diff --git a/spleeter/separator.py b/spleeter/separator.py
index 87accd5..73a1a89 100644
--- a/spleeter/separator.py
+++ b/spleeter/separator.py
@@ -98,14 +98,23 @@ class Separator(object):
         prediction.pop('audio_id')
         return prediction
 
-    def stft(self, waveform, inverse=False):
+    def stft(self, data, inverse=False):
+        """
+        Single entrypoint for both stft and istft. This computes stft and istft with librosa on stereo data. The two
+        channels are processed separately and are concatenated together in the result. The expected input formats are:
+        (n_samples, 2) for stft and (T, F, 2) for istft.
+        :param data: np.array with either the waveform or the complex spectrogram depending on the parameter inverse
+        :param inverse: should a stft or an istft be computed.
+        :return: Stereo data as numpy array for the transform. The channels are stored in the last dimension
+        """
         N = self._params["frame_length"]
         H = self._params["frame_step"]
         win = hann(N, sym=False)
         fstft = istft if inverse else stft
-        win_len_arg = "win_length" if inverse else "n_fft"
-        s1 = fstft(waveform[:, 0], hop_length=H, window=win, center=False, **{win_len_arg: N})
-        s2 = fstft(waveform[:, 1], hop_length=H, window=win, center=False, **{win_len_arg: N})
+        win_len_arg = {"win_length": None} if inverse else {"n_fft": N}
+        dl, dr = (data[:, :, 0].T, data[:, :, 1].T) if inverse else (data[:, 0], data[:, 1])
+        s1 = fstft(dl, hop_length=H, window=win, center=False, **win_len_arg)
+        s2 = fstft(dr, hop_length=H, window=win, center=False, **win_len_arg)
         s1 = np.expand_dims(s1.T, 2-inverse)
         s2 = np.expand_dims(s2.T, 2-inverse)
         return np.concatenate([s1, s2], axis=2-inverse)
@@ -127,7 +136,7 @@ class Separator(object):
             saver.restore(sess, latest_checkpoint)
             outputs = sess.run(outputs, feed_dict=input_provider.get_feed_dict(features, stft, audio_id))
             for inst in builder.instruments:
-                out[inst] = self.stft(outputs[inst], inverse=True)
+                out[inst] = self.stft(outputs[inst], inverse=True)[:waveform.shape[0], :]
         return out
 
     def separate_to_file(