Jun 10, 2023

Create Mask for Axonal Quantification Analysis with FIJI

DOI
https://dx.doi.org/10.17504/protocols.io.14egn3b9yl5d/v1
  • 1Northwestern University
Elizabeth Phelan
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DOI: https://dx.doi.org/10.17504/protocols.io.14egn3b9yl5d/v1
Protocol Citation: Oscar Moreno Ramos, Elizabeth P. 2023. Create Mask for Axonal Quantification Analysis with FIJI. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn3b9yl5d/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: June 10, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 83151
Keywords: ASAPCRN, mask for axonal quantification analysis, quantified mask from an image, quantified mask, axonal quantification analysis, axonal projection, tagged axonal projection, using fiji, mask, fluorescence, fiji, imagej software
Abstract
This is a protocol describing how to create a quantified mask from an image of fluorescence-tagged axonal projections using FIJI/ImageJ software.
Upload TIFF image of single-channel fluorescent axons to Fiji
Adjust brightness/contrast (keyboard shortcut: ctrl + shift + C)
Select Plugins -> Analyze -> Tubeness
Enter 0.5 for the sigma value
Synchronize windows: select Analyze -> Tools -> Synchronize windows
Open thresholding (shortcut: ctrl + shift + T)
Adjust the thresholding value to your needs
Select apply and create mask.
Save created mask as tiff file.