Procesado de imágenes médicas en MATLAB

La relación entre la ingeniería y la medicina cada vez se está haciendo más estrecha, y debido a esto se ha creado una nueva disciplina, la bioingeniería, ámbito en el que se centra el proyecto. Este ámbito cobra gran interés debido al rápido desarrollo de nuevas tecnologías que en particular permiten, facilitan y mejoran la obtención de diagnósticos médicos respecto de los métodos tradicionales. Dentro de la bioingeniería, el campo que está teniendo mayor desarrollo es el de la imagen médica, gracias al cual se pueden obtener imágenes del interior del cuerpo humano con métodos no invasivos y sin necesidad de recurrir a la cirugía. Mediante métodos como la resonancia magnética, rayos X, medicina nuclear o ultrasonidos, se pueden obtener imágenes del cuerpo humano para realizar diagnósticos. Para que esas imágenes puedan ser utilizadas con ese fin hay que realizar un correcto tratamiento de éstas mediante técnicas de procesado digital. En ése ámbito del procesado digital de las imágenes médicas es en el que se ha realizado este proyecto. Gracias al desarrollo del tratamiento digital de imágenes con métodos de extracción de información, mejora de la visualización o resaltado de rasgos de interés de las imágenes, se puede facilitar y mejorar el diagnóstico de los especialistas. Por todo esto en una época en la que se quieren automatizar todos los procesos para mejorar la eficacia del trabajo realizado, el automatizar el procesado de las imágenes para extraer información con mayor facilidad, es muy útil. Actualmente una de las herramientas más potentes en el tratamiento de imágenes médicas es Matlab, gracias a su toolbox de procesado de imágenes. Por ello se eligió este software para el desarrollo de la parte práctica de este proyecto, su potencia y versatilidad simplifican la implementación de algoritmos. Este proyecto se estructura en dos partes. En la primera se realiza una descripción general de las diferentes modalidades de obtención de imágenes médicas y se explican los diferentes usos de cada método, dependiendo del campo de aplicación. Posteriormente se hace una descripción de las técnicas más importantes de procesado de imagen digital que han sido utilizadas en el proyecto. En la segunda parte se desarrollan cuatro aplicaciones en Matlab para ejemplificar el desarrollo de algoritmos de procesado de imágenes médicas. Dichas implementaciones demuestran la aplicación y utilidad de los conceptos explicados anteriormente en la parte teórica, como la segmentación y operaciones de filtrado espacial de la imagen, así como otros conceptos específicos. Las aplicaciones ejemplo desarrolladas han sido: obtención del porcentaje de metástasis de un tejido, diagnóstico de las deformidades de la columna vertebral, obtención de la MTF de una cámara de rayos gamma y medida del área de un fibroadenoma de una ecografía de mama. Por último, para cada una de las aplicaciones se detallará su utilidad en el campo de la imagen médica, los resultados obtenidos y su implementación en una interfaz gráfica para facilitar su uso. ABSTRACT. The relationship between medicine and engineering is becoming closer than ever giving birth to a recently appeared science field: bioengineering. This project is focused on this subject. This recent field is becoming more and more important due to the fast development of new technologies that provide tools to improve disease diagnosis, with regard to traditional procedures. In bioengineering the fastest growing field is medical imaging, in which we can obtain images of the inside of the human body without need of surgery. Nowadays by means of the medical modalities of magnetic resonance, X ray, nuclear medicine or ultrasound, we can obtain images to make a more accurate diagnosis. For those images to be useful within the medical field, they should be processed properly with some digital image processing techniques. It is in this field of digital medical image processing where this project is developed. Thanks to the development of digital image processing providing methods for data collection, improved visualization or data highlighting, diagnosis can be eased and facilitated. In an age where automation of processes is much sought, automated digital image processing to ease data collection is extremely useful. One of the most powerful image processing tools is Matlab, together with its image processing toolbox. That is the reason why that software was chosen to develop the practical algorithms in this project. This final project is divided into two main parts. Firstly, the different modalities for obtaining medical images will be described. The different usages of each method according to the application will also be specified. Afterwards we will give a brief description of the most important image processing tools that have been used in the project. Secondly, four algorithms in Matlab are implemented, to provide practical examples of medical image processing algorithms. This implementation shows the usefulness of the concepts previously explained in the first part, such as: segmentation or spatial filtering. The particular applications examples that have been developed are: calculation of the metastasis percentage of a tissue, diagnosis of spinal deformity, approximation to the MTF of a gamma camera, and measurement of the area of a fibroadenoma in an ultrasound image. Finally, for each of the applications developed, we will detail its usefulness within the medical field, the results obtained, and its implementation in a graphical user interface to ensure ease of use

