From 9a094bcc63e6ef72096c4269550d2c97ae6cc9cf Mon Sep 17 00:00:00 2001
From: schlda00 <kai.schleicher@unibas.ch>
Date: Mon, 14 Apr 2025 17:18:48 +0200
Subject: [PATCH] Don't use z-slice option, input is a MIP
---
2d_spots_in_fibers.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 53df4a2..41ca9e4 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -765,7 +765,7 @@ 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)
+dapi_channel = BFopen_image(path_to_image, dapi_channel_number, series_number)
if threshold <= 0:
threshold = get_threshold_from_method(dapi_channel, "otsu")
dapi_binary = convert_to_binary(dapi_channel, threshold)
--
GitLab