I am a life scientist fond of image data who fell in love with computers and mathematics. I hold a MSc in Bioengineering and a PhD in Electrical Engineering, with a focus on applied maths for image processing.
My work focuses on the development of continuous representations to quantify, describe, and model objects in bioimages. My research interests include approximation and information theory, image processing, computer vision, machine learning, and life sciences.
I am leading a Bioimage Analysis research group at the EMBL-EBI in Cambridge, UK. We are interdisciplinary, doing theoretical research on approximation theory, engaging in collaborative projects with biologists, and developing image analysis software tools. We have internship opportunities in the team for enthusiastic researchers with an electrical engineering, applied maths or computer science backgound. If you like blending maths and computer vision and enjoy beautiful bioimages, drop me an e-mail!
I currently serve my second term as an associate member in the Bio Imaging and Signal Processing Technical Committee of the IEEE Signal Processing Society.
If you don't find me in the lab, I am most likely either climbing or doing something bird-related.
For more details, please refer to my curriculum vitae. Please note that this is my personal website and is not related to the institution I currently work in. As I enjoy the analog life more than the digital one, be aware that this website might not be up to date. Fortunately, Google Scholar does a decent job at keeping track of my publications.I am grateful to the Stack Overflow user community for their precious advice and help in designing this webpage.
I develop mostly Python scripts and pipelines, and Java-based plug-ins for the open-source image analysis softwares ImageJ, Fiji and Icy. I also regularly work with the Python-based softwares CellProfiler and ilastik.
I am still in the process of creating a decent code base, please bear with me in the meantime, and don't hesitate to get in touch if you are struggling to use something I developed.
I think and explain better when I doodle. Below are some illustrations of this tendency.
These are personal scribbles. In the unlikely event you would like to reuse some of them, I would appreciate to be asked first.
Illustrations of differences between cubic B-spline and cubic Hermite snakes.
Illustrations of the ability of different spline bases to approximate complex shapes by "linking the dots" and serving as a bridge between the analog and the digital worlds.
Illustrations of the real, mathematical and digital worlds.
Illustrations around Ls=w, the magical formula of my Doktorvater, Michael Unser, concieved together with Julien Fageot for the 20th birthday of the Biomedical Imaging Group at EPFL.
Illustration of Stuart's moods. Stuart is a cockatiel living in my flat.
Illustrations of a conference trip to Novossibirsk.