Neuromelanin-positive Neuron Density in Substantia Nigra Image Analysis
Hemanth Ramesh Nelvagal, Toby J Curless, Zane Jaunmuktane
Abstract
The protocol covers the steps to measure neuromelanin-positive neuron density in substantia nigra using image analysis tools including NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer, Cellpose and QuPath.
Steps
Annotation and Deconvolution
Manually annotate the substantia nigra on NZConnect (Hamamatsu), a web-based whole-slide image (WSI) viewer.
Download the annotations using a Python script, and then import into QuPath [1] using a Groovy script
Segmentation and Calculating Neuromelanin-positive Cell Density
Segment neuromelanin cells using Cellpose [2,3] via the QuPath Cellpose extension [4], followed by an object classifier to filter out non-specific detections.
Calculate neuromelanin-positive cell density by the number of neuromelanin-positive cells divided by the area of the region of interest (neuromelanin-positive cells per mm^2).
