3D crosshole ERT for aquifer characterization and monitoring of infiltrating river water

The hydrogeological properties and responses of a productive aquifer in northeastern Switzerland are investigated. For this purpose, 3D crosshole electrical resistivity tomography (ERT) is used to define the main lithological structures within the aquifer (through static inversion) and to monitor the water infiltration from an adjacent river. During precipitation events and subsequent river flooding, the river water resistivity increases. As a consequence, the electrical characteristics of the infiltrating water can be used as a natural tracer to delineate preferential flow paths and flow velocities. The focus is primarily on the experiment installation, data collection strategy, and the structural characterization of the site and a brief overview of the ERT monitoring results. The monitoring system comprises 18 boreholes each equipped with 10 electrodes straddling the entire thickness of the gravel aquifer. A multi-channel resistivity system programmed to cycle through various four-point electrode configurations of the 180 electrodes in a rolling sequence allows for the measurement of approximately 15,500 apparent resistivity values every 7 h on a continuous basis. The 3D static ERT inversion of data acquired under stable hydrological conditions provides a base model for future time-lapse inversion studies and the means to investigate the resolving capability of our acquisition scheme. In particular, it enables definition of the main lithological structures within the aquifer. The final ERT static model delineates a relatively high-resistivity, low-porosity, intermediate-depth layer throughout the investigated aquifer volume that is consistent with results from well logging and seismic and radar tomography models. The next step will be to define and implement an appropriate time-lapse ERT inversion scheme using the river water as a natural tracer. The main challenge will be to separate the superposed time-varying effects of water table height, temperature, and salinity variations associated with the infiltrating water.

On the convergence of EM-like algorithms for image segmentation using Markov random fields.

Inference of Markov random field images segmentation models is usually performed using iterative methods which adapt the well-known expectation-maximization (EM) algorithm for independent mixture models. However, some of these adaptations are ad hoc and may turn out numerically unstable. In this paper, we review three EM-like variants for Markov random field segmentation and compare their convergence properties both at the theoretical and practical levels. We specifically advocate a numerical scheme involving asynchronous voxel updating, for which general convergence results can be established. Our experiments on brain tissue classification in magnetic resonance images provide evidence that this algorithm may achieve significantly faster convergence than its competitors while yielding at least as good segmentation results.

Restitución 3D de la topografía de la antigua ciudad de Tarraco en un entorno SIG: propuestas metodológicas y primeros resultados

Durante los últimos años el Institut Català d’Arquelogia Clàssica, el Museu d’Història de Tarragona, contando con la colaboración de la Generalitat de Catalunya, han desarrallado el proyecto Planimetría Arqueológica de Tárraco, destinado a la elaboración de una planta arqueológica global en la cual se recogieran intervenciones y noticias referentes a los hallazgos arqueológicos existentes. Este trabajo fue publicado utilizando como plataforma de trabajo un SIG construido para tal fin (Macias et al. 2007). Sin embargo, un problema de difícil solución arqueológica venía dado por las transformaciones urbanísticas de la ciudad, sufridas en su mayor parte a lo largo de los siglos XIX y XX. Éstas habían provocado la pérdida irremediable de gran parte de la elevación que acogiera la ciudad romana, cambiando substancialmente su aspecto original. Ante esta situación y como proyecto paralelo a la realización de la Planimetría Arqueológica de Tarragona se plantearon formas de cubrir este vacío. Se presenta en esta comunicación una propuesta metodológica para la reconstrucción de los grandes «vacíos topográficos » originados por la evolución urbanística de Tarragona mediante la obtención e integración en un SIG de diversos tipos de información documental. En estas zonas rebajadas no resulta posible la obtención de información estratigráfica y arqueológica, por lo que es imprescindible la definición de vías metodológicas alternativas basadas en la extrapolación de datos extraídos de la cartografía histórica, panorámicas del XVI o fotografías tomadas en los siglos XIX y XX. Esta técnica permite aplicar los resultados obtenidos en los nuevos análisis interpretativos, complementando así la interpretación arqueológica de la topografía urbana de la ciudad romana. A partir de esta información, y aplicando funciones y técnicas de interpolación propias de un GIS, se propone aquí un modelo de relieve de la ciudad de Tarraco.

Automated segmentation of multiple red blood cells with digital holographic microscopy.

