higher-order jet bundle and the canonical multisymplectic form on its dual. As
both of these objects are uniquely defined, the Skinner-Rusk approach has the
advantage that it does not suffer from the arbitrariness in conventional
descriptions. The result is that we obtain a unique and global intrinsic
version of the Euler-Lagrange equations for higher-order field theories.
Several examples illustrate our construction.Comment: 21 pages; 4 diagrams; (this version) corrected typos; moved
paragraphs; publishe
Super-Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope
In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging
- …