Dilating SGNs for low-scale rendering with Imaris

Author: schilling40

scripts/dilate_sgns.py

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+import os
+
+import numpy as np
+import tifffile
+
+from elf.parallel import seeded_watershed, distance_transform
+
+LOWER_RESOLUTION_DIR = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/lower_resolution"
+
+def dilate_sgns(in_path, out_path, dilation_distance, block_shape=[64, 128, 128], halo=[8, 16, 16]):
+    print(f"Dilating {in_path} with dilation distance {dilation_distance}.")
+    seg = tifffile.imread(in_path).astype("uint32")
+
+    distances = distance_transform(seg == 0, halo=halo, sampling=(1, 1, 1), block_shape=block_shape, verbose=True)
+    extension_mask = distances < dilation_distance
+
+    extended_seg = np.zeros_like(seg)
+    extended_seg = seeded_watershed(
+        distances, seg, out=extended_seg, mask=extension_mask, block_shape=block_shape, halo=halo, verbose=True
+    )
+
+    tifffile.imwrite(out_path, extended_seg.astype("float32"), bigtiff=True, compression="zlib")
+
+
+def main():
+    cochlea = "G_EK_000049_L"
+    scale = 3
+    suffixes = ["_marker_positive", "_marker_negative", ""]
+    dilation_distances = [2, 4]
+
+    for suffix in suffixes:
+        for dilation_distance in dilation_distances:
+            in_path = os.path.join(f"{LOWER_RESOLUTION_DIR}", cochlea, f"scale{scale}", f"SGN_v2{suffix}.tif")
+            out_path = os.path.join(f"{LOWER_RESOLUTION_DIR}", cochlea, f"scale{scale}",
+                                    f"SGN_v2{suffix}_{scale}_dilated_{dilation_distance}.tif")
+            dilate_sgns(in_path, out_path, dilation_distance)
+
+
+if __name__ == "__main__":
+    main()