diff --git a/src/traccuracy/_tracking_graph.py b/src/traccuracy/_tracking_graph.py
index f6dd21fc..45dd65de 100644
--- a/src/traccuracy/_tracking_graph.py
+++ b/src/traccuracy/_tracking_graph.py
@@ -3,6 +3,7 @@
 import copy
 import enum
 import logging
+from collections import defaultdict
 from typing import TYPE_CHECKING, Hashable, Iterable
 
 import networkx as nx
@@ -169,7 +170,7 @@ def __init__(
         self.graph = graph
 
         # construct dictionaries from attributes to nodes/edges for easy lookup
-        self.nodes_by_frame: dict[int, set[Hashable]] = {}
+        self.nodes_by_frame: defaultdict[int, set[Hashable]] = defaultdict(set)
         self.nodes_by_flag: dict[NodeFlag, set[Hashable]] = {
             flag: set() for flag in NodeFlag
         }
@@ -231,22 +232,6 @@ def edges(self) -> OutEdgeView:
         """
         return self.graph.edges
 
-    def get_nodes_in_frame(self, frame: int) -> set[Hashable]:
-        """Get the node ids of all nodes in the given frame.
-
-        Args:
-            frame (int): The frame to return all node ids for.
-                If the provided frame is outside of the range
-                (self.start_frame, self.end_frame), returns an empty iterable.
-
-        Returns:
-            Iterable[Hashable]: An iterable of node ids for all nodes in frame.
-        """
-        if frame in self.nodes_by_frame.keys():
-            return self.nodes_by_frame[frame]
-        else:
-            return set()
-
     def get_location(self, node_id: Hashable) -> list[float]:
         """Get the spatial location of the node with node_id using self.location_keys.
 
diff --git a/src/traccuracy/matchers/_compute_overlap.py b/src/traccuracy/matchers/_compute_overlap.py
index e0eb1784..abd04085 100644
--- a/src/traccuracy/matchers/_compute_overlap.py
+++ b/src/traccuracy/matchers/_compute_overlap.py
@@ -46,6 +46,8 @@ def get_labels_with_overlap(gt_frame, res_frame):
     res_box_labels = np.asarray(
         [int(res_prop.label) for res_prop in res_props], dtype=np.uint16
     )
+    if len(gt_props) == 0 or len(res_props) == 0:
+        return [], [], []
 
     if gt_frame.ndim == 3:
         overlaps = compute_overlap_3D(gt_boxes, res_boxes)
diff --git a/tests/matchers/test_compute_overlap.py b/tests/matchers/test_compute_overlap.py
new file mode 100644
index 00000000..18ec557a
--- /dev/null
+++ b/tests/matchers/test_compute_overlap.py
@@ -0,0 +1,41 @@
+from traccuracy.matchers._compute_overlap import (
+    get_labels_with_overlap,
+)
+
+from tests.test_utils import get_annotated_image
+
+
+def test_get_labels_with_overlap():
+    """Get all labels IDs in gt_frame and res_frame whose bounding boxes
+    overlap.
+
+    Args:
+        gt_frame (np.ndarray): ground truth segmentation for a single frame
+        res_frame (np.ndarray): result segmentation for a given frame
+
+    Returns:
+        overlapping_gt_labels: List[int], labels of gt boxes that overlap with res boxes
+        overlapping_res_labels: List[int], labels of res boxes that overlap with gt boxes
+        intersections_over_gt: List[float], list of (intersection gt vs res) / (gt area)
+    """
+    n_labels = 3
+    image1 = get_annotated_image(
+        img_size=256, num_labels=n_labels, sequential=True, seed=1
+    )
+    image2 = get_annotated_image(
+        img_size=256, num_labels=n_labels + 1, sequential=True, seed=2
+    )
+    empty_image = get_annotated_image(
+        img_size=256, num_labels=0, sequential=True, seed=1
+    )
+
+    perfect_gt, perfect_res, perfect_ious = get_labels_with_overlap(image1, image1)
+    assert list(perfect_gt) == list(range(1, n_labels + 1))
+    assert list(perfect_res) == list(range(1, n_labels + 1))
+    assert list(perfect_ious) == [1.0] * n_labels
+    get_labels_with_overlap(image1, image2)
+    # Test empty labels array
+    empty_gt, empty_res, empty_ious = get_labels_with_overlap(image1, empty_image)
+    assert empty_gt == []
+    assert empty_res == []
+    assert empty_ious == []
diff --git a/tests/test_tracking_graph.py b/tests/test_tracking_graph.py
index 045584a4..6ed67c3d 100644
--- a/tests/test_tracking_graph.py
+++ b/tests/test_tracking_graph.py
@@ -135,9 +135,10 @@ def test_constructor(nx_comp1):
 
 
 def test_get_cells_by_frame(simple_graph):
-    assert Counter(simple_graph.get_nodes_in_frame(0)) == Counter({"1_0"})
-    assert Counter(simple_graph.get_nodes_in_frame(2)) == Counter(["1_2", "1_3"])
-    assert Counter(simple_graph.get_nodes_in_frame(5)) == Counter([])
+    assert Counter(simple_graph.nodes_by_frame[0]) == Counter({"1_0"})
+    assert Counter(simple_graph.nodes_by_frame[2]) == Counter(["1_2", "1_3"])
+    # Test non-existent frame
+    assert Counter(simple_graph.nodes_by_frame[5]) == Counter([])
 
 
 def test_get_nodes_with_flag(simple_graph):
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 1dbf6d7c..6f854ad1 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -6,6 +6,10 @@
 
 def get_annotated_image(img_size=256, num_labels=3, sequential=True, seed=1):
     np.random.seed(seed)
+    if num_labels == 0:
+        im = np.zeros((img_size, img_size))
+        return im.astype("int32")
+
     num_labels_act = False
     trial = 0
     while num_labels != num_labels_act: