Re add preprocessing

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],
     )