Dinámica Pulmonar de Estructuras Anatómicas de Interés en Imágenes 4DCT / Pulmonary Dynamics of Anatomical Structures of Interest in 4DCT Images

Resumen: El presente trabajo muestra una aplicación del algoritmo Chan-Vese para la segmentación semi-automática de estructuras anatómicas de interés (pulmones y tumor pulmonar) en imágenes de 4DCT de tórax, así como su reconstrucción tridimensional. La segmentación y reconstrucción se realizó en 10 imágenes de TAC, las cuales conforman un ciclo inspiración-espiración. Se calculó el desplazamiento máximo para el caso del tumor pulmonar usando las reconstrucciones del inicio de la inspiración, el inicio de la espiración, y la información del voxel. El método propuesto logra segmentar de manera apropiada las estructuras estudiadas sin importar su tamaño y forma. La reconstrucción tridimensional nos permite visualizar la dinámica de las estructuras de interés a lo largo del ciclo respiratorio. En un futuro se espera poder contar con mayor evidencia del buen desempeño del método propuesto y contar con la retroalimentación del experto clínico, ya que el conocimiento de características de estructuras anatómicas, como su dimensión y posición espacial, ayuda en la planificación de tratamientos de Radioterapia (RT), logrando optimizar las dosis de radiación hacia las células cancerosas y minimizarla en órganos sanos. Por lo tanto, la información encontrada en este trabajo puede resultar de interés para la planificación de tratamientos de RT.

Abstract: This paper presents an application of the Chan-Vese algorithm for a semi-automatic segmentation of anatomical structures of interest (lungs and lung tumor) in thorax 4DCT images, as well as its threedimensional reconstruction. Segmentations and reconstructions were performed in 10 CT images, which conform an inspiration-expiration cycle. The maximum displacement of the lung tumor was calculated using the reconstructions of the beginning of inspiration, beginning of expiration, and the voxel size information. The proposed method was able to succesfully segment the studied structures regardless of their size and shape. The threedimensional reconstruction allow us to visualize the dynamics of the structures of interest throughout the respiratory cycle. In the near future, we are expecting to be able to have more evidence of the good performance of the proposed segmentation approach, and to have feedback from a clinical expert, giving the fact that the knowledge of anatomical structures characteristics, such as their size and spatial location, may help in the planning of radiotherapy treatments (RT), optimizing the radiation dose to cancer cells and minimizing it in healthy organs. Therefore, the information found in this work may be of interest for the planning of RT treatments.

Sistema de Apoyo para la Cuantificación Semiautomática de Fibrosis Pulmonar en Imágenes de TAC / Support System for Semiautomatic Quantification of Pulmonary Fibrosis in CT Images

Resumen: En este trabajo se presenta un método para calcular los niveles de fibrosis pulmonar en imágenes de tomografía axial computarizada. Se utilizó un algoritmo de segmentación semiautomática basado en el método de Chan-Vese. El método mostró similitudes de forma cualitativa en la región de la fibrosis con respecto al experto clínico. Sin embargo es necesario validar los resultados con una base de datos mayor. El método propuesto aproxima un porcentaje de fibrosis de forma fácil para apoyar su implementación en la práctica clínica minimizando la subjetividad del experto médico y generando una estimación cuantitativa de la región de fibrosis.

Abstract: A method to estimate the pulmonary fibrosis in computed tomography (CT) imaging is presented. A semi-automatic segmentation algorithm based on the Chan-Vese method was used. The proposed method shows a similar fibrosis región with respect to clinical expert. However, the results need to be validated in a bigger data base. The proposed method approximates a fibrosis percentage that allows to achieve this procedure easily in order to support its implementation in the clinical practice minimizing the clinical expert subjectivity and generating a quantitative estimation of fibrosis region.

Quadratic blind linear unmixing: A graphical user interface for tissue characterization.

Spectral unmixing is the process of breaking down data from a sample into its basic components and their abundances. Previous work has been focused on blind unmixing of multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) datasets under a linear mixture model and quadratic approximations. This method provides a fast linear decomposition and can work without a limitation in the maximum number of components or end-members. Hence this work presents an interactive software which implements our blind end-member and abundance extraction (BEAE) and quadratic blind linear unmixing (QBLU) algorithms in Matlab. The options and capabilities of our proposed software are described in detail. When the number of components is known, our software can estimate the constitutive end-members and their abundances. When no prior knowledge is available, the software can provide a completely blind solution to estimate the number of components, the end-members and their abundances. The characterization of three case studies validates the performance of the new software: ex-vivo human coronary arteries, human breast cancer cell samples, and in-vivo hamster oral mucosa. The software is freely available in a hosted webpage by one of the developing institutions, and allows the user a quick, easy-to-use and efficient tool for multi/hyper-spectral data decomposition.

Deconvolution of fluorescence lifetime imaging microscopy by a library of exponentials.

Fluorescence lifetime microscopy imaging (FLIM) is an optic technique that allows a quantitative characterization of the fluorescent components of a sample. However, for an accurate interpretation of FLIM, an initial processing step is required to deconvolve the instrument response of the system from the measured fluorescence decays. In this paper, we present a novel strategy for the deconvolution of FLIM data based on a library of exponentials. Our approach searches for the scaling coefficients of the library by non-negative least squares approximations plus Thikonov/l(2) or l(1) regularization terms. The parameters of the library are given by the lower and upper bounds in the characteristic lifetimes of the exponential functions and the size of the library, where we observe that this last variable is not a limiting factor in the resulting fitting accuracy. We compare our proposal to nonlinear least squares and global non-linear least squares estimations with a multi-exponential model, and also to constrained Laguerre-base expansions, where we visualize an advantage of our proposal based on Thikonov/l(2) regularization in terms of estimation accuracy, computational time, and tuning strategy. Our validation strategy considers synthetic datasets subject to both shot and Gaussian noise and samples with different lifetime maps, and experimental FLIM data of ex-vivo atherosclerotic plaques and human breast cancer cells.

