{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T02:16:10Z","timestamp":1785204970013,"version":"3.55.0"},"reference-count":103,"publisher":"MIT Press","license":[{"start":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T00:00:00Z","timestamp":1744675200000},"content-version":"vor","delay-in-days":104,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100020899","name":"ETH Board of the Swiss Federal Institutes of Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020899","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018693","name":"European Union\u2019s Research and Innovation Program Horizon","doi-asserted-by":"publisher","award":["101147319"],"award-info":[{"award-number":["101147319"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["direct.mit.edu"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2025,5,21]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Brain atlases are indispensable tools for quantifying cellular composition across mouse brain regions. The widely used Common Coordinate Framework version 3 (CCFv3) from the Allen Institute delineates over 600 anatomical regions but lacks coverage of the most rostral and caudal brain areas, including the main olfactory bulb, cerebellum, and medulla. Additionally, the CCFv3 does not include annotations for key cerebellar layers, and its Nissl-stained reference volume is misaligned, limiting its efficiency. To overcome these limitations, we developed the Blue Brain Project (BBP) CCFv3 augmented atlas (CCFv3BBP), which includes a fully annotated mouse brain and an improved Nissl-stained reference volume aligned with the CCFv3BBP. This enhanced atlas also features the central nervous system annotation. Building on this enhanced resource, we aligned 734 Nissl-stained brains to generate an average Nissl template at 10 \u00b5m resolution. This new atlas version enabled the construction of the first comprehensive in silico model of cell distribution across the whole mouse central nervous system. This open-access resource broadens the applicability of brain atlases, supporting advancements in alignment accuracy, cell type mapping, and multimodal data integration.<\/jats:p>","DOI":"10.1162\/imag_a_00565","type":"journal-article","created":{"date-parts":[[2025,4,15]],"date-time":"2025-04-15T17:24:51Z","timestamp":1744737891000},"update-policy":"https:\/\/doi.org\/10.1162\/mitpressjournals.corrections.policy","source":"Crossref","is-referenced-by-count":2,"title":["An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain"],"prefix":"10.1162","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4419-1748","authenticated-orcid":false,"given":"S\u00e9bastien","family":"Piluso","sequence":"first","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6295-7148","authenticated-orcid":false,"given":"Csaba","family":"Veraszt\u00f3","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4111-6259","authenticated-orcid":false,"given":"Harry","family":"Carey","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9milie","family":"Delattre","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thibaud","family":"L\u2019Yvonnet","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9lo\u00efse","family":"Colnot","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6388-4286","authenticated-orcid":false,"given":"Armando","family":"Romani","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7899-906X","authenticated-orcid":false,"given":"Jan G.","family":"Bjaalie","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6164-2590","authenticated-orcid":false,"given":"Henry","family":"Markram","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3280-6255","authenticated-orcid":false,"given":"Daniel","family":"Keller","sequence":"additional","affiliation":[{"name":"Blue Brain Project, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Geneva, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"281","published-online":{"date-parts":[[2025,5,21]]},"reference":[{"key":"2025052119560817000_imag_a_00565-b1","unstructured":"Allen Institute for Brain Science. 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