Fig 1. Background schematic and CE workflow overview.

A) Studying cells in isolation disregards the effects of community interactions, which are known to direct cell fate decisions (left). Powerful micropatterning in vitro assays increase control over the cellular microenvironment and facilitate the study of context dependent cell fate acquisitions (middle). Our analysis software enhances these assays by allowing researchers to analyze cell behavior within its population context instead of as independent isolated events (right). B) CE fits into existing image analysis pipelines after initial measurements have been extracted from the images. C) Overview of the CE workflow, each step is described in detail in the methods section.