Semi supervised segmentation and graph-based tracking of 3D nuclei in time-lapse microscopy

S Shailja, Jiaxiang Jiang, BS Manjunath


We propose a novel weakly supervised method to improve the boundary of the 3D segmented nuclei utilizing an over-segmented image. This is motivated by the observation that current state-of-the-art deep learning methods do not result in accurate boundaries when the training data is weakly annotated. Towards this, a 3DU-Net is trained to get the centroid of the nuclei and integrated with a simple linear iterative clustering (SLIC) supervoxel algorithm that provides better adherence to cluster boundaries. To track these segmented nuclei, our algorithm utilizes the relative nuclei location depicting the processes of nuclei division and apoptosis.

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S Shailja, Jiaxiang Jiang, BS Manjunath,
Apr. 2021.