3D high resolution MRI small animal brain atlases
Team
Rationale and Objectives
Brain research often relies on brain atlas templates to which new data can be registered or which aids in assigning brain structures. Therefore it is often required to develop an interactive brain atlas using specific MRI tools or using a less common animal specimen for which no atlases exist. Probabilistic atlases on the other hand can be used as a template of the control situation to be compared with data obtained from a disease model induced in the same animal strains.
Methodology
In vivo and ex vivo structural MRI.
Image processing: debiasing, affine and non-rigid registration, ROI segmentation, Subject based atlas (single data) and Population based atlas (multiple data).
Previously a male zebra finch brain, male canary brain and male pigeon brain atlas have been developed.
Team
- Marleen Verhoye (Professor)
- Colline Poirier (Postdoc)
- In collaboration with Vision Lab (UA - Dept. Physics)
Rationale and Objectives
Brain research often relies on brain atlas templates to which new data can be registered or which aids in assigning brain structures. Therefore it is often required to develop an interactive brain atlas using specific MRI tools or using a less common animal specimen for which no atlases exist. Probabilistic atlases on the other hand can be used as a template of the control situation to be compared with data obtained from a disease model induced in the same animal strains.
Methodology
In vivo and ex vivo structural MRI.
Image processing: debiasing, affine and non-rigid registration, ROI segmentation, Subject based atlas (single data) and Population based atlas (multiple data).
Previously a male zebra finch brain, male canary brain and male pigeon brain atlas have been developed.
- Zebra finch brain atlas: A three-dimensional MRI atlas of brain in stereotaxic coordinates
- Canary brain atlas: MRI ATLAS OF THE CANARY BRAIN (Serinus canaria)
- Pigeon brain atlas: A 3-Dimensional Digital Atlas of the Ascending Sensory and the Descending Motor Systems in the Pigeon Brain
Examples
Fig 1 : Axial slice of T2-weighted 3D RARE images (resolution 50 micron3 [9.4 T, Bruker Biospec])
of an adult male tilapia brain (perfused with paraformaldehyde + Dotarem ® 4%)
Fig 2 : 3D surface rendering of different structures of Tilapia brain
Fig 3 : DTI-population based rat atlas : Bo-image, colored FA-map, and surface rendered view of automatic
segmented ROI corresponding to high FA-values.
Funding
- GOA
- EC RATStream
Collaborations
- Vision lab - Jan Sijbers, Dirk Van Dyck (Antwerp, Belgium)
- Micro Tomography - Nora De Clerck, Dirk Van Dyck (Antwerp, Belgium)
- Medical and Health Sciences, Anatomy - Martin Wild (Auckland, New Zealand)
- Centre for Research in Cellular and Molecular Neurobiology - Jacques Balthazart (Luik, Belgium)
- Integrative Behavioural Biology Group - Rui Oliveira (Lisbon, Portugal)
- Institute of Cognitive Neuroscience - Onur Gunturkun (Bochum, Germany)
Zebra finch atlas: rendering of the skull, the whole brain and some brain structures