diff --git a/rugnux/Rugnux.cpp b/rugnux/Rugnux.cpp
index 172a6d76..3d4c4bce 100644
--- a/rugnux/Rugnux.cpp
+++ b/rugnux/Rugnux.cpp
@@ -1008,8 +1008,13 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
                             merge_engine.ErrorModelB(),
                             merge_engine.ErrorModelB() > 0 ? 1.0 / merge_engine.ErrorModelB() : 0.0,
                             merge_engine.ErrorModelChi2());
+            // Merge-consistency filter: on floods with many spurious lattices (e.g. XFEL large cells)
+            // most indexed crystals do not correlate with the true structure; --min-image-cc drops the
+            // crystals whose per-image CC to the reference is below the limit, so the merge keeps only
+            // the coherent (real) ones.
+            const bool cc_filter = !for_search && experiment_.GetScalingSettings().GetMinCCForImage() > 0.0;
             for (size_t i = 0; i < merge_input.size(); ++i)
-                merge_engine.AddImage(merge_input[i], static_cast<int64_t>(i));
+                merge_engine.AddImage(merge_input[i], static_cast<int64_t>(i), cc_filter);
 
             ScaleMergeResult out;
             out.merged = merge_engine.ExportReflections();