Analysis of Diffusion MRI Data Biomedical Imaging Digital Signal and Image Processing Computer Graphics and Visualization Algorithm and Code Optimization Software Development

During the last 12 years the investigator has been focused on the training of students following her main research lines: Diffusion MRI data analysis, Biomedical Imaging, Digital Signal, and Image Processing, Computer Graphics and Visualization, Algorithm and Code Optimization, Software Development. The main research work is related to the processing of Diffusion MRI data for the study of brain anatomical connectivity. A wider goal is the integration of these research lines for the development of high-performance tools for the analysis and visualization of complex data.
Another R&D line is the development of software biomedical applications, in particular, the cognitive stimulation of infants. A recent line is focused on the development of virtual reality and augmented reality applications for education.

Undergraduate theses direction:

As (Assistant/Associate/Full) Professor at the Faculty of Engineering at the University of Concepción, she has directed more than 100 undergraduate theses (Biomedical Engineering (BE), Electronics Engineering (EE), and Informatics Engineering (IE)), related to the main research areas mentioned above. The main subjects are:

- "Development of a virtual reality application for the learning of neurosurgical approaches" (BE)
- "Inter-subject fiber clustering based on an autoencoder and HDBSCAN" (IE)
- “Software for the support of reading comprehension” (IE)
- “Development of a mobile application for infant stimulation and language learning” (BE)
- “Development of an application for cognitive evaluation and stimulation for the elderly” (BE)
- “Study of short association white matter fibers using clustering methods” (BE)
- “Development of an optimized tool for a high quality visualization of white matter fibers fusing GLSL” (EE)
- “Development of movement tracking processing tool for kinesiotherapy studies” (BE)
- “Development of an automatic tool for the segmentation of short association white matter fibers” (BE)
- “Parcellation of the human brain cortex based on connectivity calculated from diffusion MRI” (BE)
- “Development of a tool for the interactive manipulation of complex fiber datasets calculated from diffusion MRI” (EE)
- “Filtering and 3D interactive visualization of brain fibers calculated from diffusion MRI” (BE).
- “Registration of ultrasound and Magnetic Resonance images for neuronavigation applications” (BE).
- “Semi-automatic extraction of the trigeminal cave on Magnetic Resonance images” (BE).
- “Calculation and optimization of the diffusion tensor from diffusion MRI” (BE).
- “Study of the variability of short brain association bundles using diffusion MRI” (EE).
- “Optimization of an algorithm of white matter fiber classification based on a multi-subject bundle atlas” (BE, co-director).

Courses:

The investigator has been also dedicated to teaching different undergraduate courses: “Object-Oriented Programming”, “Programming Laboratory”, “Algorithms and Programming Languages”, “Digital Image Processing”, “Digital Signal Processing”, “Computer Graphics ", "Visualization” and “Scientific Python” and "Medical Image Analysis".

Between 2001 and 2005 she collaborated as a teaching assistant in the graduate courses: “Fundamentals of Computer Graphics”, “Advances in Computer Visualization” and “Object-Oriented Programming for Economy applications”.

In 2013, she designed and taught the course “Scientific Python” for undergraduate and graduate students. This course aims to give the knowledge for the design and implementation of efficient and interactive solutions for scientific and engineering problems using the Python language. The focus is on the efficient development of computational solutions, with the integration of scientific computing modules, 2D and 3D visualization, user interface, and a number of other tools depending on the application area. It integrates concepts such as object-oriented programming and optimization, for efficient implementation of algorithms. The course has a strong emphasis on scientific computing, starting with the optimized use of matrices and tools for the efficient management of information. We study various areas of analysis, especially digital signal and image processing, and information manipulation and visualization.

In 2017, she designed and taught the course “Medical Image Analysis” for graduate students. This course aims to give basic knowledge of the state-of-the-art techniques and software used in the biomedical community, mainly in the neuroimaging area. Software such as Freesurfer, DSI-Studio, and Brainvisa/Anatomist are used, combined with tools and new developments in Python and MATLAB.

