The authors have adequately addressed all my comments and I compliment them on the excellent quality of their work.

I specially appreciated the use of a unified evaluation criteria (MLDS on 6 brains), together with quantitative deformation metrics, which greatly adds robustness and clarity to the paper in my opinion. The flowcharts in Fig. 1, 3, 4 together with the before/after comparison in Additional Fig. 4 greatly help guide the reader. The updated reporting of statistical significance, variability across landmarks and datasets and N was also greatly improved.

I include some minor comments/suggestions below,

• I expect this atlas to become a reference in the scientific community. It is likely that other researchers will try to register their own datasets to the resource following the same methodology. Apart from sharing the individual brain scans and reference brain in "Availability of Supporting Data", would it be possible to share as well the coordinates of the different landmark points and cells used for evaluation? (Additional Figures 1-3) This will allow to easily evaluate the precision of future registered datasets (and perhaps alternative methods) to the results reported in this paper
• Fig. 1b, replace y label "Hausdorff distance" by "Hausdorff distance (um)"
• Fig. 2a, typo on the y label: "Mean Landmark Distance (ANTS)"

Are the methods appropriate to the aims of the study, are they well described, and are necessary controls included? If not, please specify what is required in your comments to the authors.
Yes

Are the conclusions adequately supported by the data shown? If not, please explain in your comments to the authors. Yes

oes the manuscript adhere to the journal’s guidelines on minimum standards of reporting? If not, please specify what is required in your comments to the author
Yes

Are you able to assess all statistics in the manuscript, including the appropriateness of statistical tests used? (If an additional statistical review is recommended, please specify what aspects require further assessment in your comments to the editors.)
Yes, and I have assessed the statistics in my report.

Quality of written English Please indicate the quality of language in the manuscript:
Acceptable

Declaration of competing interests Please complete a declaration of competing interests, consider the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this manuscript? If you can answer no to all of the above, write ‘I declare that I have no competing interests’ below. If your reply is yes to any, please give details below.
I declare that I have no competing interests.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published.
I agree to the open peer review policy of the journal.

Authors' response to reviews:

We corrected the two typos noted by Reviewer 2. Also uploaded to GigaDB the landmark points that Reviewer 2 requested, and added this information to the manuscript.

Editor asked we add funding information - added. The RRIDs added by the editor are fine, thank you.