We present a method to automatically segment red blood cells (RBCs) visualized by digital holographic microscopy (DHM), which is based on the marker-controlled watershed algorithm. Quantitative phase images of RBCs can be obtained by using off-axis DHM along to provide some important information about each RBC, including size, shape, volume, hemoglobin content, etc. The most important process of segmentation based on marker-controlled watershed is to perform an accurate localization of internal and external markers. Here, we first obtain the binary image via Otsu algorithm. Then, we apply morphological operations to the binary image to get the internal markers. We then apply the distance transform algorithm combined with the watershed algorithm to generate external markers based on internal markers. Finally, combining the internal and external markers, we modify the original gradient image and apply the watershed algorithm. By appropriately identifying the internal and external markers, the problems of oversegmentation and undersegmentation are avoided. Furthermore, the internal and external parts of the RBCs phase image can also be segmented by using the marker-controlled watershed combined with our method, which can identify the internal and external markers appropriately. Our experimental results show that the proposed method achieves good performance in terms of segmenting RBCs and could thus be helpful when combined with an automated classification of RBCs.

Performance analysis of software run-time behaviour using 3D-visualisation

Monimutkaisen tietokonejärjestelmän suorituskykyoptimointi edellyttää järjestelmän ajonaikaisen käyttäytymisen ymmärtämistä. Ohjelmiston koon ja monimutkaisuuden kasvun myötä suorituskykyoptimointi tulee yhä tärkeämmäksi osaksi tuotekehitysprosessia. Tehokkaampien prosessorien käytön myötä myös energiankulutus ja lämmöntuotto ovat nousseet yhä suuremmiksi ongelmiksi, erityisesti pienissä, kannettavissa laitteissa. Lämpö- ja energiaongelmien rajoittamiseksi on kehitetty suorituskyvyn skaalausmenetelmiä, jotka edelleen lisäävät järjestelmän kompleksisuutta ja suorituskykyoptimoinnin tarvetta. Tässä työssä kehitettiin visualisointi- ja analysointityökalu ajonaikaisen käyttäytymisen ymmärtämisen helpottamiseksi. Lisäksi kehitettiin suorituskyvyn mitta, joka mahdollistaa erilaisten skaalausmenetelmien vertailun ja arvioimisen suoritusympäristöstä riippumatta, perustuen joko suoritustallenteen tai teoreettiseen analyysiin. Työkalu esittää ajonaikaisesti kerätyn tallenteen helposti ymmärrettävällä tavalla. Se näyttää mm. prosessit, prosessorikuorman, skaalausmenetelmien toiminnan sekä energiankulutuksen kolmiulotteista grafiikkaa käyttäen. Työkalu tuottaa myös käyttäjän valitsemasta osasta suorituskuvaa numeerista tietoa, joka sisältää useita oleellisia suorituskykyarvoja ja tilastotietoa. Työkalun sovellettavuutta tarkasteltiin todellisesta laitteesta saatua suoritustallennetta sekä suorituskyvyn skaalauksen simulointia analysoimalla. Skaalausmekanismin parametrien vaikutus simuloidun laitteen suorituskykyyn analysoitiin.

Quantitative morphometry analysis of the fetal brain using clinical MR imaging

In vivo fetal magnetic resonance imaging provides aunique approach for the study of early human braindevelopment [1]. In utero cerebral morphometry couldpotentially be used as a marker of the cerebralmaturation and help to distinguish between normal andabnormal development in ambiguous situations. However,this quantitative approach is a major challenge becauseof the movement of the fetus inside the amniotic cavity,the poor spatial resolution provided by very fast MRIsequences and the partial volume effect. Extensiveefforts are made to deal with the reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution [2,3,4]. Frameworkswere developed for the segmentation of specific regionsof the fetal brain such as posterior fossa, brainstem orgerminal matrix [5,6], or for the entire brain tissue[7,8], applying the Expectation-Maximization MarkovRandom Field (EM-MRF) framework. However, many of theseprevious works focused on the young fetus (i.e. before 24weeks) and use anatomical atlas priors to segment thedifferent tissue or regions. As most of the gyraldevelopment takes place after the 24th week, acomprehensive and clinically meaningful study of thefetal brain should not dismiss the third trimester ofgestation. To cope with the rapidly changing appearanceof the developing brain, some authors proposed a dynamicatlas [8]. To our opinion, this approach however faces arisk of circularity: each brain will be analyzed /deformed using the template of its biological age,potentially biasing the effective developmental delay.Here, we expand our previous work [9] to proposepost-processing pipeline without prior that allow acomprehensive set of morphometric measurement devoted toclinical application. Data set & Methods: Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences (TR 7000 ms, TE 180 ms, FOV 40 x 40 cm,slice thickness 5.4mm, in plane spatial resolution1.09mm). For each fetus, 6 axial volumes shifted by 1 mmwere acquired under motherâeuro?s sedation (about 1min pervolume). First, each volume is segmentedsemi-automatically using region-growing algorithms toextract fetal brain from surrounding maternal tissues.Inhomogeneity intensity correction [10] and linearintensity normalization are then performed. Brain tissues(CSF, GM and WM) are then segmented based on thelow-resolution volumes as presented in [9]. Ahigh-resolution image with isotropic voxel size of 1.09mm is created as proposed in [2] and using B-splines forthe scattered data interpolation [11]. Basal gangliasegmentation is performed using a levet setimplementation on the high-resolution volume [12]. Theresulting white matter image is then binarized and givenas an input in FreeSurfer software(http://surfer.nmr.mgh.harvard.edu) to providetopologically accurate three-dimensional reconstructionsof the fetal brain according to the local intensitygradient. References: [1] Guibaud, Prenatal Diagnosis29(4) (2009). [2] Rousseau, Acad. Rad. 13(9), 2006. [3]Jiang, IEEE TMI 2007. [4] Warfield IADB, MICCAI 2009. [5]Claude, IEEE Trans. Bio. Eng. 51(4) 2004. [6] Habas,MICCAI 2008. [7] Bertelsen, ISMRM 2009. [8] Habas,Neuroimage 53(2) 2010. [9] Bach Cuadra, IADB, MICCAI2009. [10] Styner, IEEE TMI 19(39 (2000). [11] Lee, IEEETrans. Visual. And Comp. Graph. 3(3), 1997. [12] BachCuadra, ISMRM 2010.

