Pycro-Manager: open-source software for customized and reproducible microscope control

Cutting-edge innovations in biological microscopy are increasingly blurring the line between data acquisition and data analysis. Computational microscopy and machine-learning-based methods take this paradigm to an extreme, often producing raw measurements that are not human-interpretable without postprocessing. Furthermore, new data-adaptive imaging methods rely on data processing during acquisition to actively control various hardware settings of the microscope. To address these needs, we present here Pycro-Manager. Pycro-Manager is built on a translation layer that converts Java objects, functions and data into language-agnostic messages that are reconstituted as Python objects or functions and as NumPy arrays. As a result, the existing capabilities of µManager can be called as if they had been written in Python, without forcing users to learn Java, forcing Java developers to learn Python, or abandoning of the relative strengths of either language.