Add background correction method

1_identify_fibers.py

@@ -107,20 +107,31 @@ def fix_BF_czi_imagetitle(imp):
     return image_title
 
 
-def preprocess_membrane_channel(imp):
-    """apply myosoft pre-processing steps for the membrane channel
+def do_background_correction(imp, gaussian_radius=20):
+    """Perform background correction on an image.
+
+    This is done by applying a Gaussian blur to the image and then dividing the
+    original image by the blurred image.
 
     Parameters
     ----------
-    imp : ImagePlus
-        a single channel image of the membrane staining
+    imp : ij.ImagePlus
+        The image to be corrected.
+    gaussian_radius : int
+        The radius of the Gaussian filter to be used. Default value is 20.
+
+    Returns
+    -------
+    ij.ImagePlus
+        The background-corrected image.
     """
-    IJ.run(imp, "Enhance Contrast", "saturated=0.35")
-    IJ.run(imp, "Apply LUT", "")
-    IJ.run(imp, "Enhance Contrast", "saturated=1")
-    IJ.run(imp, "8-bit", "")
-    IJ.run(imp, "Invert", "")
-    IJ.run(imp, "Convolve...", "text1=[-1.0 -1.0 -1.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 0\n-1.0 -1.0 24.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 -1.0\n-1.0 -1.0 -1.0 -1.0 0] normalize")
+    imp_bgd = imp.duplicate()
+    IJ.run(
+        imp_bgd,
+        "Gaussian Blur...",
+        "sigma=" + str(gaussian_radius) + " scaled",
+    )
+    return ImageCalculator.run(imp, imp_bgd, "Divide create 32-bit")
 
 
 def get_threshold_from_method(imp, channel, method):