CCB Brown Bag Seminar

Presenter: Lisa Brown, Ph.D., Senior Data Scientist, Developmental Dynamics

Topic: Lineage Reconstruction for Preimplantation Mouse Embryogenesis

I will present our work in reconstructing cell lineages from time-lapse light-sheet microscopy of the pre-implantation mouse embryo. Using the per-frame outputs of instance segmentation of nuclei, I will describe the methods we are using for first registering the frames in the sequence and then tracking the nuclei across frames including through divisions. Using semi-automatic techniques, we are creating an initial dataset of ground truth lineages. From this data, we are measuring several features which we are leveraging using a global graph optimization scheme. Once we collect sufficient lineage data, we hope to train a convolutional neural network to determine and potentially predict the lineage.