Angel Udías

Design and performance evaluation of a coplanar multimodality scanner for rodent imaging

This work reports on the development and performance evaluation of the VrPET/CT, a new multimodality scanner with coplanar geometry for in vivo rodent imaging. The scanner design is based on a partial-ring PET system and a small-animal CT assembled on a rotatory gantry without axial displacement between the geometric centers of both fields of view (FOV). We report on the PET system performance based on the NEMA NU-4 protocol; the performance characteristics of the CT component are not included herein. The accuracy of inter-modality alignment and the imaging capability of the whole system are also evaluated on phantom and animal studies. Tangential spatial resolution of PET images ranged between 1.56 mm at the center of the FOV and 2.46 at a radial offset of 3.5 cm. The radial resolution varies from 1.48 mm to 1.88 mm, and the axial resolution from 2.34 mm to 3.38 mm for the same positions. The energy resolution was 16.5% on average for the entire system. The absolute coincidence sensitivity is 2.2% for a 100-700 keV energy window with a 3.8 ns coincident window. The scatter fraction values for the same settings were 11.45% for a mouse-sized phantom and 23.26% for a rat-sized phantom. The peak noise equivalent count rates were also evaluated for those phantoms obtaining 70.8 kcps at 0.66 MBq/cc and 31.5 kcps at 0.11 MBq/cc, respectively. The accuracy of inter-modality alignment is below half the PET resolution, and the image quality of biological specimens agrees with measured performance parameters. The assessment presented in this study shows that the VrPET/CT system is a good performance small-animal imager, while the cost derived from a partial ring detection system is substantially reduced as compared with a full-ring PET tomograph.

Software architecture for multi-bed FDK-based reconstruction in X-ray CT scanners

Most small-animal X-ray computed tomography (CT) scanners are based on cone-beam geometry with a flat-panel detector orbiting in a circular trajectory. Image reconstruction in these systems is usually performed by approximate methods based on the algorithm proposed by Feldkamp et al. (FDK). Besides the implementation of the reconstruction algorithm itself, in order to design a real system it is necessary to take into account numerous issues so as to obtain the best quality images from the acquired data. This work presents a comprehensive, novel software architecture for small-animal CT scanners based on cone-beam geometry with circular scanning trajectory. The proposed architecture covers all the steps from the system calibration to the volume reconstruction and conversion into Hounsfield units. It includes an efficient implementation of an FDK-based reconstruction algorithm that takes advantage of system symmetries and allows for parallel reconstruction using a multiprocessor computer. Strategies for calibration and artifact correction are discussed to justify the strategies adopted. New procedures for multi-bed misalignment, beam-hardening, and Housfield units calibration are proposed. Experiments with phantoms and real data showed the suitability of the proposed software architecture for an X-ray small animal CT based on cone-beam geometry.

On a selection and scheduling problem in automatic storage and retrieval warehouses

Warehousing is one of the main components of the supply chain and its optimisation is crucial to achieve global efficiency. Warehouse operations involve receiving, shipping, storing and order picking, among other things, and the coordinated optimisation of all these different operations is highly complex. This paper examines a real selection and scheduling problem that arises in an automatic storage/retrieval warehouse system involving the scheduling of forklift pickup operations. The objective is to minimise the total loading time of the vehicles performing transportation, while respecting their departure due dates. This complex problem is approached via a two-phase decomposition method, combining both exact and heuristic procedures. The performance of the proposed solution method is evaluated using extensive computational results from several scenarios from a real case study using data from a real mattress warehouse.

Design an development of a high performance micro-CT system for small animal imaging

The goal of this work was the development of a low-cost micro-CT scanner, which could be used as an add-on in our previously developed PET systems for small-animals. The scanner design consists of a single-processor computer controlling a micro-focus X-ray tube and a flat panel detector, assembled in a common rotating gantry. The geometrical configuration was selected to achieve a spatial resolution of about 12 lp/mm with a field of view appropriate for small animals such as mice and rats. The radiated dose is controlled during the acquisition by two different elements: an aluminium filter and a tungsten shutter, attached to the X-ray source. The shutter is controlled by the computer in synchronism with the gantry rotation and the detector image integration. In order to achieve high performance with regards to per-animal screening time and cost, the acquisition protocol is able to take advantage from the highest frame rate of the detector also performing on-the-fly corrections for the detector raw data. These corrections include geometrical misalignments, sensor non-uniformities and defective elements, as well as conversion to attenuation images. An FDK reconstruction algorithm adapted to the specific cone-beam geometry has been implemented. Symmetries are exploited to accelerate the algorithm and fast back-projection techniques have been developed for those protocols where high resolution is not a requirement.

