Deadline for full application: December 15th, 2013

Interviews: March, 2014

Start of the Ph.D.: October 1st, 2014




Department: Cell Biology and Infection

Title of the PhD project: Compressive Sensing Holographic Microscopy

Name of the lab: Quantitative Image Analysis

Head of the lab: Jean-Christophe Olivo-Marin

PhD advisor: Jean-Christophe Olivo-Marin

Email address: jcolivo@pasteur.fr

Web site address of the lab: www.bioimageanalysis.org

Doctoral school affiliation and University: EDITE de Paris, Paris 6


Presentation of the laboratory and its research topics:

The Quantitative Image Analysis (QuIA) unit is dedicated to design innovative and rigorous quantitative image analysis and cosmputer vision methods for the processing and quantification of multi-channel temporal 3D sequences in biological imaging, especially at cellular and molecular levels.


Description of the project:

The goal of this project is to take advantage of the Compressed Sensing (CS) framework to improve drastically on holography microscopy (DHM). Over the last few years, in collaboration with teams at ESPCI-Paristech and Télécom-Paristech, we have developed experiments demonstrating the feasibility of CS microscopy (including DHM) imaging, as well as identifying bottlenecks that need to be worked out for practical implementation. We are among the very first groups worldwide having proposed and applied the concepts of compressive sensing in biological imaging and demonstrated it in a real biological context (Marim et al., 2010; Le Montagner et al., 2012).

This project proposes to elaborate dynamic CS DHM imaging protocols and setups based on Fourier-domain measurements with random array detectors and dedicated parameterization of image reconstruction processes. The project will consider the design and implementation of dedicated dynamic compressed sensing acquisition protocols for DHM microscopy imaging. It will specifically address the following items: 1) design and validation of fast CS-based dynamic sensing protocols in holographic optical microscopy via specific acquisition devices, and the setup of dynamic sensing protocols for CS holographic compressed sensing ; 2) design of compressed holographic microscopy instruments to experimentally establish and test an optimized CS holographic microscope.

The resulting advances in CS-DHM imaging will lead to massively increased image acquisition rates with guaranteed resolution and quality for a given acquisition rate and will enable the design of optimized dynamic imaging protocols, dedicated to specific biological paradigms and experimental conditions.



  1. Marim, M., M. Atlan, E. Angelini, J.C. Olivo-Marin (2010) « Compressed Sensing with off-axis frequency-shifting holography ». Optics Letter 35(6): 871-873.
  2. Le Montagner, Y., Angelini, E., Olivo-Marin, J.-C. (2012) « Video reconstruction using compressed sensing measurements and 3D Total Variation regularization for bio-imaging applications ». IEEE Intern. Conf. on Image Processing, ICIP 2012, Orlando, USA



Digital Holography, Compressive sensing, optimization


Expected profile of the candidate (optional):

Computer Science, Physics, Applied Mathematics, Electrical Engineering



Jean-Christophe Olivo-Marin (jcolivo@pasteur.fr)

Mis à jour le 16/09/2013