From 58b620abada05dc84ef056bb256c4c717d1aa78b Mon Sep 17 00:00:00 2001
From: Laurent Guerard <laurent.guerard@unibas.ch>
Date: Wed, 11 Dec 2024 17:01:55 +0100
Subject: [PATCH] Re add preprocessing
---
1_identify_fibers.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index ee5bc97..bb73a5a 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -694,8 +694,11 @@ IJ.log( "MHC positive fiber channel = " + str(fiber_channel) )
IJ.log( "sub-tiling = " + str(tiling_factor) )
IJ.log( " -- settings used -- ")
-# image (pre)processing and segmentation (-> ROIs)# imp, firstC, lastC, firstZ, lastZ, firstT, lastT
-imp_result = run_tm(raw, membrane_channel, cellpose_dir.getPath(), PretrainedModel.CYTO2, 30.0, area_thresh=[minAr, maxAr], circularity_thresh=[minCir, maxCir],
+# image (pre)processing and segmentation (-> ROIs)# imp, firstC, lastC, firstZ,
+# lastZ, firstT, lastT
+membrane = Duplicator().run(raw, membrane_channel, membrane_channel, 1, 1, 1, 1)
+preprocess_membrane_channel(membrane)
+imp_result = run_tm(membrane, 1, cellpose_dir.getPath(), PretrainedModel.CYTO2, 30.0, area_thresh=[minAr, maxAr], circularity_thresh=[minCir, maxCir],
perimeter_thresh=[minPer, maxPer],
# feret_thresh=[minMinFer, maxMinFer],
)
--
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