Improving minimum rate predictors algorithm for compression of volumetric medical images

Medical imaging technologies are experiencing a growth in terms of usage and image resolution, namely in diagnostics systems that require a large set of images, like CT or MRI. Furthermore, legal restrictions impose that these scans must be archived for several years. These facts led to the increase of storage costs in medical image databases and institutions. Thus, a demand for more efficient compression tools, used for archiving and communication, is arising. Currently, the DICOM standard, that makes recommendations for medical communications and imaging compression, recommends lossless encoders such as JPEG, RLE, JPEG-LS and JPEG2000. However, none of these encoders include inter-slice prediction in their algorithms. This dissertation presents the research work on medical image compression, using the MRP encoder. MRP is one of the most efficient lossless image compression algorithm. Several processing techniques are proposed to adapt the input medical images to the encoder characteristics. Two of these techniques, namely changing the alignment of slices for compression and a pixel-wise difference predictor, increased the compression efficiency of MRP, by up to 27.9%. Inter-slice prediction support was also added to MRP, using uni and bi-directional techniques. Also, the pixel-wise difference predictor was added to the algorithm. Overall, the compression efficiency of MRP was improved by 46.1%. Thus, these techniques allow for compression ratio savings of 57.1%, compared to DICOM encoders, and 33.2%, compared to HEVC RExt Random Access. This makes MRP the most efficient of the encoders under study.

Dosimetric Evaluation of Metal Artefact Reduction using Metal Artefact Reduction (MAR) Algorithm and Dual-energy Computed Tomography (CT) Method

Purpose: Computed Tomography (CT) is one of the standard diagnostic imaging modalities for the evaluation of a patient’s medical condition. In comparison to other imaging modalities such as Magnetic Resonance Imaging (MRI), CT is a fast acquisition imaging device with higher spatial resolution and higher contrast-to-noise ratio (CNR) for bony structures. CT images are presented through a gray scale of independent values in Hounsfield units (HU). High HU-valued materials represent higher density. High density materials, such as metal, tend to erroneously increase the HU values around it due to reconstruction software limitations. This problem of increased HU values due to metal presence is referred to as metal artefacts. Hip prostheses, dental fillings, aneurysm clips, and spinal clips are a few examples of metal objects that are of clinical relevance. These implants create artefacts such as beam hardening and photon starvation that distort CT images and degrade image quality. This is of great significance because the distortions may cause improper evaluation of images and inaccurate dose calculation in the treatment planning system. Different algorithms are being developed to reduce these artefacts for better image quality for both diagnostic and therapeutic purposes. However, very limited information is available about the effect of artefact correction on dose calculation accuracy. This research study evaluates the dosimetric effect of metal artefact reduction algorithms on severe artefacts on CT images. This study uses Gemstone Spectral Imaging (GSI)-based MAR algorithm, projection-based Metal Artefact Reduction (MAR) algorithm, and the Dual-Energy method.

Materials and Methods: The Gemstone Spectral Imaging (GSI)-based and SMART Metal Artefact Reduction (MAR) algorithms are metal artefact reduction protocols embedded in two different CT scanner models by General Electric (GE), and the Dual-Energy Imaging Method was developed at Duke University. All three approaches were applied in this research for dosimetric evaluation on CT images with severe metal artefacts. The first part of the research used a water phantom with four iodine syringes. Two sets of plans, multi-arc plans and single-arc plans, using the Volumetric Modulated Arc therapy (VMAT) technique were designed to avoid or minimize influences from high-density objects. The second part of the research used projection-based MAR Algorithm and the Dual-Energy Method. Calculated Doses (Mean, Minimum, and Maximum Doses) to the planning treatment volume (PTV) were compared and homogeneity index (HI) calculated.

Results: (1) Without the GSI-based MAR application, a percent error between mean dose and the absolute dose ranging from 3.4-5.7% per fraction was observed. In contrast, the error was decreased to a range of 0.09-2.3% per fraction with the GSI-based MAR algorithm. There was a percent difference ranging from 1.7-4.2% per fraction between with and without using the GSI-based MAR algorithm. (2) A range of 0.1-3.2% difference was observed for the maximum dose values, 1.5-10.4% for minimum dose difference, and 1.4-1.7% difference on the mean doses. Homogeneity indexes (HI) ranging from 0.068-0.065 for dual-energy method and 0.063-0.141 with projection-based MAR algorithm were also calculated.

