HelioScan: A software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility

► HelioScan, a software framework for vivo microscopy control applications, written in the LabVIEW environment, is introduced. ► HelioScan application assembles at run-time from configurable software components and provides high flexibility and easy extendibility. ► We present four use cases demonstrating HelioScan's capabilities, in particular with regard to recent trends in the field of in vivo calcium imaging. ► A variety of imaging modalities are supported (video camera, galvanometric scan mirrors, acousto-optic deflectors, resonant scanners). ► We recommend HelioScan as a convenient software framework for the in vivo imaging community. Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community.