1,273 research outputs found
Locally Orderless Registration
Image registration is an important tool for medical image analysis and is
used to bring images into the same reference frame by warping the coordinate
field of one image, such that some similarity measure is minimized. We study
similarity in image registration in the context of Locally Orderless Images
(LOI), which is the natural way to study density estimates and reveals the 3
fundamental scales: the measurement scale, the intensity scale, and the
integration scale.
This paper has three main contributions: Firstly, we rephrase a large set of
popular similarity measures into a common framework, which we refer to as
Locally Orderless Registration, and which makes full use of the features of
local histograms. Secondly, we extend the theoretical understanding of the
local histograms. Thirdly, we use our framework to compare two state-of-the-art
intensity density estimators for image registration: The Parzen Window (PW) and
the Generalized Partial Volume (GPV), and we demonstrate their differences on a
popular similarity measure, Normalized Mutual Information (NMI).
We conclude, that complicated similarity measures such as NMI may be
evaluated almost as fast as simple measures such as Sum of Squared Distances
(SSD) regardless of the choice of PW and GPV. Also, GPV is an asymmetric
measure, and PW is our preferred choice.Comment: submitte
Enhancement of Underwater Video Mosaics for Post-Processing
Mosaics of seafloor created from still images or video acquired underwater have proved to be useful for construction of maps of forensic and archeological sites, species\u27 abundance estimates, habitat characterization, etc. Images taken by a camera mounted on a stable platform are registered (at first pair-wise and then globally) and assembled in a high resolution visual map of the surveyed area. While this map is usually sufficient for a human orientation and even quantitative measurements, it often contains artifacts that complicate an automatic post-processing (for example, extraction of shapes for organism counting, or segmentation for habitat characterization). The most prominent artifacts are inter-frame seams caused by inhomogeneous artificial illumination, and local feature misalignments due to parallax effects - result of an attempt to represent a 3D world on a 2D map. In this paper we propose two image processing techniques for mosaic quality enhancement - median mosaic-based illumination correction suppressing appearance of inter-frame seams, and micro warping decreasing influence of parallax effects
An Improved Observation Model for Super-Resolution under Affine Motion
Super-resolution (SR) techniques make use of subpixel shifts between frames
in an image sequence to yield higher-resolution images. We propose an original
observation model devoted to the case of non isometric inter-frame motion as
required, for instance, in the context of airborne imaging sensors. First, we
describe how the main observation models used in the SR literature deal with
motion, and we explain why they are not suited for non isometric motion. Then,
we propose an extension of the observation model by Elad and Feuer adapted to
affine motion. This model is based on a decomposition of affine transforms into
successive shear transforms, each one efficiently implemented by row-by-row or
column-by-column 1-D affine transforms.
We demonstrate on synthetic and real sequences that our observation model
incorporated in a SR reconstruction technique leads to better results in the
case of variable scale motions and it provides equivalent results in the case
of isometric motions
Numerical methods for coupled reconstruction and registration in digital breast tomosynthesis.
Digital Breast Tomosynthesis (DBT) provides an insight into the fine details of normal fibroglandular tissues and abnormal lesions by reconstructing a pseudo-3D image of the breast. In this respect, DBT overcomes a major limitation of conventional X-ray mam- mography by reducing the confounding effects caused by the superposition of breast tissue. In a breast cancer screening or diagnostic context, a radiologist is interested in detecting change, which might be indicative of malignant disease. To help automate this task image registration is required to establish spatial correspondence between time points. Typically, images, such as MRI or CT, are first reconstructed and then registered. This approach can be effective if reconstructing using a complete set of data. However, for ill-posed, limited-angle problems such as DBT, estimating the deformation is com- plicated by the significant artefacts associated with the reconstruction, leading to severe inaccuracies in the registration. This paper presents a mathematical framework, which couples the two tasks and jointly estimates both image intensities and the parameters of a transformation. Under this framework, we compare an iterative method and a simultaneous method, both of which tackle the problem of comparing DBT data by combining reconstruction of a pair of temporal volumes with their registration. We evaluate our methods using various computational digital phantoms, uncom- pressed breast MR images, and in-vivo DBT simulations. Firstly, we compare both iter- ative and simultaneous methods to the conventional, sequential method using an affine transformation model. We show that jointly estimating image intensities and parametric transformations gives superior results with respect to reconstruction fidelity and regis- tration accuracy. Also, we incorporate a non-rigid B-spline transformation model into our simultaneous method. The results demonstrate a visually plausible recovery of the deformation with preservation of the reconstruction fidelity
Scalable Machine Learning Methods for Massive Biomedical Data Analysis.
