Add test and fix saving to set axes to zyx instead of default qyx.

brainglobe_utils/image_io/save.py

@@ -58,7 +58,12 @@ def to_tiff(img_volume, dest_path, photometric="minisblack"):
         Use 'minisblack' (default) for grayscale and 'rgb' for rgb
     """
     dest_path = Path(dest_path)
-    tifffile.imwrite(dest_path, img_volume, photometric=photometric)
+    tifffile.imwrite(
+        dest_path,
+        img_volume,
+        photometric=photometric,
+        metadata={"axes": "ZYX"},
+    )
 
 
 def to_tiffs(img_volume, path_prefix, path_suffix="", extension=".tif"):

tests/tests/test_image_io.py

@@ -350,6 +350,19 @@ def test_image_size_dir(tmp_path, array_3d):
     assert image_shape["z"] == array_3d.shape[0]
 
 
+def test_image_size_tiff_stack(tmp_path, array_3d):
+    """
+    Test that image size can be detected from a directory of 2D tiffs
+    """
+    filename = tmp_path.joinpath("image_size_tiff_stack.tif")
+    save.save_any(array_3d, filename)
+
+    image_shape = load.get_size_image_from_file_paths(filename)
+    assert image_shape["x"] == array_3d.shape[2]
+    assert image_shape["y"] == array_3d.shape[1]
+    assert image_shape["z"] == array_3d.shape[0]
+
+
 def test_image_size_txt(txt_path, array_3d):
     """
     Test that image size can be detected from a text file containing the paths