Section: Scientific Foundations
Biological Image Analysis
In biology, a huge number of images of living systems are produced every day to study the basic mechanisms of life and pathologies. If some bio-imaging principles are the same as the ones used for medical applications (e.g. MR, CT, US, PET or SPECT), the bio-imaging devices are usually customized to produce images of higher resolution (This is the case with micro-MRI, Micro-CT, Micro-US devices, and to a less extent with Micro-SPECT and Micro-PET devices.) for the observation of small animals (typically rodents). In addition, Optical Imaging (OI) techniques and biophotonics are developing very fast. This includes traditional or Confocal Microscopy (CM), multi-photon confocal microscopy, Optical Coherent Tomography (OCT), near-infrared imaging, diffuse optical imaging, phased array imaging, etc. A very new and promising development concerns micro-endoscopy, which allows cellular imaging at the end of a very small optical fiber  .
Most of these imaging techniques can be used for Molecular Imaging, an activity aiming at the in vivo characterization and measurement of biological processes at cellular and molecular levels. With optical techniques, molecular imaging makes an extensive use of the fluorescent properties of certain molecules (in particular proteins, e.g. GFP (Green Fluorescent Protein.)) for imaging of gene expression in vivo. With other modalities (like PET, SPECT, MR, CT and even US), molecular imaging can use specific contrast agents or radioactive molecules. For clinical applications, the ultimate goal of molecular imaging is to find the ways to probe much earlier the molecular anomalies that are the basis of a disease rather than to image only its end effects  .
Some of the recent advances made in Medical Image Analysis could be directly applied (or easily adapted) to Biological Image Analysis. However, the specific nature of biological images (higher resolution, different anatomy and functions, different contrast agents, etc.), requires specific image analysis methods (one can refer to the recent tutorial  and to the Mouse Brain Atlas Project  ). This is particularly true when dealing with in vivo microscopic images of cells and vessels.
Our research efforts will be focused to the following generic problems applied to in vivo microscopic images: