Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies

Abstract

In experimental neuroscientific research, anatomical location is a key attribute of experimental observations and critical for interpretation of results, replication of findings, and comparison of data across studies. With steadily rising numbers of publications reporting basic experimental results, there is an increasing need for integration and synthesis of data. Since comparison of data relies on consistently defined anatomical locations, it is a major concern that practices and precision in the reporting of location of observations from different types of experimental studies seem to vary considerably. To elucidate and possibly meet this challenge, we have evaluated and compared current practices for interpreting and documenting the anatomical location of measurements acquired from murine brains with different experimental methods. Our observations show substantial differences in approach, interpretation and reproducibility of anatomical locations among reports of different categories of experimental research, and strongly indicate that ambiguous reports of anatomical location can be attributed to missing descriptions. Based on these findings, we suggest a set of minimum requirements for documentation of anatomical location in experimental murine brain research. We furthermore demonstrate how these requirements have been applied in the EU Human Brain Project to optimize workflows for integration of heterogeneous data in common reference atlases. We propose broad adoption of some straightforward steps for improving the precision of location metadata and thereby facilitating interpretation, reuse and integration of data.

Neurons in the Intermediate Reticular Nucleus Coordinate Postinspiratory Activity, Swallowing, and Respiratory-Sympathetic Coupling in the Rat

“…In brief, montage images of sections lying between the hypoglossal nucleus and the middle of the facial nucleus were captured (10ϫ/0.30 NA M27 objective lens), and labeled neurons were manually annotated. Sections from mice or rats were aligned to the Allen or Waxholm (Papp et al, 2014) volumetric brain atlases, respectively, using the QuickNII alignment tool (Bjerke et al, 2018) (https://www.nitrc.org/projects/quicknii), transforming the pixel coordinates of neurons identified in 2D images to 3D Cartesian coordinates. For each mouse, the distribution of ChAT ϩ IRt neurons was projected into 2D grayscale heat maps using a 5 voxel smoothing coefficient, as described previously (Dempsey et al, 2017).…”

An executive center for the intake of liquids

“…Images of sections were aligned to the Allen Brain Atlas using QuickNII ( 64 ) (https://www.nitrc.org/projects/quicknii). Labelled neurons were manually annotated as IRt seed neurons (GFP + mCherry + ) or monosynaptic input neurons (mCherry + ) in ImageJ.…”

Enhanced and unified anatomical labeling for a common mouse brain atlas

“…To make it worse, the labels in the Allen CCF released in 2017 (CCFv3) also introduced significant changes from its original ARA labels that were based on 2D Nissl stained sections. This has created confusion and misinterpretation of experimental results 21 . These issues motivated us to create a unified and highly segmented anatomical labeling system in the adult mouse brain based on the Allen CCF.…”