Figure 1: Experimental set-up.
From: Spatial clustering of tuning in mouse primary visual cortex
(a) Activity of cells in the primary visual cortex was imaged with a two-photon scanning microscope while the mouse observed a continuous visual stimulus on a freely rotating platform. The position of the platform was monitored with an optical rotary encoder. An infrared light-reflective glass (red line) allowed a camera to image the pupil while allowing for unobstructed visual stimulation. The visual stimulus consisted of a sequence of pseudo-random sinusoidal gratings (see Methods for details). (b) Two segments illustrating the process of inferring spiking activity from imaging data. First, the calcium fluorescence corresponding to cell bodies (raw signal) and their immediate neighbourhood (neuropil) as a function of time are extracted after compensating for motion in the imaging plane. Here both the raw signal and the neuropil are normalized by the s.d. of the raw signal. The vertical scale bar corresponds to five times the s.d. of the signals. A potential contamination of the signal by the neuropil is ameliorated by projecting out a robust linear prediction of the signal based on the neuropil. Finally, the probability of spiking is inferred by non-negative deconvolution (see Methods for details). The result is a trace that is nearly identical to zero in regions devoid of spiking activity (red trace), further minimizing small contributions of the neuropil to background activity. The spike inference trace is plotted in arbitrary units.
