diff --git a/src/geomtools/sfx/optimiser.py b/src/geomtools/sfx/optimiser.py
index a6cb6e8bdb9e4830a658eb15e16be6f58d553f4d..adc9c961887a2646b8b7aa70bbef05c8488a3d97 100644
--- a/src/geomtools/sfx/optimiser.py
+++ b/src/geomtools/sfx/optimiser.py
@@ -21,6 +21,8 @@ def refine():
                         help="Collection of rigid groups to pose")
     parser.add_argument('-m', '--min-counts', type=int, default=50,
                         help="Minimum counts per group")
+    parser.add_argument('--snr', type=float, default=4,
+                        help="SNR for bad pixels threshold")
     parser.add_argument('-o', '--output', type=pathlib.Path,
                         default=pathlib.Path("refined.geom"),
                         help="File to store refined geometry")
@@ -69,7 +71,7 @@ def refine():
     panels_new, transform, clen = refine_geometry(
         ma, panels, layout, 1.0, args.min_counts, args.connected)
 
-    px = badpixels_mask(pe, panels)
+    px = badpixels_mask(pe, panels, snr=args.snr)
     badpx = pixels_to_image(shape, px)
 
     geom_fn = args.output
diff --git a/src/geomtools/sfx/report.ipynb b/src/geomtools/sfx/report.ipynb
index 527d86eae5fbcd3c082adeeef70180337cd86d35..678cbaa1b84432321fa5b484236ffdb2ae11d72e 100644
--- a/src/geomtools/sfx/report.ipynb
+++ b/src/geomtools/sfx/report.ipynb
@@ -205,7 +205,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "px = badpixels_mask(pe, panels)\n",
+    "px = badpixels_mask(pe, panels, snr=4)\n",
     "shape = get_detector_shape(panels)\n",
     "msk = pixels_to_image(shape, px, 'msk')\n",
     "fig, ax = plot_data_on_detector(msk, panels, colorbar=False, cmap=plt.cm.copper)"
@@ -284,7 +284,7 @@
  "metadata": {
   "celltoolbar": "Raw Cell Format",
   "kernelspec": {
-   "display_name": "Python 3.9",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -298,7 +298,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.11.7"
   },
   "title": "Detector geometry optimisation report"
  },