Research

My research focus is on image processing, graphics, computer vision and machine learning, with special interest on biomedical image registration and segmentation and their applications on neuroscience and developmental biology.

Postdoc at INRA

From May 2013 to August 2015 I worked as a postdoc at the Modeling and Digital Imaging lab in the Institut Jean-Pierre Bourgin (INRA-Versailles, France). My main project was part of the Tefor infrastructure and aimed at creating statistically-plausible templates of model species, in particular for Drosophila adult brains and embryos.

Postdoc at MIT

From November 2009 to April 2013, I worked as a postdoctoral fellow at Sebastian Seung's lab at the Massachusetts Institute of Technology. During this period, I investigated novel solutions to some of the challenges of modern computational neuroscience. In particular, I studied machine learning approaches for the segmentation of neural processes in electron microscopy.

The main lines of the lab research project are described on the following video:

PhD thesis

On June 26th 2009 I defended the PhD thesis "Registration and 3D Reconstruction of Histological Sections: Application to Mammary Gland Development" and obtained the mark "A - Cum Laudem". It was awarded as well with the Doctor Europeus mention and the department Annual PhD thesis award.

My thesis work focused on developing novel image processing algorithms to study the mammary gland morphology in mice. In particular, I developed novel approaches for the alignment of long sequences of histological sections and the 3D reconstruction and the statistical analysis of the ductal system of the mouse mammary gland. Most of the methods are available as ImageJ and Fiji plugins. If you are interested, have a look at my software page.