Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets
Abstract Mesoscale maps of brain architecture are important tools for characterizing the chemo- and cytoarchitectonic organization of the brain. These maps are essential for advancing our understanding of normal and pathologic brain function because they provide a bridge between neuron-level micro-s...
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| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08267-6 |
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| _version_ | 1849761674226040832 |
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| author | Thomas Funck Konrad Wagstyl Claude Lepage Mona Omidyeganeh Paule-Joanne Toussaint Ting Xu Katrin Amunts Alexander Thiel Nicola Palomero-Gallagher Alan C. Evans |
| author_facet | Thomas Funck Konrad Wagstyl Claude Lepage Mona Omidyeganeh Paule-Joanne Toussaint Ting Xu Katrin Amunts Alexander Thiel Nicola Palomero-Gallagher Alan C. Evans |
| author_sort | Thomas Funck |
| collection | DOAJ |
| description | Abstract Mesoscale maps of brain architecture are important tools for characterizing the chemo- and cytoarchitectonic organization of the brain. These maps are essential for advancing our understanding of normal and pathologic brain function because they provide a bridge between neuron-level micro-scale imagining and macro-level population brain imaging. Here we introduce a method and software package called BrainBuilder for reconstructing 3-dimensional cortical maps from data sets of 2-dimensional post-mortem serial brain sections processed for the visualization of multiple different biological features. This pipeline can be applied to the brains from different species, without the strict need for a corresponding reference volume from the brain donor. As a proof of principle, we reconstruct data showing the distribution of multiple neurotransmitter receptor binding sites, and cell and myelin stained sections in the human and macaque brain. We show that BrainBuilder can serve as the basis for the development of future mesoscale 3D atlases. |
| format | Article |
| id | doaj-art-336a006f63a04891bc09d8104d4331b5 |
| institution | DOAJ |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-336a006f63a04891bc09d8104d4331b52025-08-20T03:05:56ZengNature PortfolioCommunications Biology2399-36422025-07-018111710.1038/s42003-025-08267-6Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data setsThomas Funck0Konrad Wagstyl1Claude Lepage2Mona Omidyeganeh3Paule-Joanne Toussaint4Ting Xu5Katrin Amunts6Alexander Thiel7Nicola Palomero-Gallagher8Alan C. Evans9Child Mind InstituteWellcome Center for Human Neuroimaging, University College LondonMontreal Neurological Institute, McGill UniversityMontreal Neurological Institute, McGill UniversityMontreal Neurological Institute, McGill UniversityChild Mind InstituteInstitute of Neuroscience and Medicine (INM-1), Research Centre JülichLady Davis Institute, Jewish General Hospital, McGill UniversityInstitute of Neuroscience and Medicine (INM-1), Research Centre JülichMontreal Neurological Institute, McGill UniversityAbstract Mesoscale maps of brain architecture are important tools for characterizing the chemo- and cytoarchitectonic organization of the brain. These maps are essential for advancing our understanding of normal and pathologic brain function because they provide a bridge between neuron-level micro-scale imagining and macro-level population brain imaging. Here we introduce a method and software package called BrainBuilder for reconstructing 3-dimensional cortical maps from data sets of 2-dimensional post-mortem serial brain sections processed for the visualization of multiple different biological features. This pipeline can be applied to the brains from different species, without the strict need for a corresponding reference volume from the brain donor. As a proof of principle, we reconstruct data showing the distribution of multiple neurotransmitter receptor binding sites, and cell and myelin stained sections in the human and macaque brain. We show that BrainBuilder can serve as the basis for the development of future mesoscale 3D atlases.https://doi.org/10.1038/s42003-025-08267-6 |
| spellingShingle | Thomas Funck Konrad Wagstyl Claude Lepage Mona Omidyeganeh Paule-Joanne Toussaint Ting Xu Katrin Amunts Alexander Thiel Nicola Palomero-Gallagher Alan C. Evans Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets Communications Biology |
| title | Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets |
| title_full | Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets |
| title_fullStr | Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets |
| title_full_unstemmed | Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets |
| title_short | Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets |
| title_sort | brainbuilder a software pipeline for 3d reconstruction of cortical maps from multi modal 2d data sets |
| url | https://doi.org/10.1038/s42003-025-08267-6 |
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