Modern data acquisition techniques have enabled biomedical researchers to collect and analyze datasets of substantial size and complexity. The massive size of these datasets allows us to comprehensively study the biological system of interest at an unprecedented level of detail, which may lead to the discovery of clinically relevant biomarkers. Nonetheless, the dimensionality of these datasets presents critical computational and statistical challenges, as traditional statistical methods break down when the number of predictors dominates the number of observations, a setting frequently encountered in biomedical data analysis. This difficulty is compounded by the fact that biological data tend to be noisy and often possess complex correlation patterns among the predictors. The central goal of this dissertation is to develop a computationally tractable machine learning framework that allows us to extract scientifically meaningful information from these massive and highly complex biomedical datasets. We motivate the scope of our study by considering two important problems with clinical relevance: (1) uncertainty analysis for biomedical image registration, and (2) psychiatric disease prediction based on functional connectomes, which are high dimensional correlation maps generated from resting state functional MRI.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111354/1/takanori_1.pd
Achieving Consistent Doppler Measurements from SDO/HMI Vector Field Inversions
NASA's Solar Dynamics Observatory is delivering vector field observations of
the full solar disk with unprecedented temporal and spatial resolution;
however, the satellite is in a highly inclined geostationary orbit. The
relative spacecraft-Sun velocity varies by ~km/s over a day which
introduces major orbital artifacts in the Helioseismic Magnetic Imager data. We
demonstrate that the orbital artifacts contaminate all spatial and temporal
scales in the data. We describe a newly-developed three stage procedure for
mitigating these artifacts in the Doppler data derived from the Milne-Eddington
inversions in the HMI Pipeline. This procedure was applied to full disk images
of AR11084 to produce consistent Dopplergrams. The data adjustments reduce the
power in the orbital artifacts by 31dB. Furthermore, we analyze in detail the
corrected images and show that our procedure greatly improve the temporal and
spectral properties of the data without adding any new artifacts. We conclude
that this new and easily implemented procedure makes a dramatic improvement in
the consistency of the HMI data and in its usefulness for precision scientific
studies.Comment: 58 pages, 19 figures, submitted to Ap
Distributed-memory large deformation diffeomorphic 3D image registration
We present a parallel distributed-memory algorithm for large deformation
diffeomorphic registration of volumetric images that produces large isochoric
deformations (locally volume preserving). Image registration is a key
technology in medical image analysis. Our algorithm uses a partial differential
equation constrained optimal control formulation. Finding the optimal
deformation map requires the solution of a highly nonlinear problem that
involves pseudo-differential operators, biharmonic operators, and pure
advection operators both forward and back- ward in time. A key issue is the
time to solution, which poses the demand for efficient optimization methods as
well as an effective utilization of high performance computing resources. To
address this problem we use a preconditioned, inexact, Gauss-Newton- Krylov
solver. Our algorithm integrates several components: a spectral discretization
in space, a semi-Lagrangian formulation in time, analytic adjoints, different
regularization functionals (including volume-preserving ones), a spectral
preconditioner, a highly optimized distributed Fast Fourier Transform, and a
cubic interpolation scheme for the semi-Lagrangian time-stepping. We
demonstrate the scalability of our algorithm on images with resolution of up to
on the "Maverick" and "Stampede" systems at the Texas Advanced
Computing Center (TACC). The critical problem in the medical imaging
application domain is strong scaling, that is, solving registration problems of
a moderate size of ---a typical resolution for medical images. We are
able to solve the registration problem for images of this size in less than
five seconds on 64 x86 nodes of TACC's "Maverick" system.Comment: accepted for publication at SC16 in Salt Lake City, Utah, USA;
November 201
- …