Multimodal Correlative Preclinical Whole Body Imaging and Segmentation.
Segmentation of anatomical structures and particularly abdominal organs is a fundamental problem for quantitative image analysis in preclinical research. This paper presents a novel approach for whole body segmentation of small animals in a multimodal setting of MR, CT and optical imaging. The algorithm integrates multiple imaging sequences into a machine learning framework, which generates supervoxels by an efficient hierarchical agglomerative strategy and utilizes multiple SVM-kNN classifiers each constrained by a heatmap prior region to compose the segmentation. We demonstrate results showing segmentation of mice images into several structures including the heart, lungs, liver, kidneys, stomach, vena cava, bladder, tumor, and skeleton structures. Experimental validation on a large set of mice and organs, indicated that our system outperforms alternative state of the art approaches. The system proposed can be generalized to various tissues and imaging modalities to produce automatic atlas-free segmentation, thereby enabling a wide range of applications in preclinical studies of small animal imaging.
Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel.
Ayelet
A
Akselrod-Ballin
Department of Veterinary Resources Weizmann Institute, Rehovot 76100 Israel.
Hagit
H
Dafni
Department of Biological Services Weizmann Institute, Rehovot 76100 Israel.
Yoseph
Y
Addadi
Department of Veterinary Resources Weizmann Institute, Rehovot 76100 Israel.
Inbal
I
Biton
Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel.
Reut
R
Avni
Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel.
Yafit
Y
Brenner
Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel.
Michal
M
Neeman
D000825:Animal Structures / Q000000981:diagnostic imaging*; D000818:Animals; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D000069550:Machine Learning; D008279:Magnetic Resonance Imaging; D051379:Mice; D064847:Multimodal Imaging / Q000379:methods*; D061848:Optical Imaging; D014057:Tomography, X-Ray Computed; D051598:Whole Body Imaging / Q000379:methods*