Standardizing workflows in imaging transcriptomics with the abagen toolbox

Reviewer #2 (Recommendations for the authors):

Are region-region distances geodesic or Euclidean?

In our analysis of the distance-dependent relationship of gene expression ("correlated gene expression" and "CGE" in the manuscript) we used the Euclidean distance between parcel centroids. For volumetric atlases, parcel centroids were calculated as the center-of-mass of the voxels within each parcel; for surface-based atlases, parcel centroids were calculated as the coordinate of the vertex with the minimum Euclidean distance to the center-of-mass of the vertices within each parcel. We have clarified this in the revised manuscript (“Results” section, “Correlated gene expression” subsection):

“We assessed this relationship by extracting the upper triangle of the correlated gene expression matrices and correlating them with the upper triangle of a regional distance matrix, derived by computing the average Euclidean distance between brain region centroids in the Desikan-Killiany atlas.”

P13 – typo: "asses" (you meant assess).

Fixed!

Figure 3 – Panel C might benefit from a schematic. I personally found it somewhat difficult to understand exactly what was being shown.

We have attempted to clarify Figure 3c by updating the figure labels and caption to be more explicit that the correlations shown are between the maps depicted in Figure 3b.

“(c) The Pearson correlation between the cortical somatostatin (SST) maps generated by the nine pipelines shown in panel (b).”

The number of pipelines tested is written at least two different ways (746,946 and 746,496).

We have updated the number of pipelines throughout the manuscript to the correct value of 746,496.