Enhanced ex vivo 3D whole-brain mapping and automated analysis of Parkinson's disease pathologies in mice
The spatiotemporal relationships among -synuclein inclusion formation, dopaminergic degeneration, and white matter microstructural changes remain poorly defined. To address this, we unilaterally injected preformed fibrils (PFFs) or monomeric -synuclein into the substantia nigra pars compacta (SNc) of wild-type mice. At 12 and 20 weeks post-injection (wpi), we performed ex vivo magnetic resonance imaging (MRI) at 9.4T to assess microstructural, volumetric and paramagnetic changes, along with light-sheet microscopy (LSM) to map -synuclein aggregates, and dopaminergic neuron at single-cell resolution across the whole brain. We developed a Python-based, automated registration pipeline that achieves <40 {micro}m alignment error between ex vivo MRI and LSM and computes clearing-induced distortion, enabling scalable deformation analysis and multimodal multiscale data integration. Unilateral SNc injection of -syn PFFs induced dense phospho--syn pathology in the ipsilateral SNc at 12 wpi, which decreased by 20 wpi in parallel with the loss of tyrosine hydroxylase-positive dopaminergic neuron. Pathogenic -synuclein spreads along with dopaminergic denervation in the nigrostriatal pathway to the ipsilateral striatum and contralateral SNc. Our ex vivo MRI-LSM platform provides a scalable, open-source framework for understanding circuit-level and whole-brain propagation of pathology in an -synucleinopathy model and beyond. HighlightsO_LIOpen-source, automated pipeline aligns ex vivo 9.4T MRI with light-sheet microscopy (LSM) at <40 {micro}m error, quantifies clearing-induced tissue distortion, and enables multiscale, whole-brain multimodal analysis. C_LIO_LIWhole-brain, single-cell-resolution mapping of -synuclein pathology and dopaminergic neuron loss in an -synucleinopathy mouse model using an optimized iDISCO+ protocol that achieves uniform antibody penetration even in dense regions like the striatum. C_LIO_LIUnilateral SNc injection of -syn PFFs drives spread of p--syn pathology along the nigrostriatal pathway to the ipsilateral striatum, BST, CEA, and contralateral SNc, along with dopaminergic degeneration. C_LIO_LIIpsilateral SNc shows high pS129 pathology at 12 weeks post-injection but significant reduction by 20 wpi, concurrent with loss of tyrosine hydroxylase-positive neurons. C_LIO_LIMultiparametric MRI reveals microstructural and iron-related alterations in striatum, SNc, and VTA, with cross-modal correlations linking pS129 burden, TH loss, and magnetic susceptibility changes. C_LI