Computer Aided Detection and measurement of peripheral artery disease.

Computer-Aided Tomography Angiography (CTA) images are the standard for assessing Peripheral artery disease (PAD). This paper presents a Computer Aided Detection (CAD) and Computer Aided Measurement (CAM) system for PAD. The CAD stage detects the arterial network using a 3D region growing method and a fast 3D morphology operation. The CAM stage aims to accurately measure the artery diameters from the detected vessel centerline, compensating for the partial volume effect using Expectation Maximization (EM) and a Markov Random field (MRF). The system has been evaluated on phantom data and also applied to fifteen (15) CTA datasets, where the detection accuracy of stenosis was 88% and the measurement accuracy was with an 8% error.

3D culture of postnatal retinal stem cells using self assembling polymers

PURPOSE We have previously shown that retinal stem cells (RSCs) can be isolated from the radial glia population of the newborn mouse retina (Angénieux et al., 2006). These RSCs have a great capacity to renew and to generate a large number of neurons including cells differentiated towards the photoreceptor lineage (Mehri-Soussi et al., 2006). However, recent published results from our lab revealed that such cells have a poor integration and survival rate after grafting. The uncontrolled environment of a retina seems to prevent good integration and survival after grafting in vivo. To bypass this problem, we are evaluating the possibility of generating in vitro a hemi-retinal tissue before transplantation. METHODS RSC were expanded and cells passaged <10 were seeded in a solution containing poly-ethylene-glycol (PEG) polymer based hydrogels crosslinked with peptides that are chosen to be substrates for matrix metalloproteinases. Various doses of cross linkers peptides allowing connections between PEG polymers were tested. Different growth factors were studied to stimulate cell proliferation and differentiation. RESULTS Cells survived only in the presence of EGF and FGF-2 and generated colonies with a sphere shape. No cells migrated within the gel. To improve the migration and the repartition of the cells in the gels, the integrin ligand RGDSP was added into the gel. In the presence of FGF-2 and EGF, newly formed cell clusters appeared by cell proliferation within several days, but again no outspreading of cells was observed. No difference was even seen when the stiffness of the hydrogels or the concentration of the integrin ligand RGDSP were changed. However, our preliminary results show that RSCs still form spheres when laminin is entrapped in the gel, but they started to spread out having a neuronal morphology after around 2 weeks. The neuronal population was assessed by the presence of the neuronal marker b-tubulin-III. This differentiation was achieved after successive steps of stimulations including FGF-2 and EGF, and then only FGF-2. Glial cells were also present. Further characterizations are under process. CONCLUSIONS RSC can be grown in 3D. Preliminary results show that neuronal cell phenotype acquisition can be instructed by exogenous stimulations and factors linked to the gel. Further developments are necessary to form a homogenous tissue containing retinal cells.

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.

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.

Reconstruction of 3D Planar Objects with Partial Occlusion

Kolmiulotteisten kappaleiden rekonstruktio on yksi konenäön haastavimmista ongelmista, koska kappaleiden kolmiulotteisia etäisyyksiä ei voida selvittää yhdestä kaksiulotteisesta kuvasta. Ongelma voidaan ratkaista stereonäön avulla, jossa näkymän kolmiulotteinen rakenne päätellään usean kuvan perusteella. Tämä lähestymistapa mahdollistaa kuitenkin vain rekonstruktion niille kappaleiden osille, jotka näkyvät vähintään kahdessa kuvassa. Piilossa olevien osien rekonstruktio ei ole mahdollista pelkästään stereonäön avulla. Tässä työssä on kehitetty uusi menetelmä osittain piilossa olevien kolmiulotteisten tasomaisten kappaleiden rekonstruktioon. Menetelmän avulla voidaan selvittää hyvällä tarkkuudella tasomaisista pinnoista koostuvan kappaleen muoto ja paikka käyttäen kahta kuvaa kappaleesta. Menetelmä perustuu epipolaarigeometriaan, jonka avulla selvitetään molemmissa kuvissa näkyvät kappaleiden osat. Osittain piilossa olevien piirteiden rekonstruointi suoritetaan käyttämäen stereonäköä sekä tietoa kappaleen rakenteesta. Esitettyä ratkaisua voitaisiin käyttää esimerkiksi kolmiulotteisten kappaleiden visualisointiin, robotin navigointiin tai esineentunnistukseen.

Helical tomotherapy for the treatment of anal canal cancer: a dosimetric comparison with 3D conformal radiotherapy.

