Cross-modal coherent registration of whole mouse brains.
Lei QuYuanyuan LiPeng XieLijuan LiuYimin WangJun WuYu LiuTao WangLongfei LiKaixuan GuoWan WanLei OuyangFeng XiongAnna C KolstadZhuhao WuFang XuYefeng ZhengHui GongQingming LuoGuoqiang BiHongwei DongMichael J HawrylyczHongkui ZengHanchuan PengPublished in: Nature methods (2021)
Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types.
Keyphrases
- high resolution
- single cell
- resting state
- white matter
- magnetic resonance imaging
- deep learning
- functional connectivity
- cerebral ischemia
- single molecule
- rna seq
- optical coherence tomography
- computed tomography
- convolutional neural network
- high throughput
- neural network
- stem cells
- magnetic resonance
- machine learning
- mass spectrometry
- bone marrow
- cell therapy
- mesenchymal stem cells
- multiple sclerosis
- subarachnoid hemorrhage
- molecularly imprinted
- image quality
- fluorescence imaging
- liquid chromatography
- simultaneous determination