An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain

This archive contains the dataset produced by the Blue Brain Project (BBP) for improving the Common Coordinate Framework version 3 (CCFv3) mouse brain atlas from the Allen Institute for Brain Science (AIBS). The dataset nomenclature is aligned with AIBS standards, utilizing the Allen Reference Atlas (ARA) Nissl-stained volume sectioned in the coronal incidence (ARA NisslCOR) and the annotation file version 3 (ANNOTv3). Additional data were used, such as the AIBS Nissl-stained volume sectioned in the sagittal incidence (AIBS NisslSAG, Allen Mouse Brain Atlas ID 100042147) as well as a Waxholm (WAXH) Nissl-stained volume sectioned in the horizontal incidence (WAXH NisslHOR; https://www.nitrc.org/projects/incfwhsmouse).

Here is a list of the files produced and shared below with their descriptions:

ara_bbp_nisslCOR_25 - 10: ARA Nissl-stained volume sectioned in the coronal incidence at 25 and 10 μm isotropic resolution accurately aligned in the CCFv3.

arav3a_bbp_nisslCOR_25 - 10: ARA Nissl-stained volume sectioned in the coronal incidence at 25 and 10 μm isotropic resolution accurately aligned in the CCFv3 and extended for covering the entire brain.

annotv3am_bbp_manual_25: Expert manual delineation of the extended tissue based on ARAv3aBBP NisslCOR at 25 isotropic resolution as well as of the granular and molecular layers in the cerebellum.

annotv3a_bbp_25 - 10: Extended CCFv3 annotation at 25 and 10 μm isotropic resolution covering the entire mouse brain plus including new granular and molecular layers in all cerebellar lobules, assessed using ANNOTv3am.

annotv3c_bbp: Extended CCFv3aBBP annotation covering the mouse central nervous system including spinal cord as well as barrel columns in the isocortex.

aibs_bbp_nisslSAG_25: AIBS sagittal Nissl-stained volume aligned in the CCFv3aBBP at 25 μm isotropic resolution.

waxh_bbp_nisslHOR_25: WAXH horizontal Nissl-stained volume aligned in the CCFv3aBBP at 25 μm isotropic resolution.

annotation_bbp_atlas_pipeline_25: Annotation file from the Blue Brain cell atlas pipeline including the extended version annotv3a_bbp_25, plus some additional sublayers such as layer 2 and layer 3, as well as the barrel columns in the isocortex.

hierarchy_bbp_atlas_pipeline: Hierarchy file attached to the annotation_bbp_atlas_pipeline_25 version.

average_nissl_init_25_v3a_CBcorrected: Average Nissl-stained template composed of the average of arav3a_bbp_nisslCOR_25, aibs_bbp_nisslSAG_25, and waxh_bbp_nisslHOR_25 and including some automated corrections of the artifacts in the cerebellum. This was used as a reference and initialization for building the average Nissl-stained template.

average_nissl_template: Symmetric (symmetric_full) and non symmetric (nissl_average_full)  averaged Nissl-stained template in the CCFv3aBBP, as well as the number of occurences per voxel (frequency) in the averaging process.

QuickNII-CCFv3a-extended: Extended CCFv3a atlas file compatible with QuickNII software.

VisuAlign-v0.91: Extended CCFv3a atlas file compatible with VisuAlign software.

An additional video (FullBrainAtlas_bbp) is provided in that archive, presenting the different mouse brain annotations from AIBS to BBP ones, as well as the BBP computed neuron distribution among the entire mouse brain colored by regions given AIBS standards. The code for creating the data in the video is accessible at https://github.com/favreau/BioExplorer/tree/master/bioexplorer%2Fpythonsdk%2Fnotebooks%2Fccfv3.

For accessing to the code related to that work, please go to the corresponding GitHub repository: https://github.com/BlueBrain/ccfv3a-extended-atlas.

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Citation:

Piluso, S., Verasztó, C., Carey, H., Delattre, É., L’Yvonnet, T., Colnot, É., Romani, A., Bjaalie, J. G., & Keller, D. (2024). An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain. Zenodo. https://doi.org/10.5281/zenodo.13640418

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Reference paper:

Sébastien Piluso, Csaba Verasztó, Harry Carey, Émilie Delattre, Thibaud L’Yvonnet, Éloïse Colnot, Armando Romani, Jan G. Bjaalie, Henry Markram, Daniel Keller; An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain. Imaging Neuroscience 2025; doi: https://doi.org/10.1162/imag_a_00565

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Funding:

This study was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. This project/research has received funding from the European Union’s Research and Innovation Program Horizon Europe under Grant Agreement no. 101147319 (EBRAINS 2.0).