Merge pull request #159 from computational-cell-analytics/cosmetics

Precompute embeddings in 2d example; set default box extension to 0.0…

Author: constantinpape

examples/annotator_2d.py

@@ -34,7 +34,7 @@ def hela_2d_annotator(use_finetuned_model):
         embedding_path = "./embeddings/embeddings-hela2d.zarr"
         model_type = "vit_h"
 
-    annotator_2d(image, embedding_path, show_embeddings=False, model_type=model_type)
+    annotator_2d(image, embedding_path, show_embeddings=False, model_type=model_type, precompute_amg_state=True)
 
 
 def wholeslide_annotator(use_finetuned_model):

micro_sam/sam_annotator/annotator_3d.py

@@ -154,7 +154,7 @@ def _segment_slice_wigdet(v: Viewer) -> None:
 
 @magicgui(call_button="Segment Volume [V]", projection={"choices": ["default", "bounding_box", "mask", "points"]})
 def _segment_volume_widget(
-    v: Viewer, iou_threshold: float = 0.8, projection: str = "default", box_extension: float = 0.1
+    v: Viewer, iou_threshold: float = 0.8, projection: str = "default", box_extension: float = 0.05
 ) -> None:
     # step 1: segment all slices with prompts
     shape = v.layers["raw"].data.shape