Jan 22, 2025

Public workspaceImaging and Quantification for ST

DOI
dx.doi.org/10.17504/protocols.io.rm7vzk2k8vx1/v1
  • Tony Hsiao1,2,
  • Anahid Ansari Mahabadian1,2,
  • YuHong Fu1,2,
  • Glenda Halliday1,2
  • 1Brain and Mind Centre & Faculty of Medicine and Health School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia;
  • 2Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
Tony Hsiao
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DOI: dx.doi.org/10.17504/protocols.io.rm7vzk2k8vx1/v1
Protocol Citation: Tony Hsiao, Anahid Ansari Mahabadian, YuHong Fu, Glenda Halliday 2025. Imaging and Quantification for ST. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzk2k8vx1/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 22, 2025
Last Modified: January 22, 2025
Protocol Integer ID: 118850
Keywords: ASAPCRN
Abstract
Protocol for Imaging, Cropping and Quantification in Striatum
Imaging
Imaging
Images scanned with Olympus VS200 (mode: projection intensity accumulation)​
Sections viewed on OLYMPUS OlyVIA (3.4.1)​
Quantification (QuPath ver 0.4.3)
Quantification (QuPath ver 0.4.3)
Images are cropped for sections following the Bregma range (0.98mm – 0.74mm)
Channels are renamed based on their antibody (DAPI, TH, mCherry, αSyn)
Annotations are categorized in 4 quadrants for each side of Striatum as DL, DM, VL, VM.

Quadrants are annotated surrounding TH+ cells clusters and including the accumbens nucleus core landmark.
Two circular annotations of consistent size in cortical region of each section are created for background intensity values. (Neg1 and Neg2)
Intensity measures
Intensity measures
Compute intensity feature was used with the following parameters:
a. Channels: TH/mCherry/αSyn
b. Preferred pixel size: 2µm
c. Tile diameter for ROI: 25µm
d. Area: X µm2 (depending on the size of the annotation)
e. Perimeter: X µm (depending on the size of the annotation)
f. Mean intensity: 2.00 µm per pixel: (TH/ mCherry / αSyn)
Export measurement
Export measurement
‘Annotation measurement’ results of each image are then exported to excel and arranged accordingly.