diff --git a/starfish/core/experiment/builder/__init__.py b/starfish/core/experiment/builder/__init__.py
index 738714d1b..99e9b55cc 100644
--- a/starfish/core/experiment/builder/__init__.py
+++ b/starfish/core/experiment/builder/__init__.py
@@ -30,6 +30,7 @@
 
 from starfish import FieldOfView
 from starfish.core.codebook.codebook import Codebook
+from starfish.core.errors import DataFormatWarning
 from starfish.core.experiment.builder.orderediterator import join_axes_labels, ordered_iterator
 from starfish.core.experiment.version import CURRENT_VERSION
 from starfish.core.types import Axes, Coordinates
@@ -116,6 +117,14 @@ def reducer_to_sets(
                 current_ch,
                 current_zplane
             )
+            for axis in (Axes.X, Axes.Y):
+                if image.shape[axis] < max(len(rounds), len(chs), len(zplanes)):
+                    warnings.warn(
+                        f"{axis} axis appears to be smaller than rounds/chs/zplanes, which is "
+                        "unusual",
+                        DataFormatWarning
+                    )
+
             tile = Tile(
                 image.coordinates,
                 {
diff --git a/starfish/core/experiment/builder/test/test_small_axis.py b/starfish/core/experiment/builder/test/test_small_axis.py
new file mode 100644
index 000000000..0cc39e849
--- /dev/null
+++ b/starfish/core/experiment/builder/test/test_small_axis.py
@@ -0,0 +1,66 @@
+import warnings
+from typing import Callable, Collection, Mapping, Sequence
+
+import pytest
+
+from starfish.core.errors import DataFormatWarning
+from starfish.core.types import Coordinates, CoordinateValue
+from .factories.all_purpose import collection_factory
+from .factories.unique_tiles import UniqueTiles
+from .. import TileIdentifier
+
+
+@pytest.mark.parametrize(
+    "num_round_labels, num_ch_labels, num_zplane_labels, tile_height, tile_width, has_warnings",
+    (
+        (1, 1, 1, 100, 100, False),
+        (1, 1, 1000, 100, 100, True),
+        (1, 1000, 1, 100, 100, True),
+        (1000, 1, 1, 100, 100, True),
+        (1000, 1, 1, 10000, 100, True),
+        (1000, 1, 1, 100, 10000, True),
+    )
+)
+def test_small_axis(
+        num_round_labels,
+        num_ch_labels,
+        num_zplane_labels,
+        tile_height,
+        tile_width,
+        has_warnings,
+):
+    tile_identifiers: Collection[TileIdentifier] = [
+        TileIdentifier(0, round_label, ch_label, zplane_label)
+        for round_label in range(num_round_labels)
+        for ch_label in range(num_ch_labels)
+        for zplane_label in range(num_zplane_labels)
+    ]
+
+    def make_tile_coordinate_callback(
+            all_zplane_labels: Sequence[int]
+    ) -> Callable[[TileIdentifier], Mapping[Coordinates, CoordinateValue]]:
+        def tile_coordinate_callback(
+                tile_identifier: TileIdentifier
+        ) -> Mapping[Coordinates, CoordinateValue]:
+            zplane_offset = all_zplane_labels.index(tile_identifier.zplane_label)
+            return {
+                Coordinates.X: (0.0, 0.1),
+                Coordinates.Y: (0.0, 0.1),
+                Coordinates.Z: zplane_offset * 0.1,
+            }
+
+        return tile_coordinate_callback
+
+    with warnings.catch_warnings(record=True) as warnings_:
+        collection_factory(
+            UniqueTiles,
+            tile_identifiers,
+            make_tile_coordinate_callback(
+                sorted(set(tile_identifier.zplane_label for tile_identifier in tile_identifiers))),
+            tile_height,
+            tile_width,
+        )
+        assert has_warnings == (
+            0 != len(
+                [warning for warning in warnings_
+                 if issubclass(warning.category, DataFormatWarning)]))