diff --git a/2b_central_nuclei_counter.py b/2b_central_nuclei_counter.py index 29477e7cb54aaaa85d757032465be61abdf797ba..0df41e67cb7c59119be9c2bc7d1095925035184e 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) )