From f4384868d1ba4192700f04aeb55a056b405f1d0a Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Thu, 5 Nov 2020 18:18:48 +0100
Subject: [PATCH] feature: save selected rois, reports manual threshold,
removes unnecessary function
---
2a_central_nuclei_counter.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/2a_central_nuclei_counter.py b/2a_central_nuclei_counter.py
index 122aaf4..a18bdb2 100644
--- a/2a_central_nuclei_counter.py
+++ b/2a_central_nuclei_counter.py
@@ -20,7 +20,6 @@ import os
#@ File (label="Select fiber-ROIs zip-file", style="file") roi_zip
#@ File (label="Select image file", description="select your image") path_to_image
#@ File (label="Select directory for output", style="directory") output_dir
-#@ Boolean (label="close image after processing", description="tick this box when using batch mode", value=False) close_raw
#@ String (visibility=MESSAGE, value="<html><b> shrink ROIs to find nuclei </b></html>") msg3
#@ Float (label="ROI Shrinking factor", value=0.7) shrink
#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
@@ -400,14 +399,15 @@ 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%. TODO check with markus' image
- IJ.log( "nucleus intensity threshold: " + str(min_nucleus_intensity) )
+ min_nucleus_intensity = 0.524 * get_threshold_from_method(raw, nucleus_channel, "Default")[0] # relax he threshold by 50%
+ IJ.log( "automatic intensity threshold detection: True" )
+IJ.log( "nucleus intensity threshold: " + str(min_nucleus_intensity) )
central_nuclei_fibers = select_central_nuclei( raw, nucleus_channel, rm, min_nucleus_intensity )
-save_selected_rois( rm, central_nuclei_fibers, output_dir + "central_nuclei_fiber_rois.zip")
clear_ij_roi_manager(rm)
open_rois_from_zip( rm, input_rois_path )
change_subset_roi_color(rm, central_nuclei_fibers, "yellow")
+save_selected_rois( rm, central_nuclei_fibers, output_dir + "central_nuclei_fiber_rois.zip")
save_all_rois( rm, output_dir + "all_fiber_rois_central_nuclei_color-coded.zip" )
# measure size & shape, add column for pos nuclei and fiber findings, save
@@ -436,6 +436,4 @@ total_execution_time_min = (time.time() - execution_start_time) / 60.0
IJ.log("total time in minutes: " + str(total_execution_time_min))
IJ.log( "~~ all done ~~" )
IJ.selectWindow("Log")
-IJ.saveAs("Text", str(output_dir + raw_image_title + "_centralized_nuclei_Log"))
-if close_raw == True:
- raw.close()
\ No newline at end of file
+IJ.saveAs("Text", str(output_dir + raw_image_title + "_centralized_nuclei_Log"))
\ No newline at end of file
--
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