In 2019, she designed and taught the course “Seminar on Medical Signal and Image Analysis” for graduate students. This course aims to perform the study and application of state-of-the-art methods in the area of Medical Signal and Image Analysis.

Master theses direction (Faculty of Engineering, University of Concepción):

- "Parcellation of the cortical surface based on a diffusion-based white matter atlas" (M.Sc. in Electrical Engineering)
- "Short white matter fiber identification based on hierarchical clustering, using dMRI data" (M.Sc. in Electrical Engineering)
- “Development of a method for the semi-automatic segmentation of neuron processes based on High Resolution Microscopy” (M.Sc. in Electrical Engineering)
- “Optimization of an automatic white matter bundle segmentation tool for interactive applications” (co-director) (M.Sc. in Electrical Engineering)
- "Efficient method for brain fiber clustering based on point distribution" (M.Sc. in Computer Science)
- "Siting and sizing of Energy Storage Systems for congestion control in long-term planning" (M.Sc. in Electrical Engineering)
- "Support for the diagnosis of depression using EEG signal analysis and automated learning tools" (M.Sc. in Computer Science)
- “Baseline correction algorithm for quantification of in vivo 1H-MRS” (M.Sc. in Electrical Engineering) (co-guide)
- “Longitudinal analysis of anatomical changes by magnetic resonance imaging in patients with Multiple Sclerosis using FreeSurfer software” (M.Sc. in Electrical Engineering)
- “Algorithm for brain fiber filtering and its effect on the reproducibility of automatic segmentation” (M.Sc. in Electrical Engineering)
- “Relationships between white matter hyperintensities, fiber integrity and allostatic load in subjects with cognitive complaint” (Master in Biological Sciences, mention in Neurosciences, Universidad de Valparaíso) (co-guide)

PhD theses direction (Faculty of Engineering, Universidad de Concepción)

- "Algorithms and methods for the study of brain connectivity based on MRI" (Ph.D. in Electrical Engineering)
- "Study of superficial white matter fibers in data from the Human Connectome Project" (Ph.D. in Computer Science)
- "Modeling of the states from the dynamics of resting-state brain networks" (Ph.D. in Electrical Engineering)
- "Library for the analysis of brain connectivity and its application in database of tinnitus patients" (Ph.D. in Electrical Engineering)
- "Brain fiber simulator to validate fiber clustering and cortex-based fiber clustering and cortex parcellation algorithms based on structural connectivity" (Ph.D. in Electrical Engineering)

Most of the recent developments have not yet reached the transfer stage. Therefore, the main activities have been focused on the dissemination of the research areas and projects.

The investigator presented the following talks:
- “Study of human brain anatomical connectivity using DW-MRI”, to graduate students of Biomedical Imaging Center, University of Concepción, Pontificia Universidad Católica de Chile, Chile. (14/11/2012.)
- “Study of human brain anatomical connectivity using DW-MRI”, to graduate and undergraduate students of the Electrical Department, Engineering Faculty, University of Concepción, Chile. (15/11/2012.)
- “Study of human brain anatomical connectivity using DW-MRI”, to undergraduate students of Biomedical Engineering, Electrical Department, Engineering Faculty, University of Concepción, Chile. (19/03/2013.)
- “Magnetic Resonance: principles and applications to brain images”, to master students of Computer Sciences Department, Faculty of Engineering, Universidad Católica del Maule, Chile. (7/09/2013).
- Organization of the Workshop “Brain Dynamics, from the neuron to the skill”, University of Concepción, Chile. (2014)
- Organization of the Workshop “Advances in MRI techniques for the study of brain pathologies and disorders”, University of Concepción, Chile. (2015)
- Organization of the Workshop “Diffusion MRI, processing examples and applications", University of Concepción, Chile. (2015).
- Organization of the Workshop "Workshop on Biomedical Imaging: Research and clinical applications", University of Concepción, Chile. (2017).
- Organization of the "IEEE Summer School on Biomedical Signal and Image Processing - Chile 2020", University of Concepción, Chile. (2020).