Simulation and multicriteria optimization modeling approach for regional water restoration management

This paper presents a modeling framework that intends to select the optimal robust wastewater reclamation program of measures (PoM) to achieve the European Water Framework Directive (WFD) objectives in the inner Catalonia watersheds. The integrative methodological tool developed incorporates a water quality model to simulate the effects of the PoM used to reduce pollution pressures on the hydrologic network. A Multi-Objective Evolutionary Algorithm (MOEA) helps to identify efficient trade-offs between PoM cost and water quality. Interactive Decisions Map (IDM)—a multi-criteria visualization—based decision support tool is used to provide a clear idea of the trade-off between water status and the cost to achieve such situation. Lastly, a stochastic simulation model to analyze the sensitivity under varied environmental uncertainties is run. Moreover, the tool is oriented to guide water managers in their decision-making processes. Additionally, this paper analyzes the results of the application of the management tool in the inner Catalan watershed in order to perform the European WFD. This tool has had a key role in the design of part of the PoM which shall be implemented to achieve objectives of the WFD in 2015 in all the Catalan catchments.

Use of IBASPM atlas-based automatic segmentation toolbox in pathological brains: Effect of template selection

IBASPM software is an atlas-based method for automatic segmentation of brain structures, available as a freeware toolbox for the SPM package. To test the influence of the atlas when segmenting normal and pathologic brains, manual segmentation of the caudate nucleus head was compared to automatic segmentations using four different atlases: the default MNI AAL atlas; a customized atlas created from a combined sample of patients (n=20) and controls (n=18); and a customized atlas obtained separately for each group. Maximum average ratio of overlapping voxels (dice overlap) between manual and automatic segmentation was 71% for controls and 52% for patients. In both groups, overlap ratios were better when using the customized atlases, instead of the standard MNI AAL atlas. Accuracy of the method was biased between left and right hemispheres, and also between groups, individual variability being higher in patients than in controls. Volumetric measurements using the customized atlases were also more accurate than using the MNI AAL atlas. Volume data were closer to manual segmentation values than dice overlap ratio (average differences ranging from 22.7% for MNI AAL atlas to 10.1% for customized atlas of patients and controls combined). Results suggests a low overall performance of IBASPM as an automatic segmentation method for the head of the caudate nucleus. Because of the biases observed, the use of this method for analyzing caudate nucleus in patients presenting anatomical abnormalities should be cautiously carried out.

PET/CT alignment for small animal scanners based on capillary detection

Small animal PET/CT devices provide anatomical and molecular imaging at the same time, enabling the joint visualization and analysis of both modalities. An accurate PET/CT alignment is required to correctly interpret these studies. A proper calibration procedure is essential for small animal imaging, since resolution is much higher than in human devices. This work presents an alignment phantom and a method that enable a reliable and replicable measurement of the geometrical relationship between PET and CT modules. The phantom can be built with laboratory materials, and is used to estimate the rigid spatial transformation that aligns both modalities. It consists of three glass capillaries located in non-coplanar triangular geometry and filled with FDG, so they are easily identified in both modalities. The method is based on automatic line detection and localization of the corresponding points between the lines on both modalities, which allows calculating the rigid alignment parameters. Different geometric configurations of the phantom (i.e. different angles and distances between capillaries) were tested to assess the repeatability of the calculations. To measure the alignment precision achieved, we attached two additional sodium point sources to the phantom, which were neglected in the registration process. Our results show that the accuracy of the alignment estimation, measured as average misalignment of the Na sources, is below half the PET resolution. The alternative settings for the phantom layout did not affect this result, indicating the low dependency of the alignment calculated with the actual phantom layout. Our approach allows measuring the PET/CT transformation parameters using an in-house built phantom and with low computational effort and high accuracy, demonstrating that the proposed phantom is suitable for alignment calibration of dual modality systems on a real environment.