Extended output phasor representation of multi-spectral fluorescence lifetime imaging microscopy.

In this paper, we investigate novel low-dimensional and model-free representations for multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) data. We depart from the classical definition of the phasor in the complex plane to propose the extended output phasor (EOP) and extended phasor (EP) for multi-spectral information. The frequency domain properties of the EOP and EP are analytically studied based on a multiexponential model for the impulse response of the imaged tissue. For practical implementations, the EOP is more appealing since there is no need to perform deconvolution of the instrument response from the measured m-FLIM data, as in the case of EP. Our synthetic and experimental evaluations with m-FLIM datasets of human coronary atherosclerotic plaques show that low frequency indexes have to be employed for a distinctive representation of the EOP and EP, and to reduce noise distortion. The tissue classification of the m-FLIM datasets by EOP and EP also improves with low frequency indexes, and does not present significant differences by using either phasor.

Registro elástico de imágenes médicas multimodales basado en medidas de variabilidad local / Non-rigid Multimodal Medical Image Registration Based on Local Variability

En este artículo se propone un enfoque no paramétrico para el registro elástico de imágenes médicas multimodales, cuya idea principal radica en el uso de medidas de variabilidad local, basadas en la entropía, la varianza o una combination de ambas. La metodología empleada consiste en encontrar el campo vectorial de los desplazamientos entre los pixeles de las imágenes candidata y patrón empleando una tecnica compuesta por tres pasos: primero, se obtiene una aproximación del campo vectorial por medio de un registro paramétrico entre ambas imágenes; segundo, se mapean las imágenes registradas paramétricamente a un espacio de intensidades donde pueden ser comparadas; tercero, se obtiene el flujo óptico entre las imágenes en el espacio al que fueron mapeadas. El algoritmo propuesto se evalúo usando un conjunto de imágenes de resonancia magnética y tomografía computarizada adquiridas desde diferentes vistas, las cuales fueron deformadas sintéticamente. Los resultados obtenidos en la estimación del campo de desplazamientos con las cuatro medidas de variabilidad local propuestas muestran un error medio menor que 1.4 mm, y en el caso de la entropía menor a 1 mm. Además, se demuestra la convergencia del algoritmo con ayuda de la entropía conjunta. Asó, la metodología descrita representa una nueva alternativa para el registro elástico multimodal de imágenes médicas.

In this work, we present a novel approach for multimodal elastic registration of medical images, where the key idea is to use local variability measures based on entropy, variance or a combination of these metrics. The proposed methodology relies on finding the displacements vector field between pixels of a source image and a target one, using the following three steps: first, an initial approximation of the vector field is achieved by using a parametric registration based on particle filtering between the images to align; second, the images previously registered are mapped to a common space where their intensities can be compared; and third, we obtain the optical flow between the images in this new space. To evaluate the proposed algorithm, a set of computed tomography and magnetic resonance images obtained in different views, were modified with synthetic deformation fields. The results obtained with the four proposed local variability measures show an average error of less than 1.4 mm, and in the case of the entropy less than 1 mm. In addition, the convergence of the algorithm is highlighted by the joint entropy. Therefore, the described methodology could be considered as a new alternative for multimodal elastic registration of medical images.

A new method to estimate abundances of multiple components using multi-spectral fluorescence lifetime imaging microscopy.

Multi-Spectral Fluorescent Lifetime Imaging Microscopy (m-FLIM) is a technique that aims to perform noninvasive in situ clinical diagnosis of several diseases. It measures the endogenous fluorescence of molecules, recording their lifetime decay in different wavelength bands. This signal is a mixed response of multiple fluorescent components present in a tissue sample. The goal is to decompose the mixture and estimate the proportional contributions of its constituents. Estimation of such quantitative description will help to characterize the molecular constitution of a given sample. This paper presents a new method to estimate the abundances of multiple components present in a mixture measured using m-FLIM data. It provides a closed-form solution under the fully constrained linear unmixing model and assuming the number of components as well as their ideal lifetime decays are known. Its performance is tested using synthetic samples with three components, where performance can be measured accurately and the percentage error is around 6%. The algorithm was also validated performing unmixing of ex vivo data samples from atherosclerotic human tissue containing collagen, elastin and low-density lipoproteins. These experiments were validated against ground-truth maps, which only give a quantitative description, and the estimated accuracy was around 88%.

Elastic registration based on particle filter in radiotherapy images with brain deformations.

This paper presents the evaluation of the accuracy of an elastic registration algorithm, based on the particle filter and an optical flow process. The algorithm is applied in brain CT and MRI simulated image datasets, and MRI images from a real clinical radiotherapy case. To validate registration accuracy, standard indices for registration accuracy assessment were calculated: the dice similarity coefficient (DICE), the average symmetric distance (ASD) and the maximal distance between pixels (Dmax). The results showed that this registration process has good accuracy, both qualitatively and quantitatively, suggesting that this method may be considered as a good new option for radiotherapy applications like patient's follow up treatment.