From f6b804c8a44a8a797da9cade12b284bb5635b220 Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:17:16 +0200
Subject: [PATCH] Create Labelimage from ij roiset

---
 2d_spots_in_fibers.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 08f87b6..53df4a2 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -757,7 +757,12 @@ processing_channels = processing_channels_string.split(",")
 quality_thresholds_string = quality_thresholds_string.replace(" ", "")
 quality_thresholds = quality_thresholds_string.split(",")
 
-# TODO: Get the fiber segmentation and convert to labelimage
+# Get the fiber segmentation and convert to labelimage
+canvas = create_empty_image(32, image_width, image_height)
+load_rois_from_zip(fiber_segmentation_roiset)
+fiber_label_imp = convert_rois_to_labelimage(canvas)
+canvas.close()
+fiber_label_imp.show()
 
 # threshold DAPI channel and convert to binary
 dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number, z_slice_number=dapi_channel_zslice)
-- 
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