VrPET/CT: Development of a rotating multimodality scanner for small-animal imaging

This work reports on the development and evaluation of the PET component of a PET/CT system for small-animal in-vivo imaging. The PET and CT subsystems are assembled in a rotary gantry in such a way that the center of rotation for both imaging modalities is mechanically aligned. The PET scanner configuration is based on 2 detector modules, each of which consist of 2 flat-panel type PS-PMTs (Hamamatsu, H8500) and 2 (30 × 30 elements) LYSO arrays. The dimension of the crystal matrix elements are 1.4 × 1.4 mm2 in cross section and 12 mm in depth. The VrPET detector modules are positioned in opposite sides of a 140 mm diameter ring, providing a transaxial field of view of 86.6 mm diameter and an axial field of view of 45.6 mm. The experimental results obtained in the performance tests are transaxial resolution of 1.5 mm FWHM in the CFOV, and the axial resolution of 2.3 mm FWHM. The absolute coincidence sensitivity is 2.22 % for a coincidence window of 6 ns (100–700 keV). The imaging capability of the PET unit is demonstrated on phantom and animal studies.

Assessment of a new CT system for small animals

We have developed an X-ray cone beam tomograph for in vivo small-animal imaging using a flat panel detector (CMOS technology with a columnar CsI scintillator plate) and a microfocus X-ray source in a geometric configuration with 1.6 magnification and 7.5 cm2 field of view. This work presents an initial characterization of this new system. We measured the detector modulation transfer function (MTF), detector stability, system resolution, the quality of the reconstructed tomographic images and radiated dose. The system resolution was measured following the standard test method ASTM E1696-95. For image quality evaluation, we assessed signal to noise ratio (SNR) and contrast to noise ratio (CNR) with respect to radiated dose. Measurements have been performed on Hounsfield-calibrated images of quantitative phantoms. Effective dose studies have been performed introducing TLD dosimeters in representative organs (ICRU criteria) of euthanized laboratory rats for different imaging protocols. Noise measurements indicate that 50 HU can be achieved at a dose of 10 cGy. Effective dose in standard research methods is below 200 mSv, confirming that the system is appropriate for in vivo imaging. Maximum spatial resolution achieved is better than 50 microns. Experimental results on image quality phantoms as well as on in-vivo studies show that the use of CMOS flat panel is a good choice in terms of quality with respect to radiated dose.

Identifying efficient agricultural irrigation strategies in Crete

Water scarcity and droughts are a major concern in most Mediterranean countries. Agriculture is a major user of water in the region and releases significant amounts of surface and ground waters, endangering the sustainable use of the available resources. Best Management Practices (BMPs) can mitigate the agriculture impacts on quantity of surface waters in agricultural catchments. However, identification of efficient BMPs strategies is a complex task, because BMPs costs and effectiveness can vary significantly within a basin. In this study, sustainable agricultural practices were studied based on optimal allocation of irrigation water use for dominant irrigated crops in the island of Crete, Greece. A decision support tool that integrates the Soil and Water Assessment Tool (SWAT) watershed model, an economic model, and multi-objective optimization routines, was used to identify and locate optimal irrigation strategies by considering crop water requirements, impact of irrigation changes on crop productivity, management strategies costs, and crop market prices. Three spatial scales (crop type, fields, and administrative regions) were considered to point out different approaches of efficient management. According to the analysis, depending on the spatial scale and complexity of spatial optimization, water irrigation volumes could be reduced by 32%-70% while preserving current agricultural benefit. Specific management strategies also looked at ways to relocate water between administrative regions (4 prefectures in the case of Crete) to optimize crop benefit while reducing global water use. It was estimated that an optimal reallocation of water could reduce irrigation water volumes by 52% (148 Mm3/y) at the cost of a 7% (48 M€) loss of agricultural income, but maintaining the current agricultural benefit (626.9 M€). The study showed how the identification of optimal, cost-effective irrigation management strategies can potentially address the water scarcity issue that is becoming crucial for the viability of agriculture in the Mediterranean region.