AbstractCell division patterns provide crucial information for understanding the mechanisms of development of multicellular organisms. These patterns are measured manually by long‐term microscopic observation or by studying large numbers of images taken by using time‐lapse microscope systems. Because manual measurement limits the objectivity and productivity of measurement, the comprehensive cell division pattern analysis of gene knockdown embryos has been difficult. Here, we present a system that automatically measures the cell division pattern of Caenorhabditis elegans embryos from the 1‐ to 24‐cell stages with high levels of objectivity and productivity. The system automatically detects the nuclei in a set of four‐dimensional differential interference contrast microscope images of a C. elegans embryo by using image processing and measures the cell division pattern by tracking the detected nuclei over time. This system enables a comprehensive cell division pattern analysis of gene knockdown C. elegans embryos. © 2007 Wiley Periodicals, Inc. Syst Comp Jpn, 38(11): 12–24, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20783