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Analysis of such data across the whole mouse brain, registered to a reference atlas, aids in understanding the functional organization of brain circuits related to behavior. A process is described to image mouse brain sections labeled with standard histochemical techniques, reconstruct those images into a whole brain image volume and register those images to the Allen Mouse Brain Common Coordinate Framework. Image analysis tools automate detection of cell bodies and quantification of axon density labeling in the structures in the annotated reference atlas. Examples of analysis are provided for mapping the axonal projections of layer\u2010specific cortical neurons using Cre\u2010dependent AAV vectors and for mapping inputs to such neurons using retrograde transsynaptic tracing with modified rabies viral vectors.<\/jats:p>","DOI":"10.1002\/cne.24602","type":"journal-article","created":{"date-parts":[[2018,12,14]],"date-time":"2018-12-14T03:19:36Z","timestamp":1544757576000},"page":"2170-2178","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections"],"prefix":"10.1002","volume":"527","author":[{"given":"Brian S.","family":"Eastwood","sequence":"first","affiliation":[{"name":"MBF Bioscience  Williston Vermont"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0135-4284","authenticated-orcid":false,"given":"Bryan M.","family":"Hooks","sequence":"additional","affiliation":[{"name":"Department of Neurobiology University of Pittsburgh  Pittsburgh Pennsylvania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald F.","family":"Paletzki","sequence":"additional","affiliation":[{"name":"Intramural Research Program, NIMH  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathan J.","family":"O'Connor","sequence":"additional","affiliation":[{"name":"MBF Bioscience  Williston Vermont"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4463-207X","authenticated-orcid":false,"given":"Jacob R.","family":"Glaser","sequence":"additional","affiliation":[{"name":"MBF Bioscience  Williston Vermont"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9008-4882","authenticated-orcid":false,"given":"Charles R.","family":"Gerfen","sequence":"additional","affiliation":[{"name":"Intramural Research Program, NIMH  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,1,2]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.06.035"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4131"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mri.2012.05.001"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2013.10.016"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.2707-07.2007"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.3389\/fncir.2014.00076"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4332"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06928-1"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2015.11.002"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1080\/757582976"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1023\/B:VISI.0000029664.99615.94"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2008.01.002"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2018.03.040"},{"key":"e_1_2_6_15_1","doi-asserted-by":"crossref","unstructured":"Mikolajczyk K. 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