Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data
Abstract Synchrotron radiation‐based X‐ray microtomography is uniquely suited for post‐mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field‐of‐view and produces datasets of multiple tera...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-07-01
|
| Series: | Advanced Science |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/advs.202416879 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849316498741395456 |
|---|---|
| author | Mattia Humbel Christine Tanner Marta Girona Alarcón Georg Schulz Timm Weitkamp Mario Scheel Vartan Kurtcuoglu Bert Müller Griffin Rodgers |
| author_facet | Mattia Humbel Christine Tanner Marta Girona Alarcón Georg Schulz Timm Weitkamp Mario Scheel Vartan Kurtcuoglu Bert Müller Griffin Rodgers |
| author_sort | Mattia Humbel |
| collection | DOAJ |
| description | Abstract Synchrotron radiation‐based X‐ray microtomography is uniquely suited for post‐mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field‐of‐view and produces datasets of multiple terabytes in size. These data must be reconstructed, analyzed, and made accessible to domain experts who may have limited image processing knowledge. Extended‐field X‐ray microtomography is presented with 0.65μm voxel size covering an entire mouse brain. The 4495 projections from 8 × 8 offset acquisitions are stitched to reconstruct a volume of 150003 voxels. The microtomography volume was non‐rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were block‐wise transformed and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra‐explorer. This study demonstrates X‐ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3‐teravoxel dataset is publicly available and easily accessible for domain experts via browser‐based viewers. |
| format | Article |
| id | doaj-art-bbfee6b5abcb4d8a9d0eee265f346c65 |
| institution | Kabale University |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-bbfee6b5abcb4d8a9d0eee265f346c652025-08-20T03:51:43ZengWileyAdvanced Science2198-38442025-07-011228n/an/a10.1002/advs.202416879Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte DataMattia Humbel0Christine Tanner1Marta Girona Alarcón2Georg Schulz3Timm Weitkamp4Mario Scheel5Vartan Kurtcuoglu6Bert Müller7Griffin Rodgers8Biomaterials Science Center Department of Biomedical Engineering University of Basel Hegenheimermattweg 167B/C Allschwil 4123 SwitzerlandBiomaterials Science Center Department of Biomedical Engineering University of Basel Hegenheimermattweg 167B/C Allschwil 4123 SwitzerlandThe Interface Group Institute of Physiology University of Zurich Winterthurerstrasse 190 Zurich 8057 SwitzerlandBiomaterials Science Center Department of Biomedical Engineering University of Basel Hegenheimermattweg 167B/C Allschwil 4123 SwitzerlandSynchrotron SOLEIL, L'Orme des Merisiers Saint‐Aubin 91190 FranceSynchrotron SOLEIL, L'Orme des Merisiers Saint‐Aubin 91190 FranceThe Interface Group Institute of Physiology University of Zurich Winterthurerstrasse 190 Zurich 8057 SwitzerlandBiomaterials Science Center Department of Biomedical Engineering University of Basel Hegenheimermattweg 167B/C Allschwil 4123 SwitzerlandBiomaterials Science Center Department of Biomedical Engineering University of Basel Hegenheimermattweg 167B/C Allschwil 4123 SwitzerlandAbstract Synchrotron radiation‐based X‐ray microtomography is uniquely suited for post‐mortem 3D visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field‐of‐view and produces datasets of multiple terabytes in size. These data must be reconstructed, analyzed, and made accessible to domain experts who may have limited image processing knowledge. Extended‐field X‐ray microtomography is presented with 0.65μm voxel size covering an entire mouse brain. The 4495 projections from 8 × 8 offset acquisitions are stitched to reconstruct a volume of 150003 voxels. The microtomography volume was non‐rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. The data were block‐wise transformed and stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra‐explorer. This study demonstrates X‐ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The 3.3‐teravoxel dataset is publicly available and easily accessible for domain experts via browser‐based viewers.https://doi.org/10.1002/advs.202416879big dataextended field‐of‐viewmulti‐resolution open dataneuroimagingregistrationX‐ray histology |
| spellingShingle | Mattia Humbel Christine Tanner Marta Girona Alarcón Georg Schulz Timm Weitkamp Mario Scheel Vartan Kurtcuoglu Bert Müller Griffin Rodgers Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data Advanced Science big data extended field‐of‐view multi‐resolution open data neuroimaging registration X‐ray histology |
| title | Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data |
| title_full | Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data |
| title_fullStr | Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data |
| title_full_unstemmed | Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data |
| title_short | Synchrotron Radiation‐Based Tomography of an Entire Mouse Brain with Sub‐Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data |
| title_sort | synchrotron radiation based tomography of an entire mouse brain with sub micron voxels augmenting interactive brain atlases with terabyte data |
| topic | big data extended field‐of‐view multi‐resolution open data neuroimaging registration X‐ray histology |
| url | https://doi.org/10.1002/advs.202416879 |
| work_keys_str_mv | AT mattiahumbel synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT christinetanner synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT martagironaalarcon synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT georgschulz synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT timmweitkamp synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT marioscheel synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT vartankurtcuoglu synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT bertmuller synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata AT griffinrodgers synchrotronradiationbasedtomographyofanentiremousebrainwithsubmicronvoxelsaugmentinginteractivebrainatlaseswithterabytedata |