From 5147222ec3466788869a32d38d066a417f6ac7a5 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Wed, 16 Apr 2025 14:07:59 +0200
Subject: [PATCH] Pass RoiManager to functions
---
2d_spots_in_fibers.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 34332f1..4e0a816 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -456,12 +456,12 @@ for index, channel in enumerate(processing_channels):
quality_threshold = float(quality_thresholds[index])
spots_channel = BFopen_image(path_to_image, channel, series_number)
spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
- save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+ save_labelimage_as_ijroiset(spots_label_imp, rm, filename, "spots_ch" + str(channel), parent_dir)
spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")
dapi_negative_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_positive_spots_binary, "Subtract create")
- load_rois_from_zip(fiber_segmentation_roiset)
+ load_rois_from_zip(fiber_segmentation_roiset, rm)
fiber_label_IDs, n_spots_per_fiber = measure_intensity_sum(spots_binary_imp, rm)
_, n_dapi_positive_spots_per_fiber = measure_intensity_sum(dapi_positive_spots_binary, rm)
_, n_dapi_negative_spots_per_fiber = measure_intensity_sum(dapi_negative_spots_binary, rm)
--
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