AIMS AND BACKGROUND: The standard treatment of anal canal cancer (ACC) is combined chemotherapy and radiation therapy (RT), which is complex because of the shape of the target volumes and the need to minimize the irradiation of normal pelvic structures. In this study we compared the dosimetric results of helical tomotherapy (HT) plans with traditional 3D conformal RT (3DRT) plans for the treatment of ACC. METHODS AND STUDY DESIGN: Twelve patients (median age 57 years, range 38-83; F/M 8/4) treated with HT and concurrent chemotherapy for locally advanced ACC were selected. All had histologically confirmed squamous-cell carcinoma. A clinical target volume including the tumor and pelvic and inguinal lymph nodes was treated with HT to a total dose of 36 Gy in 1.8-Gy daily fractions. Then a sequential boost of 23.4 Gy in 1.8-Gy daily fractions (total dose 59.4 Gy) was delivered to the tumor and involved nodes. For all 12 patients, 3DRT plans were generated for comparison. Treatment plans were evaluated by means of standard dose-volume histograms. Dose coverage of the planning target volumes (PTVs), homogeneity index (HI), and mean doses to organs at risk (OARs) were compared. RESULTS: The coverage of PTV was comparable between the two treatment plans. HI was better in the HT vs. 3DRT plans (1.25 and 3.57, respectively; p<0.0001). HT plans resulted in better sparing of OARs (p<0.0001). CONCLUSIONS: HT showed superior target dose conformality and significant sparing of pelvic structures compared with 3DRT. Further investigation should determine if these dosimetric improvements will improve clinical outcomes regarding locoregional control, survival, and treatment-related acute and late morbidity.

ICA Cleaning procedure for EEG signals analysis: application to Alzheimer's disease detection

To develop systems in order to detect Alzheimer’s disease we want to use EEG signals. Available database is raw, so the first step must be to clean signals properly. We propose a new way of ICA cleaning on a database recorded from patients with Alzheimer's disease (mildAD, early stage). Two researchers visually inspected all the signals (EEG channels), and each recording's least corrupted (artefact-clean) continuous 20 sec interval were chosen for the analysis. Each trial was then decomposed using ICA. Sources were ordered using a kurtosis measure, and the researchers cleared up to seven sources per trial corresponding to artefacts (eye movements, EMG corruption, EKG, etc), using three criteria: (i) Isolated source on the scalp (only a few electrodes contribute to the source), (ii) Abnormal wave shape (drifts, eye blinks, sharp waves, etc.), (iii) Source of abnormally high amplitude ( �100 �V). We then evaluated the outcome of this cleaning by means of the classification of patients using multilayer perceptron neural networks. Results are very satisfactory and performance is increased from 50.9% to 73.1% correctly classified data using ICA cleaning procedure.

Eye-tracking of nodule detection in lung CT volumetric data.

PURPOSE: Signal detection on 3D medical images depends on many factors, such as foveal and peripheral vision, the type of signal, and background complexity, and the speed at which the frames are displayed. In this paper, the authors focus on the speed with which radiologists and naïve observers search through medical images. Prior to the study, the authors asked the radiologists to estimate the speed at which they scrolled through CT sets. They gave a subjective estimate of 5 frames per second (fps). The aim of this paper is to measure and analyze the speed with which humans scroll through image stacks, showing a method to visually display the behavior of observers as the search is made as well as measuring the accuracy of the decisions. This information will be useful in the development of model observers, mathematical algorithms that can be used to evaluate diagnostic imaging systems. METHODS: The authors performed a series of 3D 4-alternative forced-choice lung nodule detection tasks on volumetric stacks of chest CT images iteratively reconstructed in lung algorithm. The strategy used by three radiologists and three naïve observers was assessed using an eye-tracker in order to establish where their gaze was fixed during the experiment and to verify that when a decision was made, a correct answer was not due only to chance. In a first set of experiments, the observers were restricted to read the images at three fixed speeds of image scrolling and were allowed to see each alternative once. In the second set of experiments, the subjects were allowed to scroll through the image stacks at will with no time or gaze limits. In both static-speed and free-scrolling conditions, the four image stacks were displayed simultaneously. All trials were shown at two different image contrasts. RESULTS: The authors were able to determine a histogram of scrolling speeds in frames per second. The scrolling speed of the naïve observers and the radiologists at the moment the signal was detected was measured at 25-30 fps. For the task chosen, the performance of the observers was not affected by the contrast or experience of the observer. However, the naïve observers exhibited a different pattern of scrolling than the radiologists, which included a tendency toward higher number of direction changes and number of slices viewed. CONCLUSIONS: The authors have determined a distribution of speeds for volumetric detection tasks. The speed at detection was higher than that subjectively estimated by the radiologists before the experiment. The speed information that was measured will be useful in the development of 3D model observers, especially anthropomorphic model observers which try to mimic human behavior.

