An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain.
Harrison MansourRyan AzrakJames J CookKathryn J HornburgYi QiYuqi TianRobert W WilliamsFang-Cheng YehLeonard E WhiteG Allan JohnsonPublished in: bioRxiv : the preprint server for biology (2024)
We have combined MR histology and light sheet microscopy (LSM) of five postmortem C57BL/6J mouse brains in a stereotaxic space based on micro-CT yielding a multimodal 3D atlas with the highest spatial and contrast resolution yet reported. Brains were imaged in situ with multi gradient echo (mGRE) and diffusion tensor imaging (DTI) at 15 μm resolution (∼ 2.4 million times that of clinical MRI). Scalar images derived from the average DTI and mGRE provide unprecedented contrast in 14 complementary 3D volumes, each highlighting distinct histologic features. The same tissues scanned with LSM and registered into the stereotaxic space provide 17 different molecular cell type stains. The common coordinate framework labels (CCFv3) complete the multimodal atlas. The atlas has been used to correct distortions in the Allen Brain Atlas and harmonize it with Franklin Paxinos. It provides a unique resource for stereotaxic labeling of mouse brain images from many sources.
Keyphrases
- contrast enhanced
- single cell
- single molecule
- magnetic resonance
- diffusion weighted
- magnetic resonance imaging
- optical coherence tomography
- computed tomography
- diffusion weighted imaging
- high throughput
- white matter
- high resolution
- deep learning
- high speed
- convolutional neural network
- pain management
- gene expression
- dual energy
- drinking water
- machine learning
- blood brain barrier
- cerebral ischemia
- subarachnoid hemorrhage