Automated identification of mouse visual areas with intrinsic signal imaging

Nat Protoc. 2017 Jan;12(1):32-43. doi: 10.1038/nprot.2016.158. Epub 2016 Dec 1.


Intrinsic signal optical imaging (ISI) is a rapid and noninvasive method for observing brain activity in vivo over a large area of the cortex. Here we describe our protocol for mapping retinotopy to identify mouse visual cortical areas using ISI. First, surgery is performed to attach a head frame to the mouse skull (∼1 h). The next day, intrinsic activity across the visual cortex is recorded during the presentation of a full-field drifting bar in the horizontal and vertical directions (∼2 h). Horizontal and vertical retinotopic maps are generated by analyzing the response of each pixel during the period of the stimulus. Last, an algorithm uses these retinotopic maps to compute the visual field sign and coverage, and automatically construct visual borders without human input. Compared with conventional retinotopic mapping with episodic presentation of adjacent stimuli, a continuous, periodic stimulus is more resistant to biological artifacts. Furthermore, unlike manual hand-drawn approaches, we present a method for automatically segmenting visual areas, even in the small mouse cortex. This relatively simple procedure and accompanying open-source code can be implemented with minimal surgical and computational experience, and is useful to any laboratory wishing to target visual cortical areas in this increasingly valuable model system.

MeSH terms

  • Animals
  • Automation
  • Mice
  • Mice, Inbred C57BL
  • Optical Imaging / instrumentation
  • Optical Imaging / methods*
  • Signal Transduction*
  • Visual Cortex / cytology*
  • Visual Cortex / physiology
  • Visual Fields