Merged magnetic resonance and light sheet microscopy of the whole mouse brain.
G Allan JohnsonYuqi TianDavid George AshbrookGary P CoferJames J CookJames C GeeAdam HallKathryn J HornburgYi QiFang-Cheng YehNian WangLeonard E WhiteRobert W WilliamsPublished in: Proceedings of the National Academy of Sciences of the United States of America (2023)
We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and diffusion tensor imaging (DTI) at 15 μm isotropic resolution which is ~ 1,000 times higher than that of most preclinical MRI. Connectomes are generated with superresolution tract density images of ~5 μm. Brains are cleared, stained for selected proteins, and imaged by LSM at 1.8 μm/pixel. LSM data are registered into the reference MRH space with labels derived from the ABA common coordinate framework. The result is a hi gh- d imensional i ntegrated v olum e with r egistration ( HiDiver ) with alignment precision better than 50 µm. Throughput is sufficiently high that HiDiver is being used in quantitative studies of the impact of gene variants and aging on mouse brain cytoarchitecture and connectomics.
Keyphrases
- magnetic resonance
- single molecule
- contrast enhanced
- high resolution
- optical coherence tomography
- copy number
- white matter
- diffusion weighted
- high speed
- high throughput
- diffusion weighted imaging
- label free
- magnetic resonance imaging
- deep learning
- transcription factor
- resting state
- electronic health record
- convolutional neural network
- functional connectivity
- computed tomography
- cell therapy
- stem cells
- bone marrow
- case control
- big data
- multiple sclerosis
- cerebral ischemia
- data analysis
- gene expression
- machine learning