Thèse : Hybrid approach "compressed acquisition - visual servoing - deformable tracking" applied to medical imaging
A Ph.D. position in medical robotics and image-guided surgery is opened at FEMTO-ST Institute (Besançon, France) and Insitut Pascal (Clermon-Ferrand, France).
Institut FEMTO-ST (Besançon) – Institut Pascal (Clermont-Ferrand)
Start date: March 2017
Duration: 3 years
The NEMRO project (microrobotic nasal endoscopy by OCT: impact of the olfactory deficit on neurodegenerative diseases) is a collaborative research project coordinated by the FEMTO-ST institute, which involves several academic and clinical partners. This project aims to develop an innovative approach for the early diagnosis of neurodegenerative diseases (e.g., Alzheimer's, Parkinson's) using an OCT (Optical Coherence Tomography) probe embedded into the distal part of the endoscopic system for the in-situ characterisation of the olfactory cells and neurons.
The thesis will be carried out in collaboration between the MINAROB team of the AS2M department (FEMTO-ST) and the ENCOV team of Institut Pascal (Université Clermont Auvergne, CNRS). On the one hand, the MINAROB team develops research activities in the field of medico-micromechatronics devices as well as image-guided solutions for medical and surgical applications. On the other hand, the ENCOV team is specialized in computer vision and its applications in diagnosis and interventional gesture assistance.
Within the framework of the proposed thesis, MINAROB and ENCOV share their skills and means to propose innovative approaches associating competences in automatic control (visual servoing)   and a know-how in applied mathematics in medical images processing. The objective of this thesis is the implementation of Compressed Sensing (CS) methods , the development of innovative methods for structures (organs) deformation tracking and image-guided approaches for medical interventions. The clinical objectives are multiple; efficient and fast optical biopsies (OCT, confocal) acquisition, compensation of artefacts due to the physiological movements, control of the navigation of an endoscopic microrobot (tube-concentric robotic system ), determination of the margins for endoscopic-based tumor resection.
The aim of this PhD thesis is the development of advanced mathematical tools: compressed acquisition paradigms, tracking of deformable anatomical structures algorithms, characterization of tissue lesions by learning  in the medical images (OCT, confocal, endoscopic). This is based on a commercial OCT system that MINAROB has acquired, on a fiber confocal microscope and on an endoscope available in the ENCOV team. For instance, it should be noted that the functioning of an OCT system is based on a scanning scheme, using a 2 degrees of freedom (DOF) mirror. Thus, each pixel (more precisely each optical core) is acquired sequentially and independently. Scanning acquisition is totally adapted to the development of compressed acquisition techniques. Thus, it is not necessary to acquire all the elementary pixels but only a certain number to reconstruct an OCT image of the same resolution. The scanning paths will be defined so as to optimize the image quality, the scanning system dynamics as well as the acquisition time. The achievement of these paths will be ensured by an original visual servoing control law. This should make it possible to use OCT to perform an optical biopsy under endoscopic control of pathologies such as endometriosis . The ability to recognize this type of lesion may be one of the criteria for optimizing the scanning scheme.
his thesis work requires a multidisciplinary profile, addressing aspects of applied mathematics related to computer vision, of control, and of robotics (geometry, kinematics). The required profile is that of a MSc (or equivalent) student. He/She must have skill in programming (C++ and MATLAB).
He/She will have good written abilities of scientific documents. Open minded, He/She will be required to work within a team and must be able to communicate easily. Listening, dynamic and persevering to carry out a fundamental and experimental research works over three years.
Candidates should send a cover letter, a CV and recent transcripts in the form of a single PDF file to the following addresses.
 B. Tamadazte, N. Piat, and E. Marchand. /A direct visual servoing scheme for automatic nanopositioning/. IEEE/ASME Trans. on Mechatronics,17 :728–736, 2012.
 R. Dahmouche, N. Andreff, Y. Mezouar, O. Ait-Aider, and P. Martinet. /Visual servoing from sequential regions of interest acquisition/. Int. J. Robotic Research, 31 :520–537, 2012.
 S. Chrétien. /An alternating e11 relaxation for compressed sensing/. IEEE Signal Processing Letters, 17 :181–184, 2010.
 R. J. III Webster, J. M. Romano, and N. J. Cowan. /Mechanics of precurved-tube continuum robots/. IEEE Transactions on Robotics, 25 :67–78, 2009.
 P. Mesejo, D. Pizarro, L. Poincloux, O. Rouquette, S. Beorchia, A. Abergel and A. Bartoli/Computer-Aided Classification of Gastrointestinal Lesions in Regular Colonoscopy/ IEEE Transactions on Medical Imaging, 2016
 A. Bartoli, T. Collins, M. Canis and N. Bourdel /Computer Assisted Minimally Invasive Surgery://Is Medical Computer Vision the Answer to Improving Laparosurgery/? Medical Hypotheses, 79(6):858-863, 2012
(c) GdR 720 ISIS - CNRS - 2011-2015.