Tested Dual Channel Pipeline one channel contains beads

spim_registration/timelapse/Snakefile

@@ -7,9 +7,9 @@ if JOBDIR[-1] != "/": # this checks if jobdir ends with slash if not it adds a s
    JOBDIR+="/"
 
 # Test config file single Channel:
-configfile: "single_test.yaml"
+# configfile: "single_test.yaml"
 # Test config file dual channel one channel contains beads:
-# configfile: "dual_OneChannel.yaml"
+configfile: "dual_OneChannel.yaml"
 
 # data specific config file, expected to be inside JOBDIR
 # configfile: "tomancak_test_cluster.yaml"
@@ -266,8 +266,8 @@ rule timelapse:
 
 rule duplicate_transformations:
     input: rules.timelapse.output, merged_xml="{xml_base}_merge.xml"
-    output: rules.timelapse.output[0] + "_dublicate"
-    log: "{xml_base}_dublicate_transformations.log"
+    output: rules.timelapse.output[0] + "_duplicate"
+    log: "{xml_base}_duplicate_transformations.log"
     run:
         cmd_string = produce_string(
         	"""{fiji-prefix} {fiji-app} \

spim_registration/timelapse/cluster.json

@@ -27,7 +27,7 @@
 
     "fusion" : 
     {
-        "lsf_extra" : "-n 7 -R \"span[hosts=1] rusage[mem=100000]\""
+        "lsf_extra" : "-n 12 -R \"span[hosts=1] rusage[mem=100000]\""
     },
 
     "deconvolution" :

spim_registration/timelapse/dual_OneChannel.yaml

@@ -29,7 +29,7 @@ common: {
   # Switches between content based fusion and deconvoltion
   # "deconvolution" > for deconvolution
   # "fusion" > for content based fusion
-  fusion_switch: "deconvolution"
+  fusion_switch: "fusion"
   }
 
 define_xml_czi: {

spim_registration/timelapse/fusion.bsh

@@ -98,7 +98,7 @@ IJ.run("Fuse/Deconvolve Dataset",
 	"imglib2_container=" + imglib2_container_fusion + " " + 
 	"process_views_in_paralell=All " +
 	"interpolation=[" + interpolation + "] " + 
-	//"blend " +
+	"blend " +
 	"content-based " +
 	"output_file_directory=" + image_file_directory + " " +
 	"lossless " +

spim_registration/timelapse/single_test.yaml

@@ -229,8 +229,8 @@ hdf5_output: {
   output_multiple_channels: '"NO (one channel)"', # '"YES (one file per channel)"' or  '"NO (one channel)"'
   output_channels: "green",
   # .xml file names
-  output_xml: '"fused_Dual_Channel"',
-  output_hdf5_xml: '"hdf5_fused_Dual_Channel"',
+  output_xml: '"fused_Single"',
+  output_hdf5_xml: '"hdf5_fused_Single"',
   output_timepoints: '0-1', # Timepoints format: '1-2'
   # pixel size of output: take downsampling into account!
   output_pixel_distance_x: 0.28590106964,