diff --git a/src/palantir/utils.py b/src/palantir/utils.py
index 077926af..e5c556e0 100644
--- a/src/palantir/utils.py
+++ b/src/palantir/utils.py
@@ -729,6 +729,9 @@ def determine_multiscale_space(
         n_eigs = np.argsort(vals[: (len(vals) - 1)] - vals[1:])[-1] + 1
         if n_eigs < 3:
             n_eigs = np.argsort(vals[: (len(vals) - 1)] - vals[1:])[-2] + 1
+        if n_eigs < 3:
+            # Fix for #39
+            n_eigs = 3
 
     # Scale the data
     use_eigs = list(range(1, n_eigs))