E. Chereul

Shape Prior Integrated in an Automated 3D Region Growing Method

We propose a new automated region growing method integrating shape prior (RGISP). The aim of this work is to improve region growing segmentation by taking into account a reference model. Our algorithm is assessed on a synthesized image and compared with two other methods in order to point up the contribution of shape prior. It was also applied to segment in-vivo mu-CT images of mouse kidneys in the framework of small animal imaging. RGISP gives promising results and appears to be well adapted to satisfy small animal imaging constraints.

3D MRI heart segmentation of mouse embryos.

MRI has become an effective tool for anatomical mice studies. Currently, embryologists study the development of mouse embryos in order to understand the mechanisms of human development. The aim of the research presented in this paper, is to develop a semi-automatic image segmentation framework based 3D deformable models to identify cardiac malformations which are a major cause of death in children. The segmentation systems have been used to segment 3D mouse embryos heart structures. Results on the ventricles and on the heart muscle are presented and compared with manually segmented models.

Impact of Anesthesia Protocols on In Vivo Bioluminescent Bacteria Imaging Results.

Infectious murine models greatly benefit from optical imaging using bioluminescent bacteria to non-invasively and repeatedly follow in vivo bacterial infection. In this context, one of the most critical parameters is the bioluminescence sensitivity to reliably detect the smallest number of bacteria. Another critical point is the anesthetic approaches that have been demonstrated to impact the bioluminescence flux emission in studies with luciferase-transfected tumor cells. However, this impact has never been assessed on bacteria bioluminescent models. To this end, we investigated the effects of four anesthesia protocols on the bioluminescence flux in a central venous catheter murine model (SKH1-hrhr mice) infected by a bioluminescent S. aureus Xen36 strain. Bioluminescence imaging was performed on mice anesthetized by either ketamine/xylazine (with or without oxygen supplementation), or isoflurane carried with air or oxygen. Total flux emission was determined in vivo daily for 3 days and ex vivo at the end of the study together with a CFU counting of the biofilm in the catheter. Bioluminescence flux differences appear between the different anesthetic protocols. Using a ketamine/xylazine anesthesia (with air), bacteria detection was impossible since the bioluminescence signal remains in the background signal. Mice anesthetized with isoflurane and oxygen led to a signal significantly higher to the background all along the kinetics. The use of isoflurane in air presents a bioluminescence signal similar to the use of ketamine/xylazine with oxygen. These data highlight the importance of oxygen to improve bioluminescence flux by bacteria with isoflurane as well as with ketamine/xylazine anesthetics. As a conclusion, we recommend the use of isoflurane anesthetic with oxygen to increase the bioluminescence sensitivity in this kind of study.

Mouse embryo’s heart segmentation on μMRI acquisitions

To understand the mechanisms of human development, embryologists study the development of mouse embryos. The aim of the research, as presented in this paper, is to identify cardiac malformations which are a major cause of mortallity in childhood. With this end in view, we developed expert computer based algorithms known as segmentation. The segmentation framework is based on a tru 3D deformable models rather than a slice-by-slice 2D processing. It includes both a pre-processing step and the automatic segmetation. At this point, we tested our segmentation pipeline on the left and right ventricles (LV, RV) of different mouse embryos. Results on a standard data set with 5 mM of Gadolinium and TE of 10 ms are presented and compared with the manually segmented embryonic heart model done at Animage. We present also the segmentation of an abnormal mouse ventricle and the segmentation of the heart muscle.