Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mouse Visual Cortex

Abstract

Highlights d Software (AMaSiNe) is developed for automated neural mapping in a reference brain d Misaligned and deformed slices are calibrated using the minimum number of samples d Multiple brain data are precisely compared, mapped onto a common 3D space d Topographic neural projection from LGd to VISp is observed accurately

Visualizing anatomically registered data with brainrender

“…These can be loaded either directly as 3D mesh data after processing with dedicated software (e.g. A. L. Tyson et al 2020;Song et al 2020;Jin et al 2019) (Figure 3A), or as 3D volumetric data ( Figure 3E). For the latter, brainrender takes care of the conversion of voxels into a 3D mesh for rendering.…”

“…In particular, a critical step for visualizing anatomical data is the registration to a reference template (e.g., one of the atlases provided by the AtlasAPI). While this step can be challenging and time consuming, the brainglobe suite provides software to facilitate this process (e.g., brainreg and bg-space), and alternative software tools have been developed before for this purpose (e.g., Song et al 2020;Jin et al 2019). Additional information about data registration can be found in brainglobe's and brainrender's online documentation, as well as in the examples in brainrender's GitHub repository.…”

Brainrender: a python-based software for visualizing anatomically registered data

“…These can be loaded either directly as 3D mesh data after processing with dedicated software (e.g. Tyson, Rousseau, and Margrie 2020;Song et al 2020;Jin et al 2019) (Figure 3A), or as 3D volumetric data ( Figure 3E). For the latter, brainrender takes care of the conversion of voxels into a 3D mesh for rendering.…”

Tools for accurate post hoc determination of marker location within whole-brain microscopy images

“…This is problematic, as it does not allow researchers to use more recently developed atlases (Chon et al, 2019;Hoops et al, 2021;Kenney et al, 2021;Perens et al, 2020;Young et al, 2021), nor adapt software developed for one model organism, to another. Tools also exist for the detection and analysis of structures in whole-brain images such as neuronal somata (Furth et al, 2018;Goubran et al, 2019;Iqbal et al, 2019;Mano et al, 2020;Renier et al, 2016;Song et al, 2020;Tyson et al, 2020;Young et al, 2020), axons (Friedmann et al, 2020;Goubran et al, 2019) and vasculature (Kirst et al, 2020;Todorov et al, 2020). While mapping implanted devices within the brain has been performed using non-invasive magnetic resonance imaging (MRI) or computed tomography (CT) (Borg et al, 2015, Rangarajan et al, 2016, Király et al, 2020Kollo et al, 2020), there has been only one study using 3D whole brain microscopy (Liu et al, 2020).…”