JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Positioning an underwater vehicle through image mosaicking

Mosaics have been commonly used as visual maps for undersea exploration and navigation. The position and orientation of an underwater vehicle can be calculated by integrating the apparent motion of the images which form the mosaic. A feature-based mosaicking method is proposed in this paper. The creation of the mosaic is accomplished in four stages: feature selection and matching, detection of points describing the dominant motion, homography computation and mosaic construction. In this work we demonstrate that the use of color and textures as discriminative properties of the image can improve, to a large extent, the accuracy of the constructed mosaic. The system is able to provide 3D metric information concerning the vehicle motion using the knowledge of the intrinsic parameters of the camera while integrating the measurements of an ultrasonic sensor. The experimental results of real images have been tested on the GARBI underwater vehicle

Identificació de subjectes a partir de l'anàlisi de dades multimodals RGB-Depth

En aquest treball s'explora el camp de la identificació facial de subjectes utilitzant tècniques d'anàlisi multimodal. Això és utilitzant imatges RGB i imatges de profunditat (3D) amb l'objecte de validar les diverses tècniques emprades en el reconeixement facial i aprofundir en sistemes que incorporen informació tridimensional als algorismes de detecció i identificació facial.

Intérêt de la tomographie par émission de positons couplée à la scanographie (TEP/TDM) dans les cancers urologiques [Value of positron emission tomography and computer tomography (PET/CT) for urologic malignancies].

Positron emission tomography is a functional imaging technique that allows the detection of the regional metabolic rate, and is often coupled with other morphological imaging technique such as computed tomography. The rationale for its use is based on the clearly demonstrated fact that functional changes in tumor processes happen before morphological changes. Its introduction to the clinical practice added a new dimension in conventional imaging techniques. This review presents the current and proposed indications of the use of positron emission/computed tomography for prostate, bladder and testes, and the potential role of this exam in radiotherapy planning.

Modelling short-term ultraviolet exposure as an alternative to individual dosimetry

Background: Excessive exposure to solar Ultra-Violet (UV) light is the main cause of most skin cancers in humans. Factors such as the increase of solar irradiation at ground level (anthropic pollution), the rise in standard of living (vacation in sunny areas), and (mostly) the development of outdoor activities have contributed to increase exposure. Thus, unsurprisingly, incidence of skin cancers has increased over the last decades more than that of any other cancer. Melanoma is the most lethal cutaneous cancer, while cutaneous carcinomas are the most common cancer type worldwide. UV exposure depends on environmental as well as individual factors related to activity. The influence of individual factors on exposure among building workers was investigated in a previous study. Posture and orientation were found to account for at least 38% of the total variance of relative individual exposure. A high variance of short-term exposure was observed between different body locations, indicating the occurrence of intense, subacute exposures. It was also found that effective short-term exposure ranged between 0 and 200% of ambient irradiation, suggesting that ambient irradiation is a poor predictor of effective exposure. Various dosimetric techniques enable to assess individual effective exposure, but dosimetric measurements remain tedious and tend to be situation-specific. As a matter of facts, individual factors (exposure time, body posture and orientation in the sun) often limit the extrapolation of exposure results to similar activities conducted in other conditions. Objective: The research presented in this paper aims at developing and validating a predictive tool of effective individual exposure to solar UV. Methods: Existing computer graphic techniques (3D rendering) were adapted to reflect solar exposure conditions and calculate short-term anatomical doses. A numerical model, represented as a 3D triangular mesh, is used to represent the exposed body. The amount of solar energy received by each "triangle is calculated, taking into account irradiation intensity, incidence angle and possible shadowing from other body parts. The model take into account the three components of the solar irradiation (direct, diffuse and albedo) as well as the orientation and posture of the body. Field measurements were carried out using a forensic mannequin at the Payerne MeteoSwiss station. Short-term dosimetric measurements were performed in 7 anatomical locations for 5 body postures. Field results were compared to the model prediction obtained from the numerical model. Results: The best match between prediction and measurements was obtained for upper body parts such as shoulders (Ratio Modelled/Measured; Mean = 1.21, SD = 0.34) and neck (Mean = 0.81, SD = 0.32). Small curved body parts such as forehead (Mean = 6.48, SD = 9.61) exhibited a lower matching. The prediction is less accurate for complex postures such as kneeling (Mean = 4.13, SD = 8.38) compared to standing up (Mean = 0.85, SD = 0.48). The values obtained from the dosimeters and the ones computed from the model are globally consistent. Conclusion: Although further development and validation are required, these results suggest that effective exposure could be predicted for a given activity (work or leisure) in various ambient irradiation conditions. Using a generic modelling approach is of high interest in terms of implementation costs as well as predictive and retrospective capabilities.

