diff --git a/sae_lens/analysis/neuronpedia_runner.py b/sae_lens/analysis/neuronpedia_runner.py
index a34e970a..95b09cb7 100644
--- a/sae_lens/analysis/neuronpedia_runner.py
+++ b/sae_lens/analysis/neuronpedia_runner.py
@@ -191,6 +191,7 @@ def run(self):
                 "model_id": self.model_id,
                 "layer": str(self.layer),
                 "sae_id": self.sae_id,
+                "log_sparsity": self.sparsity_threshold,
                 "skipped_indexes": list(skipped_indexes),
             }
         )
@@ -237,6 +238,13 @@ def run(self):
                     # print(f"Skipping batch - it's after end_batch: {feature_batch_count}")
                     continue
 
+                output_file = f"{self.outputs_dir}/batch-{feature_batch_count}.json"
+                # if output_file exists, skip
+                if os.path.isfile(output_file):
+                    logline = f"\n++++++++++ Skipping Batch #{feature_batch_count} output. File exists: {output_file} ++++++++++\n"
+                    print(logline)
+                    continue
+
                 print(f"========== Running Batch #{feature_batch_count} ==========")
 
                 layout = SaeVisLayoutConfig(
@@ -421,9 +429,11 @@ def run(self):
                 json_object = json.dumps(to_write, cls=NpEncoder)
 
                 with open(
-                    f"{self.outputs_dir}/batch-{feature_batch_count}.json",
+                    output_file,
                     "w",
                 ) as f:
                     f.write(json_object)
 
+                logline = f"\n========== Completed Batch #{feature_batch_count} output: {output_file} ==========\n"
+
         return
diff --git a/tutorials/neuronpedia/neuronpedia.py b/tutorials/neuronpedia/neuronpedia.py
index aa36a6b6..24d99865 100755
--- a/tutorials/neuronpedia/neuronpedia.py
+++ b/tutorials/neuronpedia/neuronpedia.py
@@ -21,6 +21,7 @@
 from sae_lens.training.sparse_autoencoder import SparseAutoencoder
 
 OUTPUT_DIR_BASE = Path("../../neuronpedia_outputs")
+RUN_SETTINGS_FILE = "run_settings.json"
 
 app = typer.Typer(
     add_completion=False,
@@ -77,16 +78,6 @@ def generate(
 Enter value""",
         ),
     ] = 128,
-    resume_from_batch: Annotated[
-        int,
-        typer.Option(
-            min=1,
-            help="Batch number to resume from.",
-            prompt="""
-Do you want to resume from a specific batch number?
-Enter 1 to start from the beginning""",
-        ),
-    ] = 1,
     n_batches_to_sample: Annotated[
         int,
         typer.Option(
@@ -109,6 +100,16 @@ def generate(
         ),
     ] = 4096
     * 6,
+    resume_from_batch: Annotated[
+        int,
+        typer.Option(
+            min=1,
+            help="Batch number to resume from.",
+            prompt="""
+Do you want to resume from a specific batch number?
+Enter 1 to start from the beginning. Existing batch files will not be overwritten.""",
+        ),
+    ] = 1,
 ):
     """
     This will start a batch job that generates features for Neuronpedia for a specific SAE. To upload those features, use the 'upload' command afterwards.
@@ -141,19 +142,67 @@ def generate(
     )
     model_id = sparse_autoencoder.cfg.model_name
 
