Introducing Pycro-Manager

May 14, 2020

This article cross-posted from
Introducing Pycro-Manager
May 14, 2020  |   Henry Pinkard   | Forum


I’m very excited to announce the release of a project that Nico Stuurman and I have been working on, Pycro-Manager. As the name suggests, this package enables Python access to Micro-Manager. The access works through a behind-the-scenes high-speed bridge that dynamically “translates” between the Java and c++ parts of Micro-Manager and Python. This allows for Python users to use any of the existing Java/c++ APIs and plugins of micro-manager as if they had been written in pure Python. The translation between languages occurs dynamically at runtime, so any future development on the Java/c++ side will be available through Python as well.

Pycro-manager also has a flexible, high-level API to enable complex, customized data acquisition without having write all the boilerplate automation yourself. This can be used, for example, to synchronize external hardware with the acquisition process, modify acquired images on-the-fly before saving/visualization, implement your own customized data saving/visualization, and easily adapt acquisition in response to data.

If you’d like to learn more, please check out the documentation ( For any questions/suggestions/discussions, the best place is the Pycro-manager issues page (

Happy imaging,

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Henry Pinkard

Computational Biology