Figure 2
From: Accurate determination of marker location within whole-brain microscopy images
Segmentation of injection volumes using brainreg-segment. (a) Schematic of the injection segmentation experiment timeline. Top: Injection of an AAV carrying the fluorescent protein GFP in the primary visual cortex (VISp) of a Ntsr1-cre transgenic mouse at a depth of 900 μm (layer 6, L6). Bottom: Expression of GFP by a subset of cortical neurons (Ntsr1-positive cells). (b) Plot showing the 3D position of the segmented region centroids of each rater (open circles, n = 3 centroids per rater). The average centroid for all raters is also shown (grey circle). (c) Left: Box plot showing the distance from consensus for all centroids and for each rater. Right: Plot showing the standard deviation of each brain and for each rater. (d) Left: Box plot showing the total segmented volume for each rater. Right: Box plot showing the DICE scores for each rater. (e) Box plot showing the percentage of segmented volume in each CCFv3 brain region. (f) Left: coronal image of the primary visual cortex (inset) and projection of the first 850 brain images (green channel) acquired with serial two-photon tomography, overlaid with the UAA atlas. Scale bar = 500 μm. (g) Rendering of the segmented regions within the primary visual cortex.