Conclusion: (1) Percent error without using the GSI-based MAR algorithm may deviate as high as 5.7%. This error invalidates the goal of Radiation Therapy to provide a more precise treatment. Thus, GSI-based MAR algorithm was desirable due to its better dose calculation accuracy. (2) Based on direct numerical observation, there was no apparent deviation between the mean doses of different techniques but deviation was evident on the maximum and minimum doses. The HI for the dual-energy method almost achieved the desirable null values. In conclusion, the Dual-Energy method gave better dose calculation accuracy to the planning treatment volume (PTV) for images with metal artefacts than with or without GE MAR Algorithm.

Pyramid Multi-resolution Scanning for Two-sample Comparison

Testing for two-sample differences is challenging when the differences are local and only involve a small portion of the data. To solve this problem, we apply a multi- resolution scanning framework that performs dependent local tests on subsets of the sample space. We use a nested dyadic partition of the sample space to get a collection of windows and test for sample differences within each window. We put a joint prior on the states of local hypotheses that allows both vertical and horizontal message passing among the partition tree to reflect the spatial dependency features among windows. This information passing framework is critical to detect local sample differences. We use both the loopy belief propagation algorithm and MCMC to get the posterior null probability on each window. These probabilities are then used to report sample differences based on decision procedures. Simulation studies are conducted to illustrate the performance. Multiple testing adjustment and convergence of the algorithms are also discussed.

Monthly Arctic sea ice lead fraction in 0.5° x 0.5° resolution from SARAL/Altika altimeter, link to datasets in NetCDF 4 format

Sea ice leads play an essential role in ocean-ice-atmosphere exchange, in ocean circulation, geochemistry, and in ice dynamics. Their precise detection is crucial for altimetric estimations of sea ice thickness and volume. This study evaluates the performance of the SARAL/AltiKa (Satellite with ARgos and ALtiKa) altimeter to detect leads and to monitor their spatio-temporal dynamics. We show that a pulse peakiness parameter (PP) used to detect leads by Envisat RA-2 and ERS-1,-2 altimeters is not suitable because of saturation of AltiKa return echoes over the leads. The signal saturation results in loss of 6-10% of PP data over sea ice. We propose a different parameter-maximal power of waveform-and define the threshold to discriminate the leads. Our algorithm can be applied from December until May. It detects well the leads of small and medium size from 200 m to 3-4 km. So the combination of the high-resolution altimetric estimates with low-resolution thermal infra-red or radiometric lead fraction products could enhance the capability of remote sensing to monitor sea ice fracturing.

High-resolution image reconstruction from multiple low-resolution images.

In this paper, we demonstrate a digital signal processing (DSP) algorithm for improving spatial resolution of images captured by CMOS cameras. The basic approach is to reconstruct a high resolution (HR) image from a shift-related low resolution (LR) image sequence. The aliasing relationship of Fourier transforms between discrete and continuous images in the frequency domain is used for mapping LR images to a HR image. The method of projection onto convex sets (POCS) is applied to trace the best estimate of pixel matching from the LR images to the reconstructed HR image. Computer simulations and preliminary experimental results have shown that the algorithm works effectively on the application of post-image-captured processing for CMOS cameras. It can also be applied to HR digital image reconstruction, where shift information of the LR image sequence is known.

A Pyramidal Genetic Algorithm for Multiple-Choice Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence, higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

Partnering Strategies for Fitness Evaluation in a Pyramidal Evolutionary Algorithm

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes for (sub-)fitness evaluation purposes are examined for two multiple-choice optimisation problems. It is shown that random partnering strategies perform best by providing better sampling and more diversity.

A Pyramidal Evolutionary Algorithm with Different Inter-Agent Partnering Strategies for Scheduling Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

Partnering Strategies for Fitness Evaluation in a Pyramidal Evolutionary Algorithm

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes for (sub-)fitness evaluation purposes are examined for two multiple-choice optimisation problems. It is shown that random partnering strategies perform best by providing better sampling and more diversity.

