From 2a8c420f4b7600801c48a838f03955a488f83c30 Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Thu, 19 Nov 2020 16:51:50 +0100
Subject: [PATCH] feature: find_nuclei function uses much more sensitive
threshold method
---
2b_central_nuclei_counter.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/2b_central_nuclei_counter.py b/2b_central_nuclei_counter.py
index 29477e7..0df41e6 100644
--- a/2b_central_nuclei_counter.py
+++ b/2b_central_nuclei_counter.py
@@ -261,7 +261,7 @@ def select_central_nuclei( imp, channel, rm, min_intensity ):
for i, roi in enumerate(all_rois):
imp.setRoi(roi)
stats = imp.getStatistics()
- if stats.stdDev > 250 and stats.max > min_intensity:
+ if stats.max > min_intensity:
selected_rois.append(i)
return selected_rois
@@ -399,7 +399,7 @@ renumber_rois(rm)
save_all_rois( rm, output_dir + "all_fiber_rois_shrunk.zip" )
if min_nucleus_intensity == 0:
- min_nucleus_intensity = 0.524 * get_threshold_from_method(raw, nucleus_channel, "Default")[0] # relax he threshold by 50%
+ min_nucleus_intensity = get_threshold_from_method(raw, nucleus_channel, "Mean")[0]
IJ.log( "automatic intensity threshold detection: True" )
IJ.log( "nucleus intensity threshold: " + str(min_nucleus_intensity) )
--
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