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    16Jul

    How to quantify astrocytes: example macro

    by Elazadeh,  0 Comments

    GFAP, a class-III intermediate filament, is a 50kDa protein which is found in the mature and developing astrocytes in the CNS, non-myelinating Schwann cells in the PNS, enteric glial cells (enteric nervous system/ENS), ependymal cells, and radial glia of the developing brain. GFAP antibodies are the most popular marker for astrocytes in neurological studies and along with its breakdown products (BDPs), GFAP has been proposed as a useful candidates for biofluid-based markers for numerous neurological conditions especially during traumatic brain/spinal cord injury and stroke.

    Use the following macro code in FIJI/ImageJ to quantify the number of GFAP+ cells 

    • run(“Subtract Background…”, “rolling=50 light”);

      run(“Unsharp Mask…”, “radius=100 mask=0.60”);

      run(“Gaussian Blur…”, “sigma=4”);

      run(“Unsharp Mask…”, “radius=100 mask=0.60”);

      run(“Gaussian Blur…”, “sigma=6”);

      run(“Subtract Background…”, “rolling=50 light”);

      //run(“Brightness/Contrast…”);

      setMinAndMax(63, 191);

      setMinAndMax(63, 191);

      run(“Unsharp Mask…”, “radius=100 mask=0.60”);

      setMinAndMax(36, 194);

      setMinAndMax(36, 194);

      run(“Unsharp Mask…”, “radius=100 mask=0.60”);

      run(“8-bit”);

      setAutoThreshold(“Default”);

      //run(“Threshold…”);

      //setThreshold(0, 152);

      setOption(“BlackBackground”, false);

      run(“Convert to Mask”);

      run(“Fill Holes”);

      run(“Options…”, “iterations=10 count=1 do=Close”);

      run(“Fill Holes”);

      run(“Analyze Particles…”, “size=527-Infinity circularity=0.20-1.00 show=Outlines display exclude include summarize”);FIJI

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