Add optional calibration parameter

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()