+    # make the outputs subdirectory if it doesn't exist, ensure it's not a file
     outputs_subdir = f"{model_id}_{sae_id}_{sparse_autoencoder.cfg.hook_point}"
     outputs_dir = OUTPUT_DIR_BASE.joinpath(outputs_subdir)
     if outputs_dir.exists() and outputs_dir.is_file():
         print(f"Error: Output directory {outputs_dir.as_posix()} exists and is a file.")
         raise typer.Abort()
     outputs_dir.mkdir(parents=True, exist_ok=True)
-    # Check if output_dir has any files starting with "batch_"
-    batch_files = list(outputs_dir.glob("batch-*.json"))
-    if len(batch_files) > 0 and resume_from_batch == 1:
-        print(
-            f"Error: Output directory {outputs_dir.as_posix()} has existing batch files. This is only allowed if you are resuming from a batch. Please delete or move the existing batch-*.json files."
-        )
-        raise typer.Abort()
+
+    # Check if output_dir has a run_settings.json file. If so, load those settings.
+    run_settings_path = outputs_dir.joinpath(RUN_SETTINGS_FILE)
+    print("\n")
+    if run_settings_path.exists() and run_settings_path.is_file():
+        # load the json file
+        with open(run_settings_path, "r") as f:
+            run_settings = json.load(f)
+            print(
+                f"[yellow]Found existing run_settings.json in {run_settings_path.as_posix()}, checking them."
+            )
+            if run_settings["log_sparsity"] != log_sparsity:
+                print(
+                    f"[red]Error: log_sparsity in {run_settings_path.as_posix()} doesn't match the current log_sparsity:\n{run_settings['log_sparsity']} vs {log_sparsity}"
+                )
+                raise typer.Abort()
+            if run_settings["sae_id"] != sae_id:
+                print(
+                    f"[red]Error: sae_id in {run_settings_path.as_posix()} doesn't match the current sae_id:\n{run_settings['sae_id']} vs {sae_id}"
+                )
+                raise typer.Abort()
+            if run_settings["sae_path"] != sae_path_string:
+                print(
+                    f"[red]Error: sae_path in {run_settings_path.as_posix()} doesn't match the current sae_path:\n{run_settings['sae_path']} vs {sae_path_string}"
+                )
+                raise typer.Abort()
+            if run_settings["n_batches_to_sample"] != n_batches_to_sample:
+                print(
+                    f"[red]Error: n_batches_to_sample in {run_settings_path.as_posix()} doesn't match the current n_batches_to_sample:\n{run_settings['n_batches_to_sample']} vs {n_batches_to_sample}"
+                )
+                raise typer.Abort()
+            if run_settings["n_prompts_to_select"] != n_prompts_to_select:
+                print(
+                    f"[red]Error: n_prompts_to_select in {run_settings_path.as_posix()} doesn't match the current n_prompts_to_select:\n{run_settings['n_prompts_to_select']} vs {n_prompts_to_select}"
+                )
+                raise typer.Abort()
+            if run_settings["feat_per_batch"] != feat_per_batch:
+                print(
+                    f"[red]Error: feat_per_batch in {run_settings_path.as_posix()} doesn't match the current feat_per_batch:\n{run_settings['feat_per_batch']} vs {feat_per_batch}"
+                )
+                raise typer.Abort()
+            print("[green]All settings match, using existing run_settings.json.")
+    else:
+        print(f"[green]Creating run_settings.json in {run_settings_path.as_posix()}.")
+        run_settings = {
+            "sae_id": sae_id,
+            "sae_path": sae_path_string,
+            "log_sparsity": log_sparsity,
+            "n_batches_to_sample": n_batches_to_sample,
+            "n_prompts_to_select": n_prompts_to_select,
+            "feat_per_batch": feat_per_batch,
+        }
+        with open(run_settings_path, "w") as f:
+            json.dump(run_settings, f, indent=4)
 
     sparsity = load_sparsity(sae_path_string)
     # convert sparsity to logged sparsity if it's not
@@ -290,7 +339,7 @@ def upload(
             dir_okay=True,
             readable=True,
             resolve_path=True,
-            prompt="What is the absolute, full local file path to the feature outputs directory?",
+            prompt="What is the absolute local file path to the feature outputs directory?",
         ),
     ],
     host: Annotated[
@@ -347,7 +396,7 @@ def upload_dead_stubs(
             dir_okay=True,
             readable=True,
             resolve_path=True,
-            prompt="What is the absolute, full local file path to the feature outputs directory?",
+            prompt="What is the absolute local file path to the feature outputs directory?",
         ),
     ],
     host: Annotated[