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Background  Rapid improvements in light and electron microscopy imaging techniques and the development of 3D anatomical atlases necessitate new approaches for the visualization and analysis of image data. Pixel-based representations of raw light microscopy data suffer from limitations in the number of channels that can be visualized simultaneously. Complex electron microscopic reconstructions from large tissue volumes are also challenging to visualize and analyze.    Results  Here we exploit the advanced visualization capabilities and flexibility of the open-source platform Blender to visualize and analyze anatomical atlases. We use light-microscopy-based gene expression atlases and electron microscopy connectome volume data from larval stages of the marine annelid  Platynereis dumerilii . We build object-based larval gene expression atlases in Blender and develop tools for annotation and coexpression analysis. We also represent and analyze connectome data including neuronal reconstructions and underlying synaptic connectivity.    Conclusions  We demonstrate the power and flexibility of Blender for visualizing and exploring complex anatomical atlases. The resources we have developed for  Platynereis  will facilitate data sharing and the standardization of anatomical atlases for this species. The flexibility of Blender, particularly its embedded Python application programming interface, means that our methods can be easily extended to other organisms.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-015-0652-7) contains supplementary material, which is available to authorized users.

Object-based representation and analysis of light and electron microscopic volume data using Blender