PhD Defense

Title

Image Registration and Mosaicing for Dynamic In Vivo Fibered Confocal Microscopy

Date and Time

Friday January 25th 2008, starting at 10:00 AM

Lunch buffet at 1:00 PM

Location

INRIA Sophia Antipolis

2004 route des Lucioles - BP 93

06902 Sophia Antipolis Cedex

France

Room: Jacques Morgenstern Amphitheater

Gilles Kahn building

Thesis committee

Nicholas Ayache, Advisor

Valentin Becker, Medical guest

Olivier Faugeras, President

Polina Golland, Reviewer

Sacha Loiseau, Industrial guest

Nassir Navab, Reviewer

Xavier Pennec, Co-advisor

Aymeric Perchant, Industrial advisor

Abstract

Classical confocal microscopy can be used to obtain high-resolution images of cells on tissue samples or cell cultures. Translation of this technology for in vivo applications can be achieved by using optical fibers and miniature optics. Ultimately, fibered confocal microscopy should enable clinicians and biologists to perform what can be referred to as an optical biopsy: a real-time histological examination of biological tissues in the living organism directly onto the tissues of interest.

The main goal of this thesis is to move beyond current hardware limitations of these imaging devices by developing specific innovative image registration schemes. In particular, this manuscript is framed by the goal of providing, through video sequence mosaicing tools, wide field-of-view optical biopsies to the clinicians. This targeted application is seen as a pipeline that takes some raw data as input and provides wide field-of-view image mosaics as output. We detail the critical building blocks of this pipeline, namely real-time image reconstruction, linear image registration and non-rigid registration, before presenting our mosaicing framework.

The raw data that fibered confocal microscopy produces is difficult to use as it is modulated by a fiber optics bundle pattern and distorted by geometric artifacts. In this context, we show that real-time image reconstruction can be used as a preprocessing step to get readily interpretable video sequences. Since fibered confocal microscopy is a contact imaging modality, the combined movement of the imaged tissues and the flexible optical microprobe makes it sometimes difficult to get robust and accurate measurements of some parameters of interest. We have thus been investigating the problem of efficiently and robustly registering pairs of images. We show that some tools that have recently been developed in the field of vision-based robot control can outperform classical image registration solutions used in biomedical image analysis. The adequacy of these tools for linear image registration led us to revisit non-rigid registration. By casting the non-rigid registration problem into an optimization problem on a Lie group, we develop a fast non-parametric diffeomorphic image registration scheme. In addition to being diffeomorphic, our algorithm provides results that are similar to the ones from Thirion's demons algorithm but with transformations that are smoother and closer to the true ones.

Finally, we use these image reconstruction and registration building blocks to propose a robust mosaicing algorithm that is able to recover a globally consistent alignment of the input frames, to compensate for the motion distortions and to capture the non-rigid deformations. A great deal of effort has been put into incorporating our mosaicing algorithm within a multicenter clinical trial. This trial allows us to assess the clinical value of our tools for the particular application of Barrett's esophagus surveillance.

Contacts

My cell phone: +33 6 16 87 32 74

My email: tom.vercauteren@sophia.inria.fr

Isabelle Strobant (Team Assistant): +33 4 92 38 76 60

email: isabelle.strobant@sophia.inria.fr

Full Text

Available here