Figure 3
From: Accurate determination of marker location within whole-brain microscopy images
Localization of recorded cell populations according to the centroid of the labeled volume. (a) Schematic of the functional imaging experiment timeline. Top: Injection of an AAV carrying the fluorescent indicator GCaMP7f in the primary visual cortex (VISp) at a depth of 250 μm (layer 2/3, L2/3). Middle: Two-Photon calcium imaging of L2/3 neurons in awake head-fixed mice, while presenting sparse noise stimuli. Example recorded trials from one neuron are shown in grey and their average response in black, aligned to the onset of stimulus (shaded grey area). Bottom: Average Receptive Field (RF) from one neuron, shown in visual space. (b) Top: two-photon grayscale image of GCaMP7f-expressing cells. Middle: Regions Of Interest (ROIs, green) determined by automated detection of labeled cells using suite2p. Bottom: Overlay of the Two-Photon image (grayscale) and the ROIs (green). (c) Left: centroids of all RFs recorded in one animal, color-coded according to their elevation in visual space. Right: centroids of all RFs recorded in one animal, color-coded according to their azimuth position in visual space. (d) Left: rendering of the position in atlas space of all recorded cells shown in panel c, color-coded according to their elevation in visual space. Right: rendering of the position in atlas space of all recorded cells shown in panel c, color-coded according to their azimuth position in visual space.
