From 948a18cc9b8b229f8f5da1f8b1aad93ee1e25b24 Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Wed, 8 Jan 2025 14:39:06 +0100
Subject: [PATCH] Add background correction method
---
1_identify_fibers.py | 31 +++++++++++++++++++++----------
1 file changed, 21 insertions(+), 10 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index 2debeef..6017fda 100755
--- a/1_identify_fibers.py
+++ b/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):
--
GitLab