Postdoc in Small Animal Image Registration

Commissariat d'Énergie Atomique (CEA) - Paris, France

Subject: Registration of anatomical and functional information obtained
from rodents and acquired in vivo and post-mortem.

Application
The goal of this work is to develop image processing methodologies
enabling the quantitative validation of a µ-TEP system to study rodent
brains using three-dimensional autoradiographic information as a gold
standard.

Context
The development of dedicated small animal imaging systems has been the
focus of significant efforts over the last few years. Applications are
numerous, ranging from neurological studies to whole-body assays for
oncology. The possibility to acquire combined anatomical and functional
information of animals as well as to perform longitudinal follow-ups of
these animals under various conditions open significant avenues both in
fundamental research on the mechanisms involved in physiopathology as
well as in the development of new therapeutics (medical drugs, genetic
therapies). But as of today, the bulk of rodent studies were based on
classical biological techniques such as histology and autoradiography
that require a high level of interactions which hinder the ability to
perform high throughput animal studies. Furthermore, imaging devices
dedicated to animals produce images that differ significantly from
human systems which forces the revision of both registration and
segmentation methods that are to be used to exploit these images.

Objectives
The first half of this project consists of producing registration
solutions for functional and anatomical neurological images of rodents
acquired with µ-PET (FDG) and MRI scanners. Validation, possibly based
on PET and MRI numerical simulations and / or manually obtained ground
truth, shall occupy a significant portion of this first part. The
second half will aim at linking in vivo and post mortem image acquired
from the same subject. 3D deformable registration methods will be
developed to estimate deformations between MRI acquisition obtained in
vivo and reconstructed photographic / histologic volumes. A dedicated
database is currently being built and will be constituted of several
subjects for which images from all the previously mentioned imaging
modalities will be acquired.

Candidat Profile
The candidate should have a strong experience in the fields of
mathematics, computer science (Unix / Linux, C / C++, Python would be
beneficial) and medical image analysis, in particular multi-modal
registration.

Welcoming Laboratory
The Service Hospitalier Frédéric Joliot (SHFJ) is equipped with a
broad range of nuclear imaging devices. Amongst other, the centre has
human (CTI HR-RT) and animal PET scanners (Concorde FOCUS), as well as
two MRI (1.5T Signa GE and 3T Bruker). In addition, the SHFJ is the
site of multiple research groups attached to the French Commissariat
d'Énergie Atomique (CEA) that are specialized in biology as well as
the development of animal models of disease and therapeutic treatments,
largely relying on traditional post mortem imaging techniques
(histochemistry, immunohistochemisty, autoradiography, microscopy).

The SHFJ also hosts a number of groups dedicated to the development of
image processing methods which are distributed throughout the
scientific community by the way of open source software. Examples of
these are the C++ image processing library AIMS, the visualization
interface Anatomist, and the graphical interface BrainVISA (image
processing protocols, database) (http://brainvisa.info). These
developments aim at providing to end users (medical doctors,
biologists) the required tools to face the analysis of information
resulting from different imaging modalities.

The CEA is also soon opening two large scale, state of the art imaging
research centres (MIRCen and NeuroSpin). (see joint documentation)

Application detail at: http://www.tedjob.com/job_detail.php?id=4903

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Relevant Pages

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