Morphological quantitation software in breast MRI: application to neoadjuvant chemotherapy patients

The work in this thesis examines the use of texture analysis techniques and shape descriptors to analyse MR images of the breast and their application as a potential quantitative tool for prognostic indication.Textural information is undoubtedly very heavily used in a radiologist’s decision making process. However, subtle variations in texture are often missed, thus by quantitatively analysing MR images the textural properties that would otherwise be impossible to discern by simply visually inspecting the image can be obtained. Texture analysis is commonly used in image classification of aerial and satellite photography, studies have also focussed on utilising texture in MRI especially in the brain. Recent research has focussed on other organs such as the breast wherein lesion morphology is known to be an important diagnostic and prognostic indicator. Recent work suggests benefits in assessing lesion texture in dynamic contrast-enhanced (DCE) images, especially with regards to changes during the initial enhancement and subsequent washout phases. The commonest form of analysis is the spatial grey-level dependence matrix method, but there is no direct evidence concerning the most appropriate pixel separation and number of grey levels to utilise in the required co-occurrence matrix calculations. The aim of this work is to systematically assess the efficacy of DCE-MRI based textural analysis in predicting response to chemotherapy in a cohort of breast cancer patients. In addition an attempt was made to use shape parameters in order to assess tumour surface irregularity, and as a predictor of response to chemotherapy.In further work this study aimed to texture map DCE MR images of breast patients utilising the co-occurrence method but on a pixel by pixel basis in order to determine threshold values for normal, benign and malignant tissue and ultimately creating functionality within the in house developed software to highlight hotspots outlining areas of interest (possible lesions). Benign and normal data was taken from MRI screening data and malignant data from patients referred with known malignancies.This work has highlighted that textural differences between groups (based on response, nodal status, triple negative and biopsy grade groupings) are apparent and appear to be most evident 1-3 minutes post-contrast administration. Whilst the large number of statistical tests undertaken necessitates a degree of caution in interpreting the results, the fact that significant differences for certain texture parameters and groupings are consistently observed is encouraging.With regards to shape analysis this thesis has highlighted that some differences between groups were seen in shape descriptors but that shape may be limited as a prognostic indicator. Using textural analysis gave a higher proportion of significant differences whilst shape analysis results showed inconsistency across time points.With regards to the mapping this work successfully analysed the texture maps for each case and established lesion detection is possible. The study successfully highlighted hotspots in the breast patients data post texture mapping, and has demonstrated the relationship between sensitivity and false positive rate via hotspot thresholding

Modelling shape fluctuations during cell migration

Cell migration is of crucial importance for many physiological processes, including embryonic development, wound healing and immune response. Defects in cell migration are the cause of chronic in ammatory diseases, mental retardation and cancer metastasis. Cell movement is driven by actin-mediated cell protrusion, substrate adhesion and contraction of the cell body. The emergent behaviour of the intracellular processes described above is a change in the morphology of the cell. This inspires the main hypothesis of this work which is that there is a measurable relationship between cell morphology dynamics and migratory behaviour, and that quantitative models of this relationship can create useful tools for investigating the mechanisms by which a cell regulates its own motility. Here we analyse cell shapes of migrating human retinal pigment epithelial cells with the aim to map cell shape changes to cellular behaviour. We develop a non-linear model for learning the intrinsic low-dimensional structure of cell shape space and use the resultant shape representation to analyse quantitative relationships between shape and migration behaviour. The biggest algorithmic challenge overcome in this thesis was developing a method for efficiently and appropriately measuring the shape difference between pairs of cells that may have come from independent image scenes. This difference measure must be capable of coping with the widely varying morphologies exhibited by migrating epithelial cells. We present a new, rapid, landmark-free, shape difference measure called the Best Alignment Metric (BAM). We show that BAM performs highly within our framework, generating a shape space representation of a very large dataset without any prior information on the importance of any given shape feature. We demonstrate quantitative evidence for a model of cell turning based on repolarisation and discuss the impact our proposed framework could have on the continued study of migratory mechanisms