Not yet reviewed by Pith; the record is open.

Studying cell morphology changes in time is critical to understanding cell migration mechanisms. In this work, we present a deep learning-based workflow to segment cancer cells embedded in 3D collagen matrices and imaged with phase-contrast microscopy. Our approach uses transfer learning and recurrent convolutional long-short term memory units to exploit the temporal information from the past and provide a consistent segmentation result. Lastly, we propose a geometrical-characterization approach to studying cancer cell morphology. Our approach provides stable results in time, and it is robust to the different weight initialization or training data sampling. We introduce a new annotated dataset for 2D cell segmentation and tracking, and an open-source implementation to replicate the experiments or adapt them to new image processing problems.