diff --git a/pyproject.toml b/pyproject.toml
index 42dffd7..a10bfc4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -76,6 +76,7 @@ combine_segmentations = "nuc2seg.cli.combine_segmentations:main"
 combine_predictions = "nuc2seg.cli.combine_predictions:main"
 get_n_tiles = "nuc2seg.cli.get_n_tiles:main"
 segmented_xenium_to_anndata = "nuc2seg.cli.segmented_xenium_to_anndata:main"
+calculate_benchmarks = "nuc2seg.cli.calculate_benchmarks:main"
 
 [build-system]
 requires = ["setuptools>=43.0.0", "wheel"]
diff --git a/src/nuc2seg/cli/calculate_benchmarks.py b/src/nuc2seg/cli/calculate_benchmarks.py
index 49ddfc0..7801bef 100644
--- a/src/nuc2seg/cli/calculate_benchmarks.py
+++ b/src/nuc2seg/cli/calculate_benchmarks.py
@@ -2,10 +2,13 @@
 import logging
 import os
 
+import pandas
+import geopandas
+import tqdm
+
 from nuc2seg import log_config
 from nuc2seg.postprocess import (
-    calculate_average_intersection_over_union,
-    calculate_segmentation_jaccard_index,
+    calculate_benchmarks_with_nuclear_prior,
 )
 from nuc2seg.xenium import load_vertex_file, load_and_filter_transcripts_as_points
 
@@ -18,8 +21,8 @@ def get_parser():
     )
     log_config.add_logging_args(parser)
     parser.add_argument(
-        "--output-dir",
-        help="Directory for output tables and plots.",
+        "--output-file",
+        help="Output parquet file to save the results.",
         type=str,
         required=True,
     )
@@ -56,6 +59,14 @@ def get_parser():
         type=str,
         required=True,
     )
+
+    parser.add_argument(
+        "--xenium-cell-metadata",
+        help="Cell metadata.",
+        type=str,
+        required=True,
+    )
+    parser.add_argument("--chunk-size", help="Chunk size", type=int, default=5_000)
     return parser
 
 
@@ -63,34 +74,48 @@ def main():
     args = get_parser().parse_args()
 
     logger.info("Loading true boundaries.")
-    true_boundaries = load_vertex_file(args.true_boundaries)
+    true_gdf = load_vertex_file(args.true_boundaries)
 
     logger.info("Loading transcripts.")
     transcripts = load_and_filter_transcripts_as_points(args.transcripts)
 
-    segmentations = {}
-    ious = {}
-    jaccards = {}
+    nuclear_gdf = load_vertex_file(args.nuclei_boundaries)
 
-    os.makedirs(args.output_dir, exist_ok=True)
+    cell_metadata_df = pandas.read_parquet(args.xenium_cell_metadata)
+    cell_metadata_gdf = geopandas.GeoDataFrame(
+        cell_metadata_df,
+        geometry=geopandas.points_from_xy(
+            transcripts["x_centroid"], transcripts["y_centroid"]
+        ),
+    )
 
+    true_gdf = geopandas.sjoin(true_gdf, cell_metadata_gdf, how="inner")
+
+    os.makedirs(args.output_dir, exist_ok=True)
+    dfs = []
     for method_name, seg_fn in zip(
         args.segmentation_method_names, args.segmentation_files
     ):
         logger.info(f"Loading segmentation from {seg_fn}.")
-        segmentation_shapes = load_vertex_file(seg_fn)
+        method_gdf = load_vertex_file(seg_fn)
 
+        segments_chunk_size = args.chunk_size
+
+        logger.info(f"Converting transcripts to anndata")
         logger.info(f"Calculating benchmarks for {method_name}.")
-        iou = calculate_average_intersection_over_union(
-            segmentation_shapes, true_boundaries
-        )
-        jaccard = calculate_segmentation_jaccard_index(
-            transcripts, segmentation_shapes, true_boundaries
-        )
-
-        segmentations[method_name] = segmentation_shapes
-        ious[method_name] = iou
-        jaccards[method_name] = jaccard
-
-        iou.to_parquet(f"{args.output_dir}/{method_name}_iou.parquet")
-        jaccard.to_parquet(f"{args.output_dir}/{method_name}_jaccard.parquet")
+
+        for i in tqdm.tqdm(range(0, len(method_gdf), segments_chunk_size)):
+            chunk = method_gdf[i : i + segments_chunk_size]
+
+            dfs.append(
+                calculate_benchmarks_with_nuclear_prior(
+                    true_segs=true_gdf,
+                    method_segs=chunk,
+                    nuclear_segs=nuclear_gdf,
+                    transcripts_gdf=transcripts,
+                )
+            )
+
+    df = pandas.concat(dfs)
+
+    df.to_parquet(args.output_file)
diff --git a/src/nuc2seg/postprocess.py b/src/nuc2seg/postprocess.py
index 4644641..9971066 100644
--- a/src/nuc2seg/postprocess.py
+++ b/src/nuc2seg/postprocess.py
@@ -664,6 +664,12 @@ def get_jaccard_truth_segment(row):
         right_on="method_segment_id",
     )
 
+    results = results.merge(
+        true_segs[["truth_segment_id", "segmentation_method"]],
+        left_on="truth_segment_id",
+        right_on="truth_segment_id",
+    )
+
     return results