Jose L. Rubio

3D liver segmentation in preoperative CT images using a levelsets active surface method

In this work we propose an active surface method to segment complete liver volumes from preoperative CT abdominal images. The method finds the surface that minimizes an energy function combining intensity inside and outside the surface, gradient information and curvature restrictions. The implementation is based on a level set technique following a multi-resolution strategy to reduce computing time. It requires only a single seed point inside the liver to initialize the active surface. The algorithm has been validated on a set of previously diagnosed livers. Resulting segmentations have been supervised by clinicians and radiologists, and numerically evaluated in terms of volume measurements with respect to those obtained from radiologists’ manual segmentations. Additionally, radiologists analyzed the necessity of additional corrections on segmenting volumes.

GATE simulations for small animal SPECT/PET using voxelized phantoms and rotating-head detectors

GATE (Geant4 Application for Tomographic Emission) simulation toolkit has become a well validated toolkit for the simulation of SPECT and PET systems. A very important feature of GATE is that it allows modelling of time-dependent phenomena. In addition, complex voxelized object such as realistic anthropomorphic or small animal phantoms can be used as emission sources. In this work two small field of view scanners have been evaluated experimentally, modelled in GATE and mice studies have been simulated using MOBY mouse phantom. Two scanners have been simulated: The first one is a mouse sized gamma camera (field of view is 5 times 10cm) that is based on two Hamamatsu H8500 PSPMTs, a NaI pixelized scintillator and a tungsten collimator with hexagonal parallel holes. The system has been modelled in GATE and good agreement has been found between simulation and experimental results. MOBY mouse has been introduced as a voxelized source and planar and tomography simulations were carried out. The second small animal PET scanner has four heads which are equipped with a H8500 PSPMTs and a pixelated LYSO scintillator. Systems geometry has been modelled in GATE. The results of both systems simulation and comparison between simulation and experimental data are presented. In addition, mouse bone scans were simulated both for SPECT and PET and tomographic image are derived. The presented methodology is aimed to provide all necessary tools in order to perform optimized simulations of small animal emission tomography scans.

Super-resolution in 4D positron emission tomography

Respiratory synchronized acquisitions lead to noisy images. Super-resolution techniques deal with the enhancement of several slightly different low-resolution images into a single high-resolution image. A maximum a-posteriori (MAP) super-resolution algorithm has been implemented and applied to respiratory gated PET images for motion compensation. The algorithm was tested on a GATE simulated datasets. It consisted of 8 frames of the NCAT phantom with lesions between 15–22mm placed throughout the lungs. Images were reconstructed using the OPLEM algorithm. Super-resolution was performed on the gated frames through a MAP algorithm, using a Huber prior as a regularization term to ensure convergence. The optimization of the function yielded by the MAP method was performed through a steepest descent algorithm. Motion fields were recovered using a previously presented elastic registration algorithm. Image enhancement was assessed by estimating signal to noise ratio (SNR) and contrast in regions of interest.

Efficient methodology for 3D statistical reconstruction of high resolution coplanar PET/CT scanner

A fully 3D statistical image reconstruction algorithm has been developed for a high-resolution coplanar PET/CT scanner based on rotating planar PET detectors. The system matrix has been modeled with custom Monte Carlo techniques optimized for the specific scanner architecture. The system model includes positron range, non-colinearity of gamma rays and crystal interaction modelling with attenuation and Compton scattering effects. Only 0.21% of the system matrix columns are modeled in detail, obtaining the rest of the values with axial and transaxial voxel-driven symmetries. The iterative algorithm is a fully 3D approach, regularized with the anatomical registered image using a novel version of the minimum cross entropy (MXE) scheme, and accelerated employing ordered subsets. The proposed method has been shown to produce images with superior quality than 3D hybrid (FORE+2D-OSEM) algorithms applied on synthetic GATE data, as well as on real small animal acquisitions.

Multi-grid 3D-OSEM reconstruction technique for high resolution rotating-head PET scanners

A fast statistical iterative image reconstruction algorithm has been developed for high resolution PET scanners based on rotating plane detectors. The proposed technique consists of a multi-grid version of the 3D ordered subsets expectation-maximization (3D-OSEM) algorithm. The associated system matrix is precalculated for the fine grid resolution with Monte Carlo methods. Coarse grid system matrices and subset subdivision are derived at a post-process step. Only the system matrix elements associated to the fourth part of central transverse planes are stored in sparse mode format, using axial and in-plane transaxial symmetries during the reconstruction. The multi-grid proposed technique has been evaluated on 3D sinograms obtained from GATE simulations, reporting better resolution-noise trade-off than SSRB+2D-OSEM and FORE+2D-OSEM algorithms, specially in the axial direction and far from the center of the FOV. The proposed algorithm shows significantly faster convergence rate than single-grid 3D-OSEM when is applied to images with local smoothness property.

Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging

The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and µm spatial resolution [1].

Usefulness of myocardial circunferential strain in acute myocardial infarction for prediction of contractile function recovery: a MRI myocardial tagging study

Background In patients (p) with acute myocardial infarction (AMI), quantitation of myocardial regional function may be useful to differentiate between stunned and necrotic myocardium and to predict ventricular function recovery during follow-up. Different parameters exist to evaluate regional myocardial function such as circunferential /radial strain and displacement. The purpose of this study is to determine the most useful parameter for prediction of contractile function recovery obtained from tagged MRI.