atlas-rat

atlas-rat constructs a detailed atlas of the rat spinal cord by quantifying axon morphometry and white matter microstructure.

Key Features:

• Comprehensive Morphometric Data: Extracts axon diameter, axonal density, and g-ratio from full-slice scanning electron microscopy images.
• Segmentation Algorithms: Applies advanced segmentation and image-processing algorithms to delineate axonal and myelin structures in electron microscopy images.
• 4D NIfTI Volume Output: Produces a 4-dimensional NIfTI volume encoding morphometric data across spinal levels C1-C8, T1-T13, L1-L6, and S1-S4, with each slice corresponding to a specific spinal level.
• Atlas Registration: Aligns the generated atlas to the Watson spinal cord white matter atlas via registration procedures.
• Statistical Analysis: Computes statistics across metrics, spinal levels, and tracts to quantify variations in axon diameter and g-ratio.

Scientific Applications:

• Neurological Disease Research: Enables analysis of white matter microstructure to investigate pathophysiological changes in neurological disorders.
• Comparative Studies: Supports comparison of morphometric metrics across animal models or experimental conditions.

Methodology:

Processes full-slice scanning electron microscopy images with segmentation and image-processing algorithms to extract axon diameter, axonal density, and g-ratio; assembles these metrics into 4D NIfTI volumes across specified spinal levels; registers volumes to the Watson spinal cord white matter atlas; and computes statistics across metrics, spinal levels, and tracts.