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.

中文翻译：

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黑匣子里是什么？– 对低温电子显微镜软件的看法

本文哀叹真正模块化的开源图像处理系统（如 SPIDER）的消亡，近年来在低温电子显微镜中开发的三维重建工具。取而代之的是，今天的用户不得不依赖透明度很小或没有透明度的软件系统的功能。因此，此类软件包的用户不再对从输入数据流到最​​终密度图的分析路线有概念性的理解和直观的把握。讨论了使用免费软件对这种情况的可能补救措施。