diff --git a/starfish/core/spots/AssignTargets/label.py b/starfish/core/spots/AssignTargets/label.py
index e8d0fd187..4e940b2da 100644
--- a/starfish/core/spots/AssignTargets/label.py
+++ b/starfish/core/spots/AssignTargets/label.py
@@ -1,8 +1,10 @@
+import warnings
+
 import numpy as np
 
 from starfish.core.intensity_table.decoded_intensity_table import DecodedIntensityTable
 from starfish.core.morphology.binary_mask import BinaryMaskCollection
-from starfish.core.types import Features
+from starfish.core.types import Axes, Features
 from ._base import AssignTargetsAlgorithm
 
 
@@ -32,19 +34,32 @@ def _assign(
 
         decoded_intensities[Features.CELL_ID] = cell_ids
 
+        # it's 3D data.
         for _, mask in masks:
+            has_z_data = Axes.ZPLANE.value in mask.coords
+            if has_z_data:
+                z_min, z_max = float(mask.z.min()), float(mask.z.max())
+            else:
+                warnings.warn(
+                    "AssignTargets will require 3D masks in the future.", DeprecationWarning)
+                z_min, z_max = np.NINF, np.inf
             y_min, y_max = float(mask.y.min()), float(mask.y.max())
             x_min, x_max = float(mask.x.min()), float(mask.x.max())
 
             in_bbox = decoded_intensities.where(
-                (decoded_intensities.y >= y_min)
+                (decoded_intensities.z >= z_min)
+                & (decoded_intensities.z <= z_max)
+                & (decoded_intensities.y >= y_min)
                 & (decoded_intensities.y <= y_max)
                 & (decoded_intensities.x >= x_min)
                 & (decoded_intensities.x <= x_max),
                 drop=True
             )
 
-            in_mask = mask.sel(y=in_bbox.y, x=in_bbox.x)
+            selectors = {'y': in_bbox.y, 'x': in_bbox.x}
+            if has_z_data:
+                selectors['z'] = in_bbox.z
+            in_mask = mask.sel(**selectors)
             spot_ids = in_bbox[Features.SPOT_ID][in_mask.values]
             decoded_intensities[Features.CELL_ID].loc[spot_ids] = mask.name