We study mice and rats to model human disease, using magnetic resonance imaging (MRI, in vivo and ex vivo), to characterize changes in neuroanatomy, microstructure and function due to disease. Images of exquisite anatomical detail in 2D/3D formats can be obtained, particularly when performed ex vivo as resolutions in vivo will always be hampered by ethical considerations.

We use the definitive histopathology-based neuroanatomical atlases for mice and rats (Paxinos et al., 2012) to identify brain regions where changes have been detected by MRI. Sophisticated software to register study MRI data to an imaging atlas (created by registering to Paxino et al atlases) are available but difficult to use, without familiarity in programing languages and specialized MRI analysis software as well as neuroanatomy. Inevitably, we resort to manually registering MRI data to the Paxinos et al atlases; this is still difficult as MRI contrasts are insufficient to accurately delineate distinct anatomi...
We study mice and rats to model human disease, using magnetic resonance imaging (MRI, in vivo and ex vivo), to characterize changes in neuroanatomy, microstructure and function due to disease. Images of exquisite anatomical detail in 2D/3D formats can be obtained, particularly when performed ex vivo as resolutions in vivo will always be hampered by ethical considerations.

We use the definitive histopathology-based neuroanatomical atlases for mice and rats (Paxinos et al., 2012) to identify brain regions where changes have been detected by MRI. Sophisticated software to register study MRI data to an imaging atlas (created by registering to Paxino et al atlases) are available but difficult to use, without familiarity in programing languages and specialized MRI analysis software as well as neuroanatomy. Inevitably, we resort to manually registering MRI data to the Paxinos et al atlases; this is still difficult as MRI contrasts are insufficient to accurately delineate distinct anatomical regions, and even more challenging for in vivo data, often obtained at much lower resolutions. Currently, we are identifying regions of interest (ROIs) and quantifying whole and regional brain volumes and relating changes to iron homeostasis to ascertain the role of iron in ageing and neurodegeneration. We are accurately manually registering already collected 2D mouse MRI anatomical data to the Paxinos et al mouse atlas (collaboration between anatomist, Ms Chen, and MRI scientist, Dr So). We may also collect additional MRI data ex vivo and in vivo at various resolutions and/or in 3D mode to aid registration. We will learn the relationship between MRI anatomical images and established anatomical atlases and start to compile a ‘handbook’ towards publication. Good understanding of neuroanatomy and MRI is crucial for accurate matching of the Paxinos mouse atlas to MRI anatomical data. The ‘handbook’ aims to teach/assist registration of study MRI data for selection of ROIs and delineation of regional brain volumes.
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xinwei chen
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xinwei chen CEO MSc Neuroimaging student at King's College London