Pycro-manager: open-source software for integrated microscopy hardware control and image processing

Henry Pinkard, Nico Stuurman, Laura Waller

arXiv.org
June 19, 2020

Abstract: μManager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely coupled. This is because μManager libraries are written in C++ and Java, whereas image processing is increasingly carried out with data science and machine learning tools most easily accessible through the Python programming language. We present Pycro-Manager, a tool that enables rapid development of such experiments, while also providing access to the wealth of existing tools within μManager through Python.

 

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Featured Fellows

Henry Pinkard

Computational Biology
Alumni - DATA SCIENCE FELLOW

Laura Waller

Electrical Engineering and Computer Sciences, UC Berkeley
BIDS Faculty Council