Initial commit

mask_cutout.py

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+import os
+from tifffile import imread, imwrite
+import numpy as np
+import shutil
+
+# Configure these three fields to match the directories containin the outputs from syGlass
+# and the directory where you'd like the result images to be written
+IMAGE_DIR = r'C:\Users\natha\Downloads\88-0412-OG_647_ROI-2\Image'
+MASK_DIR = r'C:\Users\natha\Downloads\88-0412-OG_647_ROI-2\Mask'
+RESULTS_DIR = r'C:\Users\natha\Downloads\mask_labels_results'
+
+# Ensure that results directory exists
+if not os.path.exists(RESULTS_DIR):
+    os.makedirs(RESULTS_DIR)
+
+# Determine the masks present in the mask TIFFs
+mask_ids = set()
+for mask_path in os.listdir(MASK_DIR):
+    img = imread(f"{MASK_DIR}/{mask_path}")
+    mask_ids.update(np.unique(img))
+mask_ids.discard(0)
+print(f"\nMask IDs detected:\n{mask_ids}\n")
+
+# Write new image TIFFs for each mask, only where that mask exists
+mask_paths = os.listdir(MASK_DIR)
+image_paths = os.listdir(IMAGE_DIR)
+for mask_id in mask_ids:
+    mask_dir = f"{RESULTS_DIR}/Mask{mask_id}"
+    if os.path.exists(mask_dir):
+        shutil.rmtree(mask_dir)
+    os.makedirs(mask_dir)
+    for i in range(0, len(mask_paths)):
+        image = imread(f"{IMAGE_DIR}/{image_paths[i]}")
+        mask = imread(f"{MASK_DIR}/{mask_paths[i]}")
+        result = np.where(mask == mask_id, image, 0).astype(image.dtype)
+        result_path = f"{mask_dir}/{image_paths[i][:-5]}_Mask-{mask_id}.tiff"
+        imwrite(result_path, result, compression = 'zlib')
+    print(f"Created TIFF stack for mask ID {mask_id}")
+print("\nFinished!")