From 8113ea6709168c360de4522b0270f0540cf35056 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@informatik.uni-goettingen.de>
Date: Sat, 15 Mar 2025 10:05:26 +0100
Subject: [PATCH] Add code for cryo lamella segmentation

---
 scripts/cryo/lamella/.gitignore               |  2 ++
 .../lamella/mito_segmentation_micro_sam.py    | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+)
 create mode 100644 scripts/cryo/lamella/.gitignore
 create mode 100644 scripts/cryo/lamella/mito_segmentation_micro_sam.py

diff --git a/scripts/cryo/lamella/.gitignore b/scripts/cryo/lamella/.gitignore
new file mode 100644
index 0000000..73b3a7a
--- /dev/null
+++ b/scripts/cryo/lamella/.gitignore
@@ -0,0 +1,2 @@
+embeddings/
+segmentations/
diff --git a/scripts/cryo/lamella/mito_segmentation_micro_sam.py b/scripts/cryo/lamella/mito_segmentation_micro_sam.py
new file mode 100644
index 0000000..2f813b2
--- /dev/null
+++ b/scripts/cryo/lamella/mito_segmentation_micro_sam.py
@@ -0,0 +1,19 @@
+from micro_sam.sam_annotator import image_folder_annotator
+
+ROOT = "/home/pape/Work/data/fernandez-busnadiego/lamella/Filtered_lamellae"
+
+
+def main():
+    tile_shape = (384, 384)
+    halo = (64, 64)
+    image_folder_annotator(
+        ROOT, "./segmentations",
+        model_type="vit_b_lm", embedding_path="./embeddings",
+        tile_shape=tile_shape, halo=halo,
+        precompute_amg_state=True,
+        skip_segmented=False,
+    )
+
+
+if __name__ == "__main__":
+    main()