Towards Automatic Embryo Staging in 3D+T Microscopy Images using Convolutional Neural Networks and PointNets

10/01/2019

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by   Manuel Traub, et al.

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Automatic analyses and comparisons of different stages of embryonic development largely depend on a highly accurate spatio-temporal alignment of the investigated data sets. In this contribution, we compare multiple approaches to perform automatic staging of developing embryos that were imaged with time-resolved 3D light-sheet microscopy. The methods comprise image-based convolutional neural networks as well as an approach based on the PointNet architecture that directly operates on 3D point clouds of detected cell nuclei centroids. The proof-of-concept experiments with four wild-type zebrafish embryos render both approaches suitable for automatic staging with average deviations of 0.45 - 0.57 hours.