diff --git a/tools/scripts/ss2_h5ad_merge.py b/tools/scripts/ss2_h5ad_merge.py
new file mode 100644
index 00000000..8920516b
--- /dev/null
+++ b/tools/scripts/ss2_h5ad_merge.py
@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+
+import argparse
+import anndata as ad
+import os
+
+def merge_h5ads(input_h5ad_files, output_h5ad_file):
+    """
+    Merge multiple H5AD files into a single H5AD file.
+    
+    Args:
+        input_h5ad_files (list of str): Paths to input H5AD files.
+        output_h5ad_file (str): Path to output merged H5AD file.
+    """
+    # Initialize an empty list to store the loaded AnnData objects
+    adata_list = []
+
+    # Load each H5AD file and append it to the list
+    for h5ad_file in input_h5ad_files:
+        print(f"Loading {h5ad_file}...")
+        adata = ad.read_h5ad(h5ad_file)
+        adata_list.append(adata)
+    
+    # Concatenate all the AnnData objects along the observation (cell) axis
+    print("Merging H5AD files...")
+    merged_adata = ad.concat(adata_list, axis=0)
+    
+    # Save the merged AnnData object to a new H5AD file
+    print(f"Saving merged H5AD file to {output_h5ad_file}...")
+    merged_adata.write_h5ad(output_h5ad_file)
+    print("Merge complete!")
+
+def main():
+    description = "Merge multiple H5AD files into a single H5AD file."
+    parser = argparse.ArgumentParser(description=description)
+    parser.add_argument('--input-h5ad-files',
+                        dest='input_h5ad_files',
+                        nargs="+",
+                        required=True,
+                        help="Paths to input H5AD files")
+    parser.add_argument('--output-h5ad-file',
+                        dest='output_h5ad_file',
+                        required=True,
+                        help="Path to output merged H5AD file")
+    args = parser.parse_args()
+
+    merge_h5ads(args.input_h5ad_files, args.output_h5ad_file)
+
+if __name__ == '__main__':
+    main()
+