A Lifespan Atlas of the Zebrafish

Zebrafish (Danio rerio) have become an increasingly popular genetic model over the past twenty years. In our lab we use the zebrafish for cancer research, and it is the basis for this histological atlas. The atlas spans the life of the zebrafish from embryo to adult and contains sections of tissue from three anatomical planes (sagittal, coronal, and transverse).

adult wild-type zebrafish
Adult, wild-type zebrafish (Danio rerio)

The Zebrafish Atlas contains 2- and 3-dimensional, anatomical reference slides of zebrafish to support research and education worldwide. Hematoxylin & eosin histological slides, at various points in the lifespan of the zebrafish, are scanned at 40x resolution and available here through a virtual slide viewer originally developed by Steven Peckins at Penn State.

The size of the zebrafish allows sections to fall conveniently within the dimensions of the common 1" x 3" glass slide. We present slices cut in three orthogonal directions, chosen from multiple candidate fish and slices that were cut in complete sets. Our hope is for the site to increasingly function as a scaffold for collaborative research and educational activity.

For the publication “Comparative Analysis of Fixation and Embedding Techniques for Optmized Histological Preparation of Zebrafish” full resolution figure slides and replicates can be found here

zebrafish tissue section


Virtual slide technology enables users to view high resolution imagery with a significantly reduced download time. Virtual slides are panned and zoomed in a manner similar to a traditional microscope but offer labeling, comparison, and collaborative possibilities beyond the limitations of physical microscopy. We now seek contributions of high-resolution, high-quality 2D and 3D images for inclusion in this resource.