diff --git a/rastermap/rastermap.py b/rastermap/rastermap.py
index 9deb25f..e7a4b12 100644
--- a/rastermap/rastermap.py
+++ b/rastermap/rastermap.py
@@ -339,8 +339,8 @@ def fit(self, data=None, Usv=None, Vsv=None, U_nodes=None, itrain=None,
         self.sv = np.nansum((self.Usv**2), axis=0)**0.5
         if not hasattr(self, "Vsv"):
             if Vsv is None:
-                U = self.Usv.copy() / self.sv
-                self.Vsv = X.T @ U 
+                U = self.Usv[igood].copy() / self.sv
+                self.Vsv = X[igood].T @ U
             elif Vsv is not None:
                 self.Vsv = Vsv
 
@@ -491,7 +491,7 @@ def fit(self, data=None, Usv=None, Vsv=None, U_nodes=None, itrain=None,
             if (bin_size==0 or n_samples < bin_size or 
                 (bin_size == 50 and n_samples < 1000)):
                 bin_size = max(1, n_samples // 500)
-            self.X_embedding = zscore(bin1d(X[igood][self.isort], bin_size, axis=0), axis=1)
+            self.X_embedding = zscore(bin1d(X[self.isort], bin_size, axis=0), axis=1)
 
         rmap_logger.info(f"rastermap complete, time {time.time() - t0:0.2f}sec")