Three Dimensional Nuclei Segmentation and Classification of Fluorescence Microscopy Images

Abstract

Segmentation and classification of cell nuclei in fluorescence 3D microscopy image volumes are fundamental steps for image analysis. However, accurate cell nuclei segmentation and detection in microscopy image volumes are hampered by poor image quality, crowding of nuclei, and large variation in nuclei size and shape. In this paper, we present an unsupervised volume to volume translation approach adapted from the Recycle-GAN using modified Hausdorff distance loss for synthetically generating nuclei with better shapes. A 3D CNN with a regularization term is used for nuclei segmentation and classification followed by nuclei boundary refinement. Experimental results demonstrate that the proposed method can successfully segment nuclei and identify individual nuclei.