Searching patterns in painting images with computer vision techniques

This paper presents a pattern recognition method focused on paintings images. The purpose is construct a system able to recognize authors or art styles based on common elements of his work (here called patterns). The method is based on comparing images that contain the same or similar patterns. It uses different computer vision techniques, like SIFT and SURF, to describe the patterns in descriptors, K-Means to classify and simplify these descriptors, and RANSAC to determine and detect good results. The method are good to find patterns of known images but not so good if they are not.

Functional calibration procedure for 3D knee joint angle description using inertial sensors.

Measurement of three-dimensional (3D) knee joint angle outside a laboratory is of benefit in clinical examination and therapeutic treatment comparison. Although several motion capture devices exist, there is a need for an ambulatory system that could be used in routine practice. Up-to-date, inertial measurement units (IMUs) have proven to be suitable for unconstrained measurement of knee joint differential orientation. Nevertheless, this differential orientation should be converted into three reliable and clinically interpretable angles. Thus, the aim of this study was to propose a new calibration procedure adapted for the joint coordinate system (JCS), which required only IMUs data. The repeatability of the calibration procedure, as well as the errors in the measurement of 3D knee angle during gait in comparison to a reference system were assessed on eight healthy subjects. The new procedure relying on active and passive movements reported a high repeatability of the mean values (offset<1 degrees) and angular patterns (SD<0.3 degrees and CMC>0.9). In comparison to the reference system, this functional procedure showed high precision (SD<2 degrees and CC>0.75) and moderate accuracy (between 4.0 degrees and 8.1 degrees) for the three knee angle. The combination of the inertial-based system with the functional calibration procedure proposed here resulted in a promising tool for the measurement of 3D knee joint angle. Moreover, this method could be adapted to measure other complex joint, such as ankle or elbow.

Detailed 3D seismic imaging of a fault zone beneath Lake Geneva, Switzerland

An efficient high-resolution (HR) three-dimensional (3D) seismic reflection system for small-scale targets in lacustrine settings was developed. In Lake Geneva, near the city of Lausanne, Switzerland, the offshore extension of a complex fault zone well mapped on land was chosen for testing our system. A preliminary two-dimensional seismic survey indicated structures that include a thin (<40 m) layer of subhorizontal Quaternary sediments that unconformably overlie south-east-dipping Tertiary Molasse beds and a major fault zone (Paudeze Fault Zone) that separates Plateau and Subalpine Molasse (SM) units. A 3D survey was conducted over this test site using a newly developed three-streamer system. It provided high-quality data with a penetration to depths of 300 m below the water bottom of non-aliased signal for dips up to 30degrees and with a maximum vertical resolution of 1.1 m. The data were subjected to a conventional 3D processing sequence that included post-stack time migration. Tests with 3D pre-stack depth migration showed that such techniques can be applied to HR seismic surveys. Delineation of several horizons and fault surfaces reveals the potential for small-scale geologic and tectonic interpretation in three dimensions. Five major seismic facies and their detailed 3D geometries can be distinguished. Three fault surfaces and the top of a molasse surface were mapped in 3D. Analysis of the geometry of these surfaces and their relative orientation suggests that pre-existing structures within the Plateau Molasse (PM) unit influenced later faulting between the Plateau and SM. In particular, a change in strike of the PM bed dip may indicate a fold formed by a regional stress regime, the orientation of which was different from the one responsible for the creation of the Paudeze Fault Zone. This structure might have later influenced the local stress regime and caused the curved shape of the Paudeze Fault in our surveyed area.

Anàlisi de l'aplicació Geomedia 3D

Anàlisi de les diferents funcionalitats de l'aplicació Geomedia 3D i la seva utilitat dins del terreny dels sistemes d'informació geogràfica.

Evolution of a debris flow channel monitored using a 3D terrestrial laser scanner

