Script for counting cells in segmentation

Author: schilling40

scripts/prediction/count_cells.py

@@ -0,0 +1,32 @@
+import argparse
+import os
+import sys
+
+from elf.parallel import unique
+from elf.io import open_file
+
+sys.path.append("../..")
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-o", "--output_folder", type=str, required=True, help="Output directory containing segmentation.zarr")
+    parser.add_argument("-m", "--min_size", type=int, default=1000, help="Minimal number of voxel size for counting object")
+    args = parser.parse_args()
+
+    seg_path = os.path.join(args.output_folder, "segmentation.zarr")
+    seg_key = "segmentation"
+
+    file = open_file(seg_path, mode='r')
+    dataset = file[seg_key]
+
+    ids, counts = unique(dataset, return_counts=True)
+
+    # You can change the minimal size for objects to be counted here:
+    min_size = args.min_size
+
+    counts = counts[counts > min_size]
+    print("Number of objects:", len(counts))
+
+if __name__ == "__main__":
+    main()