2,212 research outputs found
GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging
Tomography has made a radical impact on diverse fields ranging from the study
of 3D atomic arrangements in matter to the study of human health in medicine.
Despite its very diverse applications, the core of tomography remains the same,
that is, a mathematical method must be implemented to reconstruct the 3D
structure of an object from a number of 2D projections. In many scientific
applications, however, the number of projections that can be measured is
limited due to geometric constraints, tolerable radiation dose and/or
acquisition speed. Thus it becomes an important problem to obtain the
best-possible reconstruction from a limited number of projections. Here, we
present the mathematical implementation of a tomographic algorithm, termed
GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between
real and reciprocal space, GENFIRE searches for a global solution that is
concurrently consistent with the measured data and general physical
constraints. The algorithm requires minimal human intervention and also
incorporates angular refinement to reduce the tilt angle error. We demonstrate
that GENFIRE can produce superior results relative to several other popular
tomographic reconstruction techniques by numerical simulations, and by
experimentally by reconstructing the 3D structure of a porous material and a
frozen-hydrated marine cyanobacterium. Equipped with a graphical user
interface, GENFIRE is freely available from our website and is expected to find
broad applications across different disciplines.Comment: 18 pages, 6 figure
Compressed Sensing with off-axis frequency-shifting holography
This work reveals an experimental microscopy acquisition scheme successfully
combining Compressed Sensing (CS) and digital holography in off-axis and
frequency-shifting conditions. CS is a recent data acquisition theory involving
signal reconstruction from randomly undersampled measurements, exploiting the
fact that most images present some compact structure and redundancy. We propose
a genuine CS-based imaging scheme for sparse gradient images, acquiring a
diffraction map of the optical field with holographic microscopy and recovering
the signal from as little as 7% of random measurements. We report experimental
results demonstrating how CS can lead to an elegant and effective way to
reconstruct images, opening the door for new microscopy applications.Comment: vol 35, pp 871-87
Linear chemically sensitive electron tomography using DualEELS and dictionary-based compressed sensing
We have investigated the use of DualEELS in elementally sensitive tilt series tomography in the scanning transmission electron microscope. A procedure is implemented using deconvolution to remove the effects of multiple scattering, followed by normalisation by the zero loss peak intensity. This is performed to produce a signal that is linearly dependent on the projected density of the element in each pixel. This method is compared with one that does not include deconvolution (although normalisation by the zero loss peak intensity is still performed). Additionaly, we compare the 3D reconstruction using a new compressed sensing algorithm, DLET, with the well-established SIRT algorithm. VC precipitates, which are extracted from a steel on a carbon replica, are used in this study. It is found that the use of this linear signal results in a very even density throughout the precipitates. However, when deconvolution is omitted, a slight density reduction is observed in the cores of the precipitates (a so-called cupping artefact). Additionally, it is clearly demonstrated that the 3D morphology is much better reproduced using the DLET algorithm, with very little elongation in the missing wedge direction. It is therefore concluded that reliable elementally sensitive tilt tomography using EELS requires the appropriate use of DualEELS together with a suitable reconstruction algorithm, such as the compressed sensing based reconstruction algorithm used here, to make the best use of the limited data volume and signal to noise inherent in core-loss EELS
Compressive Wavefront Sensing with Weak Values
We demonstrate a wavefront sensor based on the compressive sensing,
single-pixel camera. Using a high-resolution spatial light modulator (SLM) as a
variable waveplate, we weakly couple an optical field's transverse-position and
polarization degrees of freedom. By placing random, binary patterns on the SLM,
polarization serves as a meter for directly measuring random projections of the
real and imaginary components of the wavefront. Compressive sensing techniques
can then recover the wavefront. We acquire high quality, 256x256 pixel images
of the wavefront from only 10,000 projections. Photon-counting detectors give
sub-picowatt sensitivity
Projected gradient descent for non-convex sparse spike estimation
We propose a new algorithm for sparse spike estimation from Fourier
measurements. Based on theoretical results on non-convex optimization
techniques for off-the-grid sparse spike estimation, we present a projected
gradient descent algorithm coupled with a spectral initialization procedure.
Our algorithm permits to estimate the positions of large numbers of Diracs in
2d from random Fourier measurements. We present, along with the algorithm,
theoretical qualitative insights explaining the success of our algorithm. This
opens a new direction for practical off-the-grid spike estimation with
theoretical guarantees in imaging applications
- …