From 312bc8e763fb35d0043f6dc6b847526de876fbc6 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Fri, 25 Apr 2025 13:40:28 +0200
Subject: [PATCH] Add optional calibration parameter
---
2d_spots_in_fibers.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 18161e8..78054ef 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -227,7 +227,7 @@ def get_threshold_from_method(imp, method):
return threshold_value
-def convert_to_binary(imp, threshold=1, scale_binary=True):
+def convert_to_binary(imp, threshold=1, scale_binary=True, cal=None):
"""Convert grayscale image to a mask / binary image
Parameters
@@ -238,6 +238,8 @@ def convert_to_binary(imp, threshold=1, scale_binary=True):
the threshold above which pixels are considered foreground, by default 1
scale_binary : bool, optional
scale the mask image from 0/255 to 0/1, by default True
+ cal : ImagePlus Calibration, optional
+ apply the calibration if given, by default None
Returns
-------
@@ -257,6 +259,9 @@ def convert_to_binary(imp, threshold=1, scale_binary=True):
IJ.run(mask_imp, "Divide...", "value=255")
IJ.run(mask_imp, "Enhance Contrast", "saturated=0.35")
mask_imp.changes = False
+
+ if cal != None:
+ mask_imp.setCalibration(cal)
return mask_imp
@@ -502,7 +507,7 @@ quality_thresholds = quality_thresholds_string.split(",")
dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu")
-dapi_binary = convert_to_binary(dapi_channel, threshold)
+dapi_binary = convert_to_binary(dapi_channel, threshold, cal=dapi_channel.getCalibration())
# detect spots and count them per fiber
results_table = ResultsTable()
--
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