Enable using fine-tuned model in the image series annotator

Author: constantinpape

examples/image_series_annotator.py

@@ -2,18 +2,29 @@
 from micro_sam.sample_data import fetch_image_series_example_data
 
 
-def series_annotation():
-    """Annotate a series of images. Example runs for three different example images.
+def series_annotation(use_finetuned_model):
+    """Annotate a series of images. Example runs for three different images.
     """
+
+    if use_finetuned_model:
+        embedding_path = "./embeddings/series-embeddings-vit_h_lm"
+        model_type = "vit_h_lm"
+    else:
+        embedding_path = "./embeddings/series-embeddings"
+        model_type = "vit_h"
+
     example_data = fetch_image_series_example_data("./data")
     image_folder_annotator(
-        example_data, "./data/series-segmentation-result", embedding_path="./embeddings/series-embeddings",
-        pattern="*.tif", model_type="vit_b"
+        example_data, "./data/series-segmentation-result", embedding_path=embedding_path,
+        pattern="*.tif", model_type=model_type
     )
 
 
 def main():
-    series_annotation()
+    # whether to use the fine-tuned SAM model
+    # this feature is still experimental!
+    use_finetuned_model = False
+    series_annotation(use_finetuned_model)
 
 
 if __name__ == "__main__":