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

TL;DR

Pycro-Manager is an open-source Python-based tool that simplifies the integration of microscopy hardware control with image processing, bridging the gap between acquisition and analysis for advanced experiments.

Contribution

It introduces a Python interface for {b5}Manager, enabling seamless coupling of hardware control and image analysis, which was difficult with previous Java and C++ libraries.

Findings

Facilitates rapid development of integrated microscopy experiments.

Provides access to existing {b5}Manager tools through Python.

Enhances usability for data science and machine learning applications.

Abstract

{\mu}Manager, 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 {\mu}Manager 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 {\mu}Manager through Python.