Computational Image Analysis Reveals Intrinsic Multigenerational Differences between Anterior and Posterior Cerebral Cortex Neural Progenitor Cells

Time-lapse microscopy can capture patterns of development through multiple divisions for an entire clone of proliferating cells. Images are taken every few minutes over many days, generating data too vast to process completely by hand. Computational analysis of this data can benefit from occasional human guidance. Here we combine improved automated algorithms with minimized human validation to produce fully corrected segmentation, tracking, and lineaging results with dramatic reduction in effort. A web-based viewer provides access to data and results. The improved approach allows efficient analysis of large numbers of clones. Using this method, we studied populations of progenitor cells derived from the anterior and posterior embryonic mouse cerebral cortex, each growing in a standardized culture environment. Progenitors from the anterior cortex were smaller, less motile, and produced smaller clones compared to those from the posterior cortex, demonstrating cell-intrinsic differences that may contribute to the areal organization of the cerebral cortex. [Display omitted] •Open-source automated software designed to track stem/progenitor clones in time-lapse movies•Software tools for easy data validation and visualization greatly improve efficiency•Lineage tree reconstruction from hundreds of embryonic mouse forebrain clones•Intrinsic differences in progenitor behavior from anterior/posterior cerebral cortex Cohen, Temple, and colleagues describe new techniques for segmenting, tracking, and lineaging stem and progenitor cells through multiple rounds of division in time-lapse phase contrast images. Manual validation is combined with automated analysis, minimizing effort to correct any errors. Progenitors from anterior and posterior mouse cerebral cortex cultured identically exhibited differences in behavior, indicating early encoding of cortex area identity.