Semi-supervised 3D neural networks to track iPS cell division in label-free phase contrast time series images

In order to predict cell population behavior, it is important to understand the dynamic characteristics of individual cells. Individual induced pluripotent stem (iPS) cells in colonies have been difficult to track over long times, both because segmentation is challenging due to close proximity of cells and because cell morphology at the time of cell division does not change dramatically in phase contrast images; image features do not provide sufficient discrimination for 2D neural network models of label-free images. However, these cells do not move significantly during division, and they display a distinct temporal pattern of morphologies. As a result, we can detect cell division with images overlaid in time. Using a combination of a 3D neural network applied over time-lapse data to find regions of cell division activity, followed by a 2D neural network for images in these selected regions to find individual dividing cells, we developed a robust detector of iPS cell division. We created an initial 3D neural network to find 3D image regions in (x,y,t) in which identified cell divisions occurred, then used semi-supervised training with additional stacks of images to create a more refined 3D model. These regions were then inferenced with our 2D neural network to find the location and time immediately before cells divide when they contain two sets of chromatin, information needed to track the cells after division. False positives from the 3D inferenced results were identified and removed with the addition of the 2D model. We successfully identified 37 of the 38 cell division events in our manually annotated test image stack, and specified the time and (x,y) location of each cell just before division within an accuracy of 10 pixels.