Optical Coherence Tomography (OCT) is a promising research tool for neuroimaging. However, persistent challenges remain in following a large population of neurons and axonal tracts over time and across the entire depth due to system limitations. Here we introduce a label-free highly stable OCT system configuration and a novel segmentation algorithm that enable a longitudinal study of white matter axonal tracts and neuron cell bodies in a mouse brain, across 0.7 mm depth, in vivo. The system configuration enabled the acquisition of high-resolution images, which reveals thousands of neuron cell bodies across the entire volume and their interactions with multiple white matter axon tracts.
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