A segmentation analysis and segments profile of budget air travelers

Many Spanish destinations are now considering low cost airlines (LCA) important for attracting tourists. However, there is little evidence on the characteristics travelers using low cost airlines and their flight preferences. Typical segmentation of air travelers are business versus leisure travelers and business versus tourist fares. The aim of this paper is to obtain a deeper understanding of the demand of LCA through a segmentation analysis, based on 808 foreign travelers who used Girona airport, that focuses on low cost travelers’ valuations of different flight attributes and trip related characteristics

3D-muodot tuoliaihion muotopuristuksessa

Diplomityössä tutkittiin muotopuristeissa käytettävien viilujen soveltuvuutta yhteistyöyrityksen, VK Valmiskaluste Oy:n, valmistaman lepotuolin materiaaliksi. Tuoliaihion muoto edellytti viilun taivuttamista kahteen suuntaan, eli kyseessä oli ns. 3D-muoto. Muotopuristeita valmistavissa yrityksissä tehtyjen haastattelujen perusteella valittiin viilumateriaalit ja mitattiin niiden murtovenymä. Materiaaleja testattiin puristamalla tuoliaihioita. Aihionmuoto edellytti viilulta vähintään 3,3 %:n venyvyyttä. Koepuristuksetvahvistivat murtovenymätestauksen tulokset, eli tutkitun aihion pintarakenne säilyi ehjänä käyttämällä paperitaustaista viilua tai 3D-muotoihin tarkoitettua 3D-viilua. Kirjallisuusosiossa on selvitetty taivutettavuuteen vaikuttavia tekijöitä ja viilun rakenteen muokkausta taivutettavuuden parantamiseksi .

Three-Dimensional (3D) Microarchitecture Correlations with 2D Projection Image Gray-Level Variations Assessed by Trabecular Bone Score Using High-Resolution Computed Tomographic Acquisitions: Effects of Resolution and Noise.

The aim of the present study is to determine the level of correlation between the 3-dimensional (3D) characteristics of trabecular bone microarchitecture, as evaluated using microcomputed tomography (μCT) reconstruction, and trabecular bone score (TBS), as evaluated using 2D projection images directly derived from 3D μCT reconstruction (TBSμCT). Moreover, we have evaluated the effects of image degradation (resolution and noise) and X-ray energy of projection on these correlations. Thirty human cadaveric vertebrae were acquired on a microscanner at an isotropic resolution of 93μm. The 3D microarchitecture parameters were obtained using MicroView (GE Healthcare, Wauwatosa, MI). The 2D projections of these 3D models were generated using the Beer-Lambert law at different X-ray energies. Degradation of image resolution was simulated (from 93 to 1488μm). Relationships between 3D microarchitecture parameters and TBSμCT at different resolutions were evaluated using linear regression analysis. Significant correlations were observed between TBSμCT and 3D microarchitecture parameters, regardless of the resolution. Correlations were detected that were strongly to intermediately positive for connectivity density (0.711≤r(2)≤0.752) and trabecular number (0.584≤r(2)≤0.648) and negative for trabecular space (-0.407 ≤r(2)≤-0.491), up to a pixel size of 1023μm. In addition, TBSμCT values were strongly correlated between each other (0.77≤r(2)≤0.96). Study results show that the correlations between TBSμCT at 93μm and 3D microarchitecture parameters are weakly impacted by the degradation of image resolution and the presence of noise.

