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

J Neurosci Methods. 2013 Apr 30;215(1):38-52. doi: 10.1016/j.jneumeth.2013.02.006. Epub 2013 Feb 14.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology
  • Brain / physiology
  • Calcium / chemistry
  • Computer Simulation
  • Computer Systems
  • Computers
  • Data Interpretation, Statistical
  • Equipment Design
  • Image Processing, Computer-Assisted
  • Mice
  • Microscopy / instrumentation*
  • Microscopy / methods*
  • Microscopy, Confocal
  • Microscopy, Video
  • Neuroimaging / instrumentation*
  • Neuroimaging / methods*
  • Software*


  • Calcium