Like numerous torrents in mountainous regions, the Illgraben creek (canton of Wallis, SW Switzerland) produces almost every year several debris flows. The total area of the active catchment is only 4.7 km², but large events ranging from 50'000 to 400'000 m³ are common (Zimmermann 2000). Consequently, the pathway of the main channel often changes suddenly. One single event can for instance fill the whole river bed and dig new several-meters-deep channels somewhere else (Bardou et al. 2003). The quantification of both, the rhythm and the magnitude of these changes, is very important to assess the variability of the bed's cross section and long profile. These parameters are indispensable for numerical modelling, as they should be considered as initial conditions. To monitor the channel evolution an Optech ILRIS 3D terrestrial laser scanner (LIDAR) was used. LIDAR permits to make a complete high precision 3D model of the channel and its surroundings by scanning it from different view points. The 3D data are treated and interpreted with the software Polyworks from Innovmetric Software Inc. Sequential 3D models allow for the determination of the variation in the bed's cross section and long profile. These data will afterwards be used to quantify the erosion and the deposition in the torrent reaches. To complete the chronological evolution of the landforms, precise digital terrain models, obtained by high resolution photogrammetry based on old aerial photographs, will be used. A 500 m long section of the Illgraben channel was scanned on 18th of August 2005 and on 7th of April 2006. These two data sets permit identifying the changes of the channel that occurred during the winter season. An upcoming scanning campaign in September 2006 will allow for the determination of the changes during this summer. Preliminary results show huge variations in the pathway of the Illgraben channel, as well as important vertical and lateral erosion of the river bed. Here we present the results of a river bank on the left (north-western) flank of the channel (Figure 1). For the August 2005 model the scans from 3 viewpoints were superposed, whereas the April 2006 3D image was obtained by combining 5 separate scans. The bank was eroded. The bank got eroded essentially on its left part (up to 6.3 m), where it is hit by the river and the debris flows (Figures 2 and 3). A debris cone has also formed (Figure 3), which suggests that a part of the bank erosion is due to shallow landslides. They probably occur when the river erosion creates an undercut slope. These geometrical data allow for the monitoring of the alluvial dynamics (i.e. aggradation and degradation) on different time scales and the influence of debris flows occurrence on these changes. Finally, the resistance against erosion of the bed's cross section and long profile will be analysed to assess the variability of these two key parameters. This information may then be used in debris flow simulation.

Disseny i modelació en 3D d'un habitacle en le jaciment ibèric d'Els Vilars

L'objectiu del projecte és reconstruir un habitacle del jaciment ibèric dels Vilars amb els objectes de l'època pertinents. Tot això servirà per obtenir una visió de la vida i les costums dels pobladors ibèrics.

Algorismes per a la resolució de problemes de proximitat en terrenys

El modelatge, visualització i anàlisi de terrenys és de gran importància en els Sistemes d’Informació Geogràfica (GIS). Actualment és de gran interès per a aquesta comunitat disposar de software que permeti analitzar terrenys. L’objectiu principal del projecte és desenvolupar una aplicació per a la resolució de diversos problemes de proximitat en terrenys. Una part important ha d’ésser la de poder generar, visualitzar i modificar un model 3D d’un terreny a partir de dades introduïdes per l’usuari o obtingudes des d’un fitxer. Per tal de poder construir l’aplicació desitjada ha calgut dissenyar una interfície gràfica d’usuari que permetés realitzar de forma interactiva la introducció, modificació i esborrat de les diferents seus (punts, segments, polígons, poligonals...) o restriccions del terreny, així com la seva visualització

Development of model observers applied to 3D breast tomosynthesis microcalcifications and masses

The development of model observers for mimicking human detection strategies has followed from symmetric signals in simple noise to increasingly complex backgrounds. In this study we implement different model observers for the complex task of detecting a signal in a 3D image stack. The backgrounds come from real breast tomosynthesis acquisitions and the signals were simulated and reconstructed within the volume. Two different tasks relevant to the early detection of breast cancer were considered: detecting an 8 mm mass and detecting a cluster of microcalcifications. The model observers were calculated using a channelized Hotelling observer (CHO) with dense difference-of-Gaussian channels, and a modified (Partial prewhitening [PPW]) observer which was adapted to realistic signals which are not circularly symmetric. The sustained temporal sensitivity function was used to filter the images before applying the spatial templates. For a frame rate of five frames per second, the only CHO that we calculated performed worse than the humans in a 4-AFC experiment. The other observers were variations of PPW and outperformed human observers in every single case. This initial frame rate was a rather low speed and the temporal filtering did not affect the results compared to a data set with no human temporal effects taken into account. We subsequently investigated two higher speeds at 5, 15 and 30 frames per second. We observed that for large masses, the two types of model observers investigated outperformed the human observers and would be suitable with the appropriate addition of internal noise. However, for microcalcifications both only the PPW observer consistently outperformed the humans. The study demonstrated the possibility of using a model observer which takes into account the temporal effects of scrolling through an image stack while being able to effectively detect a range of mass sizes and distributions.

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis.

BACKGROUND: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. RESULTS: We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called "RodCellJ", allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. CONCLUSIONS: "RodCell" is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large number of rod-shaped cells in an extensive manner. The integration of different image-processing techniques in a single package, as well as the development of novel algorithms does not only allow to speed up the analysis with respect to the usage of existing tools, but also accounts for higher accuracy. Its utility was demonstrated on both 2D and 3D static and dynamic images to study the septation initiation network of the yeast Schizosaccharomyces pombe. More generally, it can be used in any kind of biological context where fluorescent-protein labeled structures need to be analyzed in rod-shaped cells. AVAILABILITY: RodCellJ is freely available under http://bigwww.epfl.ch/algorithms.html, (after acceptance of the publication).