Accurate determination of marker location within whole-brain microscopy images

Abstract

High-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function. Here we have developed two plugins (brainreg and brainreg-segment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. We analysed the position of dye-labelled electrode tracks and two-photon imaged cell populations expressing fluorescent proteins. The precise location of probes and cells were physiologically interrogated and revealed accurate segmentation with near-cellular resolution.

Quantitative analysis of rabies virus-based synaptic connectivity tracing

“…Our dataset is thus uniformity in terms of cell-type (L5PN), yet contains sufficient heterogeneity in terms of sub-types and starter areas to test comparative approaches. Whole brains were imaged using 2-photon tomography, then registered, segmented and annotated according to the Allen Common Coordinate Framework (CCFv3, [27]) using the open source brainreg software [28]. Starter and input cells were detected and classified using the open source software cellfinder [17].…”

Behavioral origin of sound-evoked activity in mouse visual cortex

“…Images were assembled using StitchIt (https://github.com/SainsburyWellcomeCentre/StitchIt, https://zenodo.org/badge/latestdoi/57851444). Probe location was checked using brainreg 26–28 , showing that most recordings were in area V1, and partially VISpm and VISl. The exact location of the probe in visual cortex did not affect the results so we pooled all areas together under the name of VIS.…”

“…Figure 3a-c). We used the software packages brainreg [26][27][28] to quantify the cuts and brainrender 29 to visualize their extent in 3D (Figure 3b, Suppl. Figure 3d).…”

“…Bilateral craniotomies were performed between 7 to 14 days following the transectomy, and acute bilateral recordings were acquired using 4-shank Neuropixels 2.0 probes targeting visual cortex over multiple days (3, 1 and 2 consecutive days in the three mice). The total number of cells was 1059 (ipsi) and 914 (contra) ( Probe location was checked using brainreg [26][27][28] , showing that most recordings were in area V1, and partially VISpm and VISl. The exact location of the probe in visual cortex did not affect the results so we pooled all areas together under the name of VIS.…”

“…To visualize and estimate the extent of the transectomy, we used the software brainreg [26][27][28] to register the brain to the Allen Mouse Brain Reference Atlas 43 , and manually trace the contours of the cut using brainreg-segment. The cut was identified visually by observing the massive neuronal loss (made obvious by a loss of fluorescence) and scars.…”