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Commit 63b610b1 authored by Kai Schleicher's avatar Kai Schleicher
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fix: fixes a bug, now reports manual threshold

parent ed6b58fa
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......@@ -554,8 +554,9 @@ save_all_rois( rm, output_dir + "all_fiber_rois.zip" )
if fiber_channel > 0:
if min_fiber_intensity == 0:
min_fiber_intensity = get_threshold_from_method(raw, fiber_channel, "Mean")[0]
IJ.log( "fiber intensity threshold: " + str(min_fiber_intensity) )
IJ.log( "automatic intensity threshold detection: True" )
IJ.log( "fiber intensity threshold: " + str(min_fiber_intensity) )
change_all_roi_color(rm, "blue")
positive_fibers = select_positive_fibers( raw, fiber_channel, rm, min_fiber_intensity )
change_subset_roi_color(rm, positive_fibers, "magenta")
......
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