diff --git a/test/test_sam_annotator/test_cli.py b/test/test_sam_annotator/test_cli.py
index 1df399f9..8a413e89 100644
--- a/test/test_sam_annotator/test_cli.py
+++ b/test/test_sam_annotator/test_cli.py
@@ -6,6 +6,7 @@
 
 import imageio.v3 as imageio
 import micro_sam.util as util
+import pytest
 import zarr
 from skimage.data import binary_blobs
 
@@ -35,19 +36,13 @@ def test_annotator_tracking(self):
     def test_image_series_annotator(self):
         self._test_command("micro_sam.image_series_annotator")
 
+    @pytest.mark.skipif(platform.system() == "Windows", reason="Gui test is not working on windows.")
     def test_precompute_embeddings(self):
         self._test_command("micro_sam.precompute_embeddings")
 
-    def test_automatic_segmentation(self):
-        self._test_command("micro_sam.automatic_segmentation")
-
-        # The filepaths can't be found on windows, probably due different filepath conventions.
-        # The actual functionality likely works despite this issue.
-        if platform.system() == "Windows":
-            return
-
-        # Create 3 images as testdata.
-        for i in range(3):
+        # Create 2 images as testdata.
+        n_images = 2
+        for i in range(n_images):
             im_path = os.path.join(self.tmp_folder, f"image-{i}.tif")
             image_data = binary_blobs(512).astype("uint8") * 255
             imageio.imwrite(im_path, image_data)
@@ -73,7 +68,7 @@ def test_automatic_segmentation(self):
         self.assertTrue(os.path.exists(emb_path2))
         with zarr.open(emb_path2, "r") as f:
             self.assertIn("features", f)
-            self.assertEqual(f["features"].shape[0], 3)
+            self.assertEqual(f["features"].shape[0], n_images)
         ais_path = os.path.join(emb_path2, "is_state.h5")
         self.assertTrue(os.path.exists(ais_path))
 
@@ -83,11 +78,14 @@ def test_automatic_segmentation(self):
             "micro_sam.precompute_embeddings", "-i", self.tmp_folder, "-e", emb_path3,
             "-m", self.model_type, "--pattern", "*.tif", "--precompute_amg_state"
         ])
-        for i in range(3):
+        for i in range(n_images):
             self.assertTrue(os.path.exists(os.path.join(emb_path3, f"image-{i}.zarr")))
             ais_path = os.path.join(emb_path3, f"image-{i}.zarr", "is_state.h5")
             self.assertTrue(os.path.exists(ais_path))
 
+    def test_automatic_segmentation(self):
+        self._test_command("micro_sam.automatic_segmentation")
+
 
 if __name__ == "__main__":
     unittest.main()