Index: trunk/ppStack/src/ppStackMatch.c
===================================================================
--- trunk/ppStack/src/ppStackMatch.c	(revision 18100)
+++ trunk/ppStack/src/ppStackMatch.c	(revision 18183)
@@ -126,4 +126,17 @@
         psFree(optWidths);
 
+        // Set the variance factor
+        float vfNew = psMetadataLookupF32(NULL, output->analysis, PM_SUBTRACTION_ANALYSIS_VARFACTOR);
+        float vfOld = psMetadataLookupF32(NULL, readout->concepts, "CELL.VARFACTOR");
+        if (isfinite(vfOld)) {
+            vfNew *= vfOld;
+        }
+        psMetadataItem *vfItem = psMetadataLookup(output->parent->concepts, "CELL.VARFACTOR");
+        if (!isfinite(vfItem->data.F32)) {
+            vfItem->data.F32 *= vfNew;
+        } else {
+            vfItem->data.F32 = vfNew;
+        }
+
         // Replace original images with convolved
         psFree(readout->image);