The Application of 3D Reconstruction Techniques in the Analysis of Ancient Tarraco’s Urban Topography

The widespread implementation of GIS-based 3D topographical models has been a great aid in the development and testing of archaeological hypotheses. In this paper, a topographical reconstruction of the ancient city of Tarraco, the Roman capital of the Tarraconensis province, is presented. This model is based on topographical data obtained through archaeological excavations, old photographic documentation, georeferenced archive maps depicting the pre-modern city topography, modern detailed topographical maps and differential GPS measurements. The addition of the Roman urban architectural features to the model offers the possibility to test hypotheses concerning the ideological background manifested in the city shape. This is accomplished mainly through the use of 3D views from the main city accesses. These techniques ultimately demonstrate the ‘theatre-shaped’ layout of the city (to quote Vitrubius) as well as its southwest oriented architecture, whose monumental character was conceived to present a striking aspect to visitors, particularly those arriving from the sea.

Prosessilaitosten asennusjärjestyksen simulointi 3D-malleilla

Työn tavoitteena on haihduttamon asennusjärjestyksen havainnollistaminen 3D animaatiota hyväksikäyttäen, sekä sen hyödyntäminen niin myynti- kuin asennusneuvotteluissa. Kirjallinen osio perustuu tehtyyn 3D-animaatioon, joka onjaettu kolmeen pääalueeseen. Ensimmäisessä vaiheessa kerrotaan lyhyesti Andritz Oy:n liiketoiminnasta sekä selvitetään haihduttamoprosessin toimintaperiaatteet. Toinen alue käsittää toimintaprojektin, jossa tuotettu 3D-animaatio linkitetään sen käyttöympäristöön. Kolmannessa alueessa käydään läpi 3D-animaation tekoon liittyvät asiat. Lopuksi ennen yhteenvetoa käydään vielä läpi käyttäjien kommentit tehdystä animaatiosta.

Forecasting coal resources and reserves in heterogeneous coal zones using 3D facies models (As Pontes Basin, NW Spain)

Forecasting coal resources and reserves is critical for coal mine development. Thickness maps are commonly used for assessing coal resources and reserves; however they are limited for capturing coal splitting effects in thick and heterogeneous coal zones. As an alternative, three-dimensional geostatistical methods are used to populate facies distributionwithin a densely drilled heterogeneous coal zone in the As Pontes Basin (NWSpain). Coal distribution in this zone is mainly characterized by coal-dominated areas in the central parts of the basin interfingering with terrigenous-dominated alluvial fan zones at the margins. The three-dimensional models obtained are applied to forecast coal resources and reserves. Predictions using subsets of the entire dataset are also generated to understand the performance of methods under limited data constraints. Three-dimensional facies interpolation methods tend to overestimate coal resources and reserves due to interpolation smoothing. Facies simulation methods yield similar resource predictions than conventional thickness map approximations. Reserves predicted by facies simulation methods are mainly influenced by: a) the specific coal proportion threshold used to determine if a block can be recovered or not, and b) the capability of the modelling strategy to reproduce areal trends in coal proportions and splitting between coal-dominated and terrigenousdominated areas of the basin. Reserves predictions differ between the simulation methods, even with dense conditioning datasets. Simulation methods can be ranked according to the correlation of their outputs with predictions from the directly interpolated coal proportion maps: a) with low-density datasets sequential indicator simulation with trends yields the best correlation, b) with high-density datasets sequential indicator simulation with post-processing yields the best correlation, because the areal trends are provided implicitly by the dense conditioning data.

Evaluation and comparison of current fetal ultrasound image segmentation methods for biometric measurements: a grand challenge.

This paper presents the evaluation results of the methods submitted to Challenge US: Biometric Measurements from Fetal Ultrasound Images, a segmentation challenge held at the IEEE International Symposium on Biomedical Imaging 2012. The challenge was set to compare and evaluate current fetal ultrasound image segmentation methods. It consisted of automatically segmenting fetal anatomical structures to measure standard obstetric biometric parameters, from 2D fetal ultrasound images taken on fetuses at different gestational ages (21 weeks, 28 weeks, and 33 weeks) and with varying image quality to reflect data encountered in real clinical environments. Four independent sub-challenges were proposed, according to the objects of interest measured in clinical practice: abdomen, head, femur, and whole fetus. Five teams participated in the head sub-challenge and two teams in the femur sub-challenge, including one team who tackled both. Nobody attempted the abdomen and whole fetus sub-challenges. The challenge goals were two-fold and the participants were asked to submit the segmentation results as well as the measurements derived from the segmented objects. Extensive quantitative (region-based, distance-based, and Bland-Altman measurements) and qualitative evaluation was performed to compare the results from a representative selection of current methods submitted to the challenge. Several experts (three for the head sub-challenge and two for the femur sub-challenge), with different degrees of expertise, manually delineated the objects of interest to define the ground truth used within the evaluation framework. For the head sub-challenge, several groups produced results that could be potentially used in clinical settings, with comparable performance to manual delineations. The femur sub-challenge had inferior performance to the head sub-challenge due to the fact that it is a harder segmentation problem and that the techniques presented relied more on the femur's appearance.