diff --git a/out/artifacts/TCellSim_jar/TCellSim.jar b/out/artifacts/TCellSim_jar/TCellSim.jar
index 705ce0a..f9716d7 100644
Binary files a/out/artifacts/TCellSim_jar/TCellSim.jar and b/out/artifacts/TCellSim_jar/TCellSim.jar differ
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index c3b83c8..81a2e02 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -196,12 +196,12 @@ public class Simulator {
 
         //Filter by overlap size
         if(verbose){System.out.println("Eliminating edges with weights much less than occupancy values");}
-        filterByOverlapSize(graph, alphaWellCounts, betaWellCounts);
+        filterByOverlapSize(graph, alphaWellCounts, betaWellCounts, plateVtoAMap, plateVtoBMap);
         if(verbose){System.out.println("Edges with weights much less than occupancy values set to 0.0");}
 
         //Filter by relative occupancy
         if(verbose){System.out.println("Eliminating edges between vertices of massively different occupancy");}
-        filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts);
+        filterByRelativeOccupancy(graph, alphaWellCounts, betaWellCounts, plateVtoAMap, plateVtoBMap);
         if(verbose){System.out.println("Edges between vertices of massively different occupancy set to 0.0");}
 
 
@@ -679,10 +679,12 @@ public class Simulator {
     //Remove edges for pairs with large occupancy discrepancy
     private static void filterByRelativeOccupancy(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
                                                   Map<Integer, Integer> alphaWellCounts,
-                                                  Map<Integer, Integer> betaWellCounts) {
+                                                  Map<Integer, Integer> betaWellCounts,
+                                                  Map<Integer, Integer> plateVtoAMap,
+                                                  Map<Integer, Integer> plateVtoBMap) {
         for (DefaultWeightedEdge e : graph.edgeSet()) {
-            Integer alphaOcc = alphaWellCounts.get(graph.getEdgeSource(e));
-            Integer betaOcc = betaWellCounts.get(graph.getEdgeTarget(e));
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
             //Adjust this to something cleverer later
             if (Math.abs(alphaOcc - betaOcc) >= 20) {
                 graph.setEdgeWeight(e, 0.0);
@@ -693,10 +695,12 @@ public class Simulator {
     //Remove edges for pairs where overlap size is significantly lower than the well occupancy
     private static void filterByOverlapSize(SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph,
                                             Map<Integer, Integer> alphaWellCounts,
-                                            Map<Integer, Integer> betaWellCounts) {
+                                            Map<Integer, Integer> betaWellCounts,
+                                            Map<Integer, Integer> plateVtoAMap,
+                                            Map<Integer, Integer> plateVtoBMap) {
         for (DefaultWeightedEdge e : graph.edgeSet()) {
-            Integer alphaOcc = alphaWellCounts.get(graph.getEdgeSource(e));
-            Integer betaOcc = betaWellCounts.get(graph.getEdgeTarget(e));
+            Integer alphaOcc = alphaWellCounts.get(plateVtoAMap.get(graph.getEdgeSource(e)));
+            Integer betaOcc = betaWellCounts.get(plateVtoBMap.get(graph.getEdgeTarget(e)));
             //Adjust this to something cleverer later
             Integer min = alphaOcc > betaOcc ? betaOcc : alphaOcc;
             if (min - graph.getEdgeWeight(e) >= 15) {