Abstract Micro-CT imaging is a powerful tool for generating high resolution, isotropic three-dimensional datasets of whole, small model organisms that are useful for qualitative and quantitative analysis. D. magna , one of the most common ecological model organisms used for toxicity testing and evaluation of environmental stressors, could benefit from this imaging method for enhancing whole-organism phenotype assessment. This protocol details the steps involved in Daphnia sample preparation for micro-CT imaging: euthanasia, fixation, staining, and resin embedding. The resulting 3D reconstructions of samples imaged using synchrotron micro-CT revealed histological (microanatomic) features of organ systems, tissues, and cells in the context of the entire organism at sub-micron resolution. 3D histology and renderings enabled by this imaging method could contribute to morphometric analysis of any tissue or organ system for both descriptive and hypothesis testing studies.

Staining and resin embedding of wholeDaphniasamples for micro-CT imaging