Tested Dual Channel Processing 1 channel contains beads

spim_registration/timelapse/fusion.bsh

@@ -98,8 +98,8 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"imglib2_container=" + imglib2_container_fusion + " " + 
 	"process_views_in_paralell=All " +
 	"interpolation=[" + interpolation + "] " + 
-	//"blend " +
-	//"content-based " +
+	"blend " +
+	"content-based " +
 	"output_file_directory=" + image_file_directory + " " +
 	"lossless " +
 	"imglib2_data_container=[" + imglib2_data_container + "]");

spim_registration/timelapse/tomancak_test_cluster.yaml

@@ -166,7 +166,7 @@ hdf5_output: {
   output_image_file_pattern: 'TP{{t}}_Ch{{c}}_Ill0_Ang0,72,144,216,288.tif',
   output_xml: '"fused_Dual_Channel"',
   output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
-  output_multiple_channels: '"NO (one channel)"',
+  output_multiple_channels: '"YES (one file per channel)"', # "\"YES (one file per channel)\"" or  "\"NO (one channel)\""
   output_timepoints: '0-1',
   output_pixel_distance_x: 0.28590,
   output_pixel_distance_y: 0.28590,