Add stardist postprocessing script

Author: constantinpape

scripts/la-vision/postprocess_stardist.py

@@ -0,0 +1,29 @@
+import os
+from glob import glob
+
+from tifffile import imread, imwrite
+from csbdeep.utils import normalize
+from stardist.models import StarDist3D
+
+model = StarDist3D.from_pretrained("3D_demo")
+
+
+def segment_with_stardist(ff, out):
+    axis_norm = (0, 1, 2)  # normalize channels independently
+    x = imread(ff)
+    img = normalize(x[0], 1, 99.8, axis=axis_norm)
+    labels, details = model.predict_instances(img)
+    imwrite(out, labels)
+
+
+def main():
+    files = glob("predictions/sgn-new/*.tif")
+    out_folder = "./predictions/stardist"
+    os.makedirs(out_folder, exist_ok=True)
+    for ff in files:
+        out = imread(ff)
+        segment_with_stardist(ff, out)
+
+
+if __name__ == "__main__":
+    main()