For multicellular model systems, comprehensive morphological phenotyping ideally includes assessments of every cell type in every organ system. We report the ability to use synchrotron-microCT to create 3D images of whole, fixed and metal-stained zebrafish at cellular resolutions such that virtually every cell type can be visualized and phenotyped. Sample diameters may be as large as about 1.5 mm for 0.743 micron voxel resolution and about 2.9 mm for 1.43 micron resolution. Full volumes of 3 or 4 day old zebrafish larvae at the higher resolution or 1 cm long juvenile fish at the lower resolution yield files of about 100 GB. Computer-based visualizations can be optimized for visualization of different cellular structures such as nerve tracts, blood vessels, bone, and melanocytes. This pancellular form of microCT allows volumetric measurements, the creation of slab thicknesses of any multiple of the voxel resolution, and any angle of cut. Analysis of a pola2 mutant in zebrafish shows that we are able to detect abnormalities at the cellular level including atypical nuclei, nuclear fragments, and abnormal mitoses. Since large scale projects will require far greater throughput than is currently possible, we are pursuing optimizations and standardization for sample generation and handling, instrumentation, optics, reconstruction, and visualization, under the auspices of a Synchrotron MicroCT Imaging Resource for Biology. We are recruiting partners as we plan for broad usage of this tool for samples of mm length scale, including whole worms, and flies, and parts of larger models including Arabidopsis and mammals. Automated image processing tools for phenotypic analysis are being developed in parallel with rapid imaging capabilities. Through the creation of these imaging capabilities for the research community, we hope to facilitate a far more rapid and comprehensive understanding of organismal diversity, gene function, organismal toxicity, and disease than is currently possible.