Course BMED360

In Vivo Imaging and Physiological Modelling

Course offered :

Current semester
Next semester

Current programmes of study

Master's Programme in Medical Biology

Course offered by

Number of credits	10
Course offered (semester)	Autumn/spring(minimum 2 students)
Subject overlap	HUFY372
Schedule	Schedule
Reading list	Reading list

Introduction
Course description

Language of Instruction

English

Pre-requirements

Physics, computer science, mathematics or statistics, on bachelor level. Students with bachelor's degree in biology/life sciences, and strong interest and some previous experience in biomedical image analysis and programming could also be qualified.

Learning Outcomes

The students will be able to explain the physical principles of MRI and functional MRI imaging for exploration / estimation of the physiological and morphological parameters (e.g. k-space and pulse sequences, tensor estimation and eigen-decomposition, deconvolution, compartment modeling, statistical modeling, and geometric modeling). Students will also achieve practical knowledge of software and algorithms for quantitative analysis of image-based information in space and time, and be able to install and modify these programs for use in analysis and visualization of their own data. This knowledge is particularly linked to MATLAB and Python.

After completion of the course the student should be able to:

Present knowledge about

Basic principles of MRI.
Methdos for image analysis.
Software tools for image processing.

Skills and general competence

Perform simple scripting and programming.
Install and adapt image processing tools.
Communicate and translate imaging problems between (i) a biological or medical formulation and (ii) a computational & algorithmic formulation.

Contact Information

Department of Biomedicine

studie@biomed.uib.no

(+47) 55 58 64 39 / 55 58 64 40 / 55 58 60 95

Course coordinator:

Erlend Hodneland, http://uib.no/persons/Erlend.Hodneland

Course offered (semester)

Autumn/spring(minimum 2 students)

Language of Instruction

English

Aim and Content

Obtain theoretical and practical knowledge on functional and quantitative in vivo imaging in man and animal using magnetic resonance imaging (MRI) and computer-based image analysis. The focus is on brain imaging (perfusion, diffusion, permeability mapping) and structural and functional connectivity, but also examples from functional kidney imaging and (image-based) systems biology will be presented. A major objective is also to give insight about the importance of mathematical models and computations in analysis and understanding of complex physiological processes, and the need of cross-disciplinary collaborations.

Learning Outcomes

After completion of the course the student should be able to:

Present knowledge about

Basic principles of MRI.
Methdos for image analysis.
Software tools for image processing.

Skills and general competence

Perform simple scripting and programming.
Install and adapt image processing tools.
Communicate and translate imaging problems between (i) a biological or medical formulation and (ii) a computational & algorithmic formulation.

Pre-requirements

Recommended previous knowledge

General human physiology dealing with diffusion, perfusion and microcirculation. Basic knowledge of brain anatomy and neurophysiology, and molecular and cell biology. Background in mathematics (e.g. calculus & linear algebra) and some experience with using computers in biomedical applications (e.g. statistical packages, signal processing, etc.). Access to a computer with MATLAB and Image Processing Toolbox installed, in addition to Python/Sage.

Subject Overlap

HUFY372

Teaching Methods

Lectures + programming lab and demonstrations. Term and project-task. Course materials, including links to software and data, are available from the course web page.