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    Create Mask for Axonal Quantification Analysis with FIJI

    Elizabeth Phelan, Oscar Moreno Ramos

    Published: 2023-06-10 DOI: 10.17504/protocols.io.14egn3b9yl5d/v1
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    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.

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