A statistical shape model of the human second cervical vertebra.

PURPOSE: Statistical shape and appearance models play an important role in reducing the segmentation processing time of a vertebra and in improving results for 3D model development. Here, we describe the different steps in generating a statistical shape model (SSM) of the second cervical vertebra (C2) and provide the shape model for general use by the scientific community. The main difficulties in its construction are the morphological complexity of the C2 and its variability in the population. METHODS: The input dataset is composed of manually segmented anonymized patient computerized tomography (CT) scans. The alignment of the different datasets is done with the procrustes alignment on surface models, and then, the registration is cast as a model-fitting problem using a Gaussian process. A principal component analysis (PCA)-based model is generated which includes the variability of the C2. RESULTS: The SSM was generated using 92 CT scans. The resulting SSM was evaluated for specificity, compactness and generalization ability. The SSM of the C2 is freely available to the scientific community in Slicer (an open source software for image analysis and scientific visualization) with a module created to visualize the SSM using Statismo, a framework for statistical shape modeling. CONCLUSION: The SSM of the vertebra allows the shape variability of the C2 to be represented. Moreover, the SSM will enable semi-automatic segmentation and 3D model generation of the vertebra, which would greatly benefit surgery planning.

Absence of flash-lag when judging global shape from local positions

When a flash is presented aligned with a moving stimulus, the former is perceived to lag behind the latter (the flash-lag effect). We study whether this mislocalization occurs when a positional judgment is not required, but a veridical spatial relationship between moving and flashed stimuli is needed to perceive a global shape. To do this, we used Glass patterns that are formed by pairs of correlated dots. One dot of each pair was presented moving and, at a given moment, the other dot of each pair was flashed in order to build the Glass pattern. If a flash-lag effect occurs between each pair of dots, we expect the best perception of the global shape to occur when the flashed dots are presented before the moving dots arrive at the position that physically builds the Glass pattern. Contrary to this, we found that the best detection of Glass patterns occurred for the situation of physical alignment. This result is not consistent with a low-level contribution to the flash-lag effect.

Landslide detection and monitoring capability of boat-based mobile laser scanning along Dieppe coastal cliffs, Normandy

Integrated in a wide research assessing destabilizing and triggering factors to model cliff dynamic along the Dieppe's shoreline in High Normandy, this study aims at testing boat-based mobile LiDAR capabilities by scanning 3D point clouds of the unstable coastal cliffs. Two acquisition campaigns were performed in September 2012 and September 2013, scanning (1) a 30-km-long shoreline and (2) the same test cliffs in different environmental conditions and device settings. The potentials of collected data for 3D modelling, change detection and landslide monitoring were afterward assessed. By scanning during favourable meteorological and marine conditions and close to the coast, mobile LiDAR devices are able to quickly scan a long shoreline with median point spacing up to 10cm. The acquired data are then sufficiently detailed to map geomorphological features smaller than 0.5m2. Furthermore, our capability to detect rockfalls and erosion deposits (>m3) is confirmed, since using the classical approach of computing differences between sequential acquisitions reveals many cliff collapses between Pourville and Quiberville and only sparse changes between Dieppe and Belleville-sur-Mer. These different change rates result from different rockfall susceptibilities. Finally, we also confirmed the capability of the boat-based mobile LiDAR technique to monitor single large changes, characterizing the Dieppe landslide geometry with two main active scarps, retrogression up to 40m and about 100,000m3 of eroded materials.

Mechanical closing of the paperboard package and the effect of the shape of paperboard package to its manufacturability

The main objective of this thesis was to design a hinge and a closing mechanism for the plastic rim of a paperboard package. Of the hinge and closing mechanisms the 3D-models were designed using SolidWorks program and the functionality of the mechanisms was tested with rapid prototype models. When a mechanism that worked was found, the manufacturability of the mechanisms was tested in an injection molding machine with changeable inserts. Another objective of this thesis was to test the effect of the shape of paperboard package to its manufacturability. The effect of the packages shape was tested with plastic tools made for three different shaped trays. Suggestions for further research were made according to the results of the thesis.

