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

Abstract

To interpret in vivo experiments designed to understand brain function, high-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and recorded cells in three dimensional brain space that is a critical step for data interrogation. Here we have developed Python-based tools (brainreg and brainreg-segment) to accurately map, in a common coordinate space, the position of dye-labelled probe tracks and two-photon imaged cell populations expressing fluorescent protein. The precise location of probes and cells were validated using physiological recordings and human raters that indicate accuracy levels to less than 70{micro}m. These flexible, open-source methodologies are expected to further evolve with need and to deliver the anatomical precision that is necessary for understanding the functional architecture of the brain.