What is in the black box? - A perspective on software in cryoelectron microscopy

This article bemoans the demise of truly modular open-source image processing systems, such as SPIDER, in recent years' development of tools for three-dimensional reconstruction in cryo-electron microscopy. Instead, today's users have to rely on the functionality of software systems that have little or no transparency. As a consequence, users of such packages no longer gain a conceptual understanding and intuitive grasp of the analytical routes leading from the stream of input data to the final density map. Possible remedies of this situation with free software are discussed.