Detection and transmission of Drechslera avenae from oat seed

Detection, symptoms and symptomless transmission of Drechslera avenae (teleomorph Pyrenophora avenae) from seed were investigated. The present study reported that the D. avenae is frequently found in oat (Avena sativa) seed in Argentina. The prevalence of the seed lot infected was 54%. The incidence of seeds infected by D. avenae in the various seed lots from different regions ranged from 0 to 52% (overall mean of 7%). Besides conidia on conidiophore and immature pseudothecia, D. avenae produced small, spherical to pear-shape picnidia containing tiny conidia, on the seed surface. The pathogen was efficiently transmitted at a rate of 55% from seed to coleoptile tips in symptomless seedlings and at 12.5% to plumules. The importance of the infected seed and its epidemiological role are discussed.

The Shadow Moiré method using the phase shifting technique and digital image processing: computational implementation and application to the 3D-reconstruction of a buckled plate

The Shadow Moiré fringe patterns are level lines of equal depth generated by interference between a master grid and its shadow projected on the surface. In simplistic approach, the minimum error is about the order of the master grid pitch, that is, always larger than 0,1 mm, resulting in an experimental technique of low precision. The use of a phase shift increases the accuracy of the Shadow Moiré technique. The current work uses the phase shifting method to determine the surfaces three-dimensional shape using isothamic fringe patterns and digital image processing. The current study presents the method and applies it to images obtained by simulation for error evaluation, as well as to a buckled plate, obtaining excellent results. The method hands itself particularly useful to decrease the errors in the interpretation of the Moiré fringes that can adversely affect the calculations of displacements in pieces containing many concave and convex regions in relatively small areas.

3D-tulostustekniikan hyödyntäminen diagnostisten pikatestien tuotekehityksessä

Pikamallinnustekniikat ovat kehittyneet viime vuosina nopeasti. Tämä antaa jo lähes rajat-tomat mahdollisuudet tuottaa 3D-tulostamalla erilaisia tuotteita. 3D-tulostuksen hyödyntä-minen on yleistynyt erityisesti teollisuuden ja teknologian aloilla. Tässä työssä tutkittiin miten 3D-tulostamista voidaan hyödyntää diagnostisten pikatestien tuotekehityksessä. Immunologinen lateral flow-testi on vasta-aineisiin perustuva, nopea ja helppokäyttöinen mittausmenetelmä pienten ainemäärien havaitsemiseen. Tässä työssä kehitettiin lateral flow-testikotelo, jonka suunnitteluun ja rakenteen mallintamiseen käytettiin 3D-tulostustekniikkaa. Testikotelon toimivuus lateral flow- testissä varmistettiin kehittämällä testikoteloon sopiva pikatesti, jonka suorituskykyä analysoitiin sekä visuaalisesti että Actim 1ngeni-lukulaitteella. Työ aloitettiin tutkimalla eri pikavalmistustekniikoita, joista testikotelon tulostamiseen valittiin SLA-tekniikka sen tulostustarkkuuden ja tuotteen pinnan laadun perusteella. Testikotelon suunnittelu aloitettiin määrittämällä millaisia ominaisuuksia testikotelolta haluttiin. Näitä ominaisuuksia olivat lateral flow-testin suojaaminen sekä testissä kulkevan näytteen virtauksen varmistamien. Lateral flow- testin kehityksessä hyödynnettiin osin aiemmin kehitetystä pikatestistä saatuja tietoja. Lateral flow- kasettitestin valmistusprosessi koostui seitsemästä eri prosessivaiheesta jotka olivat: Vasta-aineen/kontrollireagenssin konjugointi, näytetyynyn käsittely, konjugointityynyn käsittely, konjugointityynylle annostelu, membraanille annostelu, tikkujen laminointi ja leikkaus sekä kasettitestin kokoonpano. Kehitetyn lateral flow- kasettitestin toimivuus varmistettiin tutkimalla testin reaktiokinetiikkaa ja analyyttistä herkkyyttä sekä visuaalisesti että lukulaitteen avulla. Tutkimustulosten perusteella 3D-tulostus on erittäin hyödyllinen menetelmä pikatestien tuotekehityksessä suunniteltaessa testikotelorakenteita, näytteen annosteluvälineitä ja näiden yhdistelmiä.