[robotics-worldwide] [Jobs] PhD Position in Computer Vision and Medical Imaging

TAMADAZTE brahim.tamadazte at femto-st.fr
Thu Jul 11 06:14:06 PDT 2019

Title: Registration of 3D optical biopsies: application to medical imaging of 
high-resolution and wide field-of-view

•	FEMTO-ST Institute (UMR 6174), AS2M Department
•	25000, Besançon, France
•	36 months (start: October, 2019)

Scientific context 
FEMTO-ST Institute (Besançon, France), develop several research activities
related to surgical robotics, medical imaging, and image-guided
intracorporeal interventions. In particular, we are addressing the clinical
problem of performing of in-situ 3D optical biopsies, i.e. the optical
analysis at the micrometer resolution of biological tissues thanks to highly
efficient medical imaging without the traditional physical sampling of
suspected tissues (physical biopsy). However, tissue analysis at micrometric
resolution, using for example optical coherence tomography (OCT) or confocal
microscopy, raises the problem of the limited field of view. Actually, this
is the recurring dilemma of a wide field of view and micrometric resolution.
To remedy this, it is necessary to perform several high-resolution 3D
optical biopsies based on the micrometric motion of the imaging probe and to
assemble them to reconstruct a single high-resolution biopsy over a large

Clinical context
The clinical objectives of this investigation are numerous, among them,
achieving of 3D optical biopsies with micrometric resolution and wide field
of view as part of the in-situ characterization of the olfactory mucosa in
human subjects. The idea to find a precursor sign (earlier diagnosis) of a
future neurodegenerative disease (Alzheimer’s and Parkinson’s disease) by
studying the odor operating in its healthy and pathological states. The
diagnosis is intended to be as early as possible (5 to 10 years) before the
first signs of motor impairment or memory loss. In fact, it has been
statistically demonstrated (post-mortem studies) that loss of smell with no
apparent causes (trauma, cancer, etc.) is generally correlated with dementia
(neurodegenerative diseases, such as Alzheimer). 
Consequently, the aim is to understand what is happening in vivo in the
olfactory mucosa without taking a sampling process of tissues (physical
biopsy), which is clinically difficult to achieve. However, the in-situ
characterization of the olfactory mucosa can be carried out thanks to 3D
optical biopsies approaches.

Scientific content 
The scientific work concerns the development of accurate and robust
registration methods between 3D visual information (optical biopsies). The
PhD student will first focus on the development of calibration methods based
on local visual features (e.g., geometric type information), matching
methods, computing rigid transformations as well as reconstruction and
mapping all the acquired data on the same final volume. This first work will
provide a basis for extending these methods in aim to use global information
such as pixel/voxel intensities, wavelet coefficients or any other global
image information. In addition, several parameters and external disturbances
will be considered within this work such as physiological motion, … in order
to limit potential artifacts. 

This work will then be extended to non-rigid registration in which the
observed tissue is subjected to a global (or a local minimum) deformation
resulting, for instance, from the contact between the tissue and the imaging

Required knowledges 
•	computer vision, (medical) imaging, robotics and applied mathematics 
•	Advanced programing skills (C++, Matlab, Python)
•	Knowledges of computer vision libraries (OpenCV, PCL) will be appreciated

Supervision team 
•	Guillaume Laurent (Associate-Prof, ENSMM)    -
•	Brahim Tamadazte (Senior Scientist, CNRS)    -

Application procedure
Interested candidates should send a cover letter, a CV and transcripts (M1
and M2 or equivalent) as a single PDF file to the supervisors before 1
September 2019.

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