Figure 1
From: Accurate determination of marker location within whole-brain microscopy images
Overview of the brainreg/brainreg-segment workflow and validation of probe track tracing. (a) Atlas data including the reference anatomical image and the brain region annotations are sourced from the BrainGlobe Atlas API and used for image registration. Multiple atlases, such as the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3) and the Unified Anatomical Atlas (UAA) are supported. (b) Multichannel (e.g., labelled signal channel and a secondary autofluorescence channel) whole-brain microscopy data can be processed directly by brainreg without pre-processing (other than stitching). (c) Brainreg registers the sample data to the atlas reference image (and vice versa), allowing brain region annotations to be overlaid upon the raw data. (d) Brainreg-segment allows manual segmentation of labelled structures such as linear electrophysiological probes and fluorescent cell populations. Scale bars = 250 μm. (e) Schematic of the electrophysiological probe (Neuropixels) experiment. Top: A Neuropixels probe is coated with DiI by coming into contact with a suspended drop of the dye. Middle: The Neuropixels probe is inserted in the mouse brain above the primary visual cortical region (VISp) at a depth of 1750 or 2000 μm. Bottom: Projection of a whole-brain image (red channel) acquired with serial two-photon tomography, showing the DiI signal left by the Neuropixels probe. (f) Schematic of the probe and plot of the normalized Local Field Potential (LFP) power (500–1250 Hz) against depth. The red line shows the depth of the cortical LFP power peak, indicating the position of the middle of layer 5 (mid-VISp5). The grey arrowhead indicates the increase in LFP power when entering the hippocampal formation. (g) Left: Box plot showing the distance from landmark (mid-VISp5) for each rater (n = 7 per rater; positive distances are towards the pia). Right: Box plot showing the standard deviation of each rater (n = 7 per rater). (h) Rendering of the position of all the probe tracks (lines) within VISp (wireframe). Red arrowhead indicates the probe track shown in panel i. (i) One probe track (yellow) was identified as crossing the monocular primary cortex (V1M, brown) and the binocular primary cortex (V1B, blue) border.
