Histological assessment of developmental cell death in pupae.

This protocol describes the embedding and processing of pupae in paraffin to monitor tissue changes during development. Although multiple methods are available to evaluate developmental changes in embryos, imaging detailed changes during metamorphosis is challenging as the animal is enclosed in the cuticle, rendering it inaccessible to whole mount imaging. Here, we present a protocol that focuses on developmental clearance of the larval salivary glands in pupae that can be extended to examine other tissues/stages for similar purposes. For complete details on the use and execution of this protocol, please refer to Velentzas et al. (2018).