--- a/vpt_segment.xml	Sun May 11 12:02:47 2025 +0000
+++ b/vpt_segment.xml	Mon May 26 06:54:28 2025 +0000
@@ -82,9 +82,9 @@
         "all_z_indexes": [$indices],
         "z_positions_um": [$vpt_config.experiment_properties.z_positions_um]
     },
-    #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
-    #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
     "segmentation_tasks": [
+        #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
+        #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
         {
         "task_id": $i,
         "segmentation_family": "Cellpose2",
@@ -196,11 +196,11 @@
             "smoothing_radius": $task.polygon_parameters.smoothing_radius,
             "minimum_final_area": $task.polygon_parameters.minimum_final_area
         }
-        }
-    ]#if $j != $task_n
-    ,
-    #end if
-    #end for
+        }#if $i != $task_n
+        ,
+        #end if
+        #end for
+    ],
     "segmentation_task_fusion": {
         "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
         "fused_polygon_postprocessing_parameters": {
@@ -248,7 +248,7 @@
                         <option value="nucleus">nucleus</option>
                         <option value="both">both</option>
                     </param>
-                    <param argument="--z_layers" type="text" value="" optional="true" label="Comma-separated list of z-index images to segment." help="2D segmentation is applied to all z-layers in the experiment by default without needing to explicitly specify the behavior.">
+                    <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
                         <expand macro="sanitize_digits"/>
                     </param>
                     <section name="segmentation_properties" title="Segmentation properties">
@@ -728,8 +728,8 @@
                 <element name="metrics">
                     <assert_contents>
                         <has_text_matching expression=",Cell count,Cell volume"/>
-                        <has_text_matching expression="All cells,618,1026.0,1005.3,649.1,621.0,94.2,106.0,64.6,33.8,0.0"/>
-                        <has_text_matching expression="Cells after filtering,563,1061.2,1025.9,710.8,666.0,102.3,107.0,64.4,31.8,0.03"/>
+                        <has_text_matching expression="All cells,811,1588.0,1549.9,740.5,669.0,92.2,109.0,96.7,68.6,0.0"/>
+                        <has_text_matching expression="Cells after filtering,698,1711.6,1705.9,856.1,817.5,104.6,111.0,96.2,63.7,0.06"/>
                     </assert_contents>
                 </element>
                 <element name="sum_signals">
@@ -755,8 +755,8 @@
             <output name="vpt_qc">
                 <assert_contents>
                     <has_text text="VPT Segmentation Report (cyto2_2task)"/>
-                    <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;618&lt;/b&gt;&lt;/p&gt;"/>
-                    <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;621.0&lt;/b&gt;&lt;/p&gt;"/>
+                    <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
+                    <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
                 </assert_contents>
             </output>
             <output_collection name="vpt_config_out" type="list">