A Pyramidal Evolutionary Algorithm with Different Inter-Agent Partnering Strategies for Scheduling Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

A Pyramidal Genetic Algorithm for Multiple-Choice Problems

This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising larger parts of the problem. Hence, higher-level sub-populations search a larger search space with a lower resolution whilst lower-level sub-populations search a smaller search space with a higher resolution. The effects of different partner selection schemes amongst the agents on solution quality are examined for two multiple-choice optimisation problems. It is shown that partnering strategies that exploit problem-specific knowledge are superior and can counter inappropriate (sub-) fitness measurements.

Feature-based tracking of urethral motion in low-resolution trans-perineal ultrasound

This paper describes a novel algorithm for tracking the motion of the urethra from trans-perineal ultrasound. Our work is based on the structure-from-motion paradigm and therefore handles well structures with ill-defined and partially missing boundaries. The proposed approach is particularly well-suited for video sequences of low resolution and variable levels of blurriness introduced by anatomical motion of variable speed. Our tracking method identifies feature points on a frame by frame basis using the SURF detector/descriptor. Inter-frame correspondence is achieved using nearest-neighbor matching in the feature space. The motion is estimated using a non-linear bi-quadratic model, which adequately describes the deformable motion of the urethra. Experimental results are promising and show that our algorithm performs well when compared to manual tracking.

Feature-based tracking of urethral motion in low-resolution trans-perineal ultrasound

This paper describes a novel algorithm for tracking the motion of the urethra from trans-perineal ultrasound. Our work is based on the structure-from-motion paradigm and therefore handles well structures with ill-defined and partially missing boundaries. The proposed approach is particularly well-suited for video sequences of low resolution and variable levels of blurriness introduced by anatomical motion of variable speed. Our tracking method identifies feature points on a frame by frame basis using the SURF detector/descriptor. Inter-frame correspondence is achieved using nearest-neighbor matching in the feature space. The motion is estimated using a non-linear bi-quadratic model, which adequately describes the deformable motion of the urethra. Experimental results are promising and show that our algorithm performs well when compared to manual tracking.

Damage and fracture algorithm using the screened Poisson equation and local remeshing

We propose a crack propagation algorithm which is independent of particular constitutive laws and specific element technology. It consists of a localization limiter in the form of the screened Poisson equation with local mesh refinement. This combination allows the cap- turing of strain localization with good resolution, even in the absence of a sufficiently fine initial mesh. In addition, crack paths are implicitly defined from the localized region, cir- cumventing the need for a specific direction criterion. Observed phenomena such as mul- tiple crack growth and shielding emerge naturally from the algorithm. In contrast with alternative regularization algorithms, curved cracks are correctly represented. A staggered scheme for standard equilibrium and screened equations is used. Element subdivision is based on edge split operations using a given constitutive quantity (either damage or void fraction). To assess the robustness and accuracy of this algorithm, we use both quasi-brittle benchmarks and ductile tests.

Experimental evaluation of the z-resolution in different clinical Digital Breast Tomosynthesis systems using commercial phantoms

Digital Breast Tomosynthesis (DBT) is an advanced mammography technique based on the reconstruction of a pseudo-volumetric image. To date, image quality represents the most deficient section of DBT quality control protocols. In fact, related tests are not yet characterized by either action levels or typical values. This thesis work focuses on the evaluation of one aspect of image quality: the z-resolution. The latter is studied in terms of Artifact Spread Function (ASF), a function that describes the signal spread of a detail along the reconstructed focal planes. To quantify the ASF numerically, its Full Width at Half Maximum (FWHM) is calculated and used as a representative index of z-resolution. Experimental measurements were acquired in 24 DBT systems, of 7 different models, currently in use in 20 hospital facilities in Italy. The analysis, performed on the clinical reconstructed images, of 5 different commercial phantoms, lead to the identification of characteristic FWHM values for each type of DBT system. The ASF clearly showed a dependence on the size of the detail, providing higher FWHM values for larger objects. The z-resolution was found to be positively influenced by the acquisition angle: Fujifilm sistematically showed wider ASF profiles in ST mode (15°) than in HR mode (40°). However, no clear relationship was found between angular range and ASF, among different DBT systems, due to the influence of the peculiarities of each reconstruction algorithm. The experimental approach shown in this thesis work can be proposed as a z-resolution quality control test procedure. Contextually, the values found could be used as a starting point for identifying typical values to be included in the test, in a DBT protocol. Clearly, a statistically significant number of images is needed to do this. The equipment involved in this work is located in hospitals and is not available for research purposes, so only a limited amount of data was acquired and processed.