An open-source control system for in vivo fluorescence measurements from deep-brain structures

J Neurosci Methods. 2019 Jan 1:311:170-177. doi: 10.1016/j.jneumeth.2018.10.022. Epub 2018 Oct 17.


Background: Intracranial photometry through chronically implanted optical fibers is a widely adopted technique for measuring signals from fluorescent probes in deep-brain structures. The recent proliferation of bright, photo-stable, and specific genetically encoded fluorescent reporters for calcium and for other neuromodulators has greatly increased the utility and popularity of this technique.

New method: Here we describe an open-source, cost-effective, microcontroller-based solution for controlling optical components in an intracranial photometry system and processing the resulting signal.

Results: We show proof-of-principle that this system supports high quality intracranial photometry recordings from dorsal striatum in freely moving mice. A single system supports simultaneous fluorescence measurements in two independent color channels, but multiple systems can be integrated together if additional fluorescence channels are required. This system is designed to work in combination with either commercially available or custom-built optical components. Parts can be purchased for less than one tenth the cost of commercially available alternatives and complete assembly takes less than one day for an inexperienced user.

Comparison with existing method(s): Currently available hardware draws on a variety of commercial, custom-built, or hybrid elements for both optical and electronic components. Many of these hardware systems are either specialized and inflexible, or over-engineered and expensive.

Conclusions: This open-source system increases experimental flexibility while reducing cost relative to current commercially available components. All software and firmware are open-source and customizable, affording a degree of experimental flexibility that is not available in current commercial systems.

Keywords: Basal ganglia; Biophotonics; Fluorescence; GCaMP; Microcontrollers; Open-Source; Optical fibers; Photometry.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Calcium Signaling
  • Corpus Striatum / diagnostic imaging*
  • Corpus Striatum / metabolism
  • Equipment Design
  • Fluorometry / instrumentation*
  • Fluorometry / methods*
  • Mice
  • Optical Fibers
  • Optical Imaging / instrumentation*
  • Optical Imaging / methods*
  • Software