From 84fad588aa282ce7864d573d0bb56b38571aa057 Mon Sep 17 00:00:00 2001
From: "kai.schleicher@unibas.ch" <kai.schleicher@unibas.ch>
Date: Mon, 12 Oct 2020 17:39:02 +0200
Subject: [PATCH] feature: accepts any roi-set and only searches for central
nuclei
---
myosoft-imcf_central_nuclei_counter.py | 73 +++-----------------------
1 file changed, 6 insertions(+), 67 deletions(-)
diff --git a/myosoft-imcf_central_nuclei_counter.py b/myosoft-imcf_central_nuclei_counter.py
index 9b5bfcf..19f8f85 100644
--- a/myosoft-imcf_central_nuclei_counter.py
+++ b/myosoft-imcf_central_nuclei_counter.py
@@ -24,9 +24,7 @@ import os
#@ Float (label="ROI Shrinking factor", value=0.7) shrink
#@ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
#@ Integer (label="Nucleus staining channel number", style="slider", min=1, max=5, value=3) nucleus_channel
-#@ Integer (label="Fiber staining (MHC) channel number", style="slider", min=1, max=5, value=3) fiber_channel
#@ Integer (label="minimum nucleus intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_nucleus_intensity
-#@ Integer (label="minimum fiber intensity (0=auto)", description="0 = automatic threshold detection", value=0) min_fiber_intensity
#@ ResultsTable rt
#@ RoiManager rm
@@ -157,22 +155,6 @@ def measure_in_all_rois( imp, channel, rm ):
rm.runCommand(imp,"Measure")
-def change_all_roi_color( rm, color ):
- """change the color of all ROIs in the RoiManager
-
- Parameters
- ----------
- rm : RoiManager
- a reference of the IJ-RoiManager
- color : string
- the desired color. e.g. "green", "red", "yellow", "magenta" ...
- """
- number_of_rois = rm.getCount()
- for roi in range( number_of_rois ):
- rm.select(roi)
- rm.runCommand("Set Color", color)
-
-
def change_subset_roi_color( rm, selected_rois, color ):
"""change the color of selected ROIs in the RoiManager
@@ -285,38 +267,6 @@ def select_central_nuclei( imp, channel, rm, min_intensity ):
return selected_rois
-def select_positive_fibers( imp, channel, rm, min_intensity ):
- """For all ROIs in the RoiManager, select ROIs based on intensity measurement in given channel of imp.
- See https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html
-
- Parameters
- ----------
- imp : ImagePlus
- the imp on which to measure
- channel : integer
- the channel on which to measure. starts at 1
- rm : RoiManager
- a reference of the IJ-RoiManager
- min_intensity : integer
- the selection criterion (here: intensity threshold)
-
- Returns
- -------
- array
- a selection of ROIs which passed the selection criterion (are above the threshold)
- """
- imp.setC(channel)
- all_rois = rm.getRoisAsArray()
- selected_rois = []
- for i, roi in enumerate(all_rois):
- imp.setRoi(roi)
- stats = imp.getStatistics()
- if stats.mean > min_intensity:
- selected_rois.append(i)
-
- return selected_rois
-
-
def open_rois_from_zip( rm, path ):
"""open RoiManager ROIs from zip and adds them to the RoiManager
@@ -423,10 +373,12 @@ raw_image_title = fix_BF_czi_imagetitle(raw)
# take care of paths and directories
output_dir = os.path.dirname(str(roi_zip))
+input_roi_zip = os.path.basename(str(roi_zip))
output_dir = fix_ij_dirs(output_dir)
+input_rois_path = output_dir + input_roi_zip
# open ROIS and show on image
-open_rois_from_zip( rm, output_dir + "all_fiber_rois.zip" )
+open_rois_from_zip( rm, input_rois_path )
show_all_rois_on_image( rm, raw )
# update the log for the user
@@ -435,17 +387,9 @@ if raw_image_calibration.scaled() == False:
IJ.log("Your image is not spatially calibrated! Size measurements are only possible in [px].")
IJ.log( " -- settings used -- ")
IJ.log( "ROI Shrinking factor = " + str(shrink) )
-IJ.log( "Selected fiber-ROIs zip-file = " + str(roi_zip) )
+IJ.log( "Selected fiber-ROIs zip-file = " + str(input_rois_path) )
IJ.log( " -- settings used -- ")
-# check for positive fibers
-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) )
-
-positive_fibers = select_positive_fibers( raw, fiber_channel, rm, min_fiber_intensity )
-save_selected_rois( rm, positive_fibers, output_dir + "mhc_positive_fiber_rois.zip")
-
# shrink ROIs and look for nuclei
rm.hide()
raw.hide()
@@ -460,19 +404,14 @@ if min_nucleus_intensity == 0:
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, output_dir + "all_fiber_rois.zip" )
-change_all_roi_color(rm, "blue")
-positive_fibers_with_central_nucleus = list( set(positive_fibers).intersection(central_nuclei_fibers) )
-change_subset_roi_color(rm, positive_fibers, "magenta")
-change_subset_roi_color(rm, positive_fibers_with_central_nucleus, "yellow")
+open_rois_from_zip( rm, input_rois_path )
+change_subset_roi_color(rm, central_nuclei_fibers, "yellow")
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
IJ.run("Set Measurements...", "area perimeter shape feret's redirect=None decimal=4")
IJ.run("Clear Results", "")
measure_in_all_rois( raw, nucleus_channel, rm )
-preset_results_column( rt, "MHC Positive Fibers (magenta)", "NO" )
-add_results( rt, "MHC Positive Fibers (magenta)", positive_fibers, "YES")
preset_results_column( rt, "Centralized Nuclei (yellow)" , "NO" )
add_results( rt, "Centralized Nuclei (yellow)", central_nuclei_fibers, "YES")
rt.save(output_dir + "centralized_nuclei_results.csv")
--
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