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Commit 5147222e authored by Kai Schleicher's avatar Kai Schleicher
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Pass RoiManager to functions

parent 1725ac7f
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......@@ -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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