Category Archives: biological-data

SIFR project Ontology and web semantic

The SIFR project investigate the scientific and technical challenges in building ontology-based services to leverage biomedical ontologies.

My work is on the the annotators web service which purpose it to:

  1. Provide a unique access point to several server running the ontology annotators developed by the NCBO, such as their
  2. Wrap new functionalities around these annotators. In particular I work on adding RDF output format and the annotation scoring methods which have been published in

Rhizoscan High-throughput Root System Architecture extraciton from images

The RhizoScan is a project, founded by Rhizopolis and Numev, to develop image and graph analysis technologies to automatically process image of root systems and extract their architecture.

See the RhizoScan python package.

Poster at the 7th internation conference on Functional-Structural Plant Model
Poster at the CSHL meeting: Automated Imaging and High Throughput Phenotyping

Teaching assistant at Université de Nice Sophia-Antipolis September 2010 to August 2011

I participated on a project to study the measurement of paramecium ciliary beating from video.


Postdoc at LadHyX, Ecole Polytechnique January 2009 to March 2010

The goal of my research is to provide a metrological study comparing well-known algorithms to compute the optical flow of video sequences. In particular, we are interested by videos of plants motion (more specifically single trees) which represent particularly complex cases for image processing techniques. This work is part of a larger research project studying the bio-mechanics of plants. Here I focus on developing an experimental method to study plant dynamics and structure using video data.

Through this project, I have coded the CR matlab toolbox containing a set of algorithms that allows the extraction of motion data out of video sequences. This toolbox proposes a user friendly interface designed to be used by scientists who are not specialized in image processing.

This post-doc is founded by the ANR research project Chêne-Roseau.

Ph.D at Evasion, INRIA September 2005 to December 2008

I have done a PhD at Evasion, INRIA under the supervision of Lionel Reveret.
I studied methods to generate the motion for virtual plants. Two main approaches have been explored:

  1. Acquisition and reproduction of real motion from videos – project page
  2. Real-time simulation of the tree response to wind load  – project page