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correction to workflow for BG removal in segmantation
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ronshnapp committed Oct 23, 2024
1 parent 832073c commit bb38e31
Showing 1 changed file with 11 additions and 1 deletion.
12 changes: 11 additions & 1 deletion example/workflow.py
100644 → 100755
Original file line number Diff line number Diff line change
Expand Up @@ -624,12 +624,22 @@ def calculate_BG_image(dirname, extension):

# segmenting the image if there are more than 1 frames
if N_img is None or N_img>1:

if type(remove_BG)==str:
print('\n','using given background image')
BG = imread(remove_BG)*1.0
elif remove_BG==True:
print('\n','calculating background image')
BG = calculate_BG_image(dirname, ext)
else:
BG=False

loopSegment = loop_segmentation(dirname,
particle_size=p_size,
extension=ext,
image_start=image_start,
N_img=N_img,
remove_ststic_BG=remove_BG,
remove_ststic_BG=BG,
sigma=sigma,
median=median,
threshold=threshold,
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