From 63b610b1b7e968a47b18e61698e75a24a78732f5 Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Thu, 5 Nov 2020 18:16:15 +0100
Subject: [PATCH] fix: fixes a bug, now reports manual threshold
---
1_identify_fibers.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index ad19079..15acdcf 100644
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -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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