From volume medical images to quadratic surface patches

Projet SYNTIMIn this paper, we show how to extract reliable informations about the shape of 3D objects, obtained from volume medical images . We present an optimal region-growing algorithm, that makes use of the differential characteristics of the object sur face, and achieves a stable segmentation into a set of patches of quadratic surfaces. We show how this segmentation can be used to recognize and locate a target sub-structure on a global anatomic structure

From 4D medical images (CT, MRI, and Ultrasound) to 4D structured mesh models of the left ventricular endocardium for patient-specific simulations

With cardiovascular disease (CVD) remaining the primary cause of death worldwide, early detection of CVDs becomes essential. The intracardiac flow is an important component of ventricular function, motion kinetics, wash-out of ventricular chambers, and ventricular energetics. Coupling between Computational Fluid Dynamics (CFD) simulations and medical images can play a fundamental role in terms of patient-specific diagnostic tools. From a technical perspective, CFD simulations with moving boundaries could easily lead to negative volumes errors and the sudden failure of the simulation. The generation of high-quality 4D meshes (3D in space + time) with 1-to-l vertex becomes essential to perform a CFD simulation with moving boundaries. In this context, we developed a semiautomatic morphing tool able to create 4D high-quality structured meshes starting from a segmented 4D dataset. To prove the versatility and efficiency, the method was tested on three different 4D datasets (Ultrasound, MRI, and CT) by evaluating the quality and accuracy of the resulting 4D meshes. Furthermore, an estimation of some physiological quantities is accomplished for the 4D CT reconstruction. Future research will aim at extending the region of interest, further automation of the meshing algorithm, and generating structured hexahedral mesh models both for the blood and myocardial volume

An Overview of Rendering from Volume Data --- including Surface and Volume Rendering

Volume rendering is a title often ambiguously used in science. One meaning often quoted is: `to render any three volume dimensional data set'; however, within this categorisation `surface rendering'' is contained. Surface rendering is a technique for visualising a geometric representation of a surface from a three dimensional volume data set. A more correct definition of Volume Rendering would only incorporate the direct visualisation of volumes, without the use of intermediate surface geometry representations. Hence we state: `Volume Rendering is the Direct Visualisation of any three dimensional Volume data set; without the use of an intermediate geometric representation for isosurfaces'; `Surface Rendering is the Visualisation of a surface, from a geometric approximation of an isosurface, within a Volume data set'; where an isosurface is a surface formed from a cross connection of data points, within a volume, of equal value or density. This paper is an overview of both Surface Rendering and Volume Rendering techniques. Surface Rendering mainly consists of contouring lines over data points and triangulations between contours. Volume rendering methods consist of ray casting techniques that allow the ray to be cast from the viewing plane into the object and the transparency, opacity and colour calculated for each cell; the rays are often cast until an opaque object is `hit' or the ray exits the volume

PyHST2: an hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities

We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches. We give details of the different methods and their implementations while the code is distributed under free license. We provide methods for estimating, in the absence of ground-truth data, the optimal parameters values for a-priori techniques

A Novel Framework for Highlight Reflectance Transformation Imaging

We propose a novel pipeline and related software tools for processing the multi-light image collections (MLICs) acquired in different application contexts to obtain shape and appearance information of captured surfaces, as well as to derive compact relightable representations of them. Our pipeline extends the popular Highlight Reflectance Transformation Imaging (H-RTI) framework, which is widely used in the Cultural Heritage domain. We support, in particular, perspective camera modeling, per-pixel interpolated light direction estimation, as well as light normalization correcting vignetting and uneven non-directional illumination. Furthermore, we propose two novel easy-to-use software tools to simplify all processing steps. The tools, in addition to support easy processing and encoding of pixel data, implement a variety of visualizations, as well as multiple reflectance-model-fitting options. Experimental tests on synthetic and real-world MLICs demonstrate the usefulness of the novel algorithmic framework and the potential benefits of the proposed tools for end-user applications.Terms: "European Union (EU)" & "Horizon 2020" / Action: H2020-EU.3.6.3. - Reflective societies - cultural heritage and European identity / Acronym: Scan4Reco / Grant number: 665091DSURF project (PRIN 2015) funded by the Italian Ministry of University and ResearchSardinian Regional Authorities under projects VIGEC and Vis&VideoLa

Chromatic Illumination Discrimination Ability Reveals that Human Colour Constancy Is Optimised for Blue Daylight Illuminations

The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed