Skip to content
Snippets Groups Projects
Commit 84fad588 authored by Kai Schleicher's avatar Kai Schleicher
Browse files

feature: accepts any roi-set and only searches for central nuclei

parent 8ca6ed3a
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
myosoft-imcf_central_nuclei_counter.py
+ 6
− 67
View file @ 84fad588
......@@ -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")
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment