Move instance segmentation script to development

Author: constantinpape

examples/instance_segmentation.py development/instance_segmentation.pyexamples/instance_segmentation.py renamed to development/instance_segmentation.py

@@ -7,12 +7,12 @@
 
 
 def mito_segmentation():
-    input_path = "./data/Lucchi++/Test_In"
+    input_path = "../examples/data/Lucchi++/Test_In"
     with open_file(input_path) as f:
         raw = f["*.png"][-1, :768, :768]
 
     predictor = util.get_sam_model()
-    image_embeddings = util.precompute_image_embeddings(predictor, raw, "./embeddings/embeddings-mito2d.zarr")
+    image_embeddings = util.precompute_image_embeddings(predictor, raw, "../examples/embeddings/embeddings-mito2d.zarr")
     embedding_pca = compute_pca(image_embeddings["features"])
 
     seg, initial_seg = segment_from_embeddings(predictor, image_embeddings=image_embeddings, return_initial_seg=True)
@@ -26,14 +26,16 @@ def mito_segmentation():
 
 
 def cell_segmentation():
-    path = "./DIC-C2DH-HeLa/train/01"
+    path = "../examples/data/DIC-C2DH-HeLa/train/01"
     with open_file(path, mode="r") as f:
         timeseries = f["*.tif"][:50]
 
     frame = 11
 
     predictor = util.get_sam_model()
-    image_embeddings = util.precompute_image_embeddings(predictor, timeseries, "./embeddings/embeddings-ctc.zarr")
+    image_embeddings = util.precompute_image_embeddings(
+        predictor, timeseries, "../examples/embeddings/embeddings-ctc.zarr"
+    )
     embedding_pca = compute_pca(image_embeddings["features"][frame])
 
     seg, initial_seg = segment_from_embeddings(