Create Mask for Axonal Quantification Analysis with FIJI
Elizabeth Phelan, Oscar Moreno Ramos
Published: 2023-06-10 DOI: 10.17504/protocols.io.14egn3b9yl5d/v1
Abstract
This is a protocol describing how to create a quantified mask from an image of fluorescence-tagged axonal projections using FIJI/ImageJ software.
Steps
1.
Upload TIFF image of single-channel fluorescent axons to Fiji
2.
Adjust brightness/contrast (keyboard shortcut: ctrl + shift + C)
3.
Select Plugins -> Analyze -> Tubeness
4.
Enter 0.5 for the sigma value
5.
Synchronize windows: select Analyze -> Tools -> Synchronize windows
6.
Open thresholding (shortcut: ctrl + shift + T)
7.
Adjust the thresholding value to your needs
8.
Select apply and create mask.
9.
Save created mask as tiff file.
