--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/split.py	Fri Mar 07 08:08:05 2025 +0000
@@ -0,0 +1,44 @@
+import argparse
+import math
+
+import giatools
+import giatools.util
+import numpy as np
+import tifffile
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('input', type=str)
+parser.add_argument('axis', type=str)
+parser.add_argument('output', type=str)
+parser.add_argument('--squeeze', action='store_true', default=False)
+args = parser.parse_args()
+
+# Validate and normalize input parameters
+assert len(args.axis) == 1, 'Axis input must be a single character.'
+axis = args.axis.replace('S', 'C')
+
+# Read input image as TZYXC
+img_in = giatools.Image.read(args.input)
+
+# Determine the axis to split along
+axis_pos = img_in.axes.index(axis)
+
+# Perform the splitting
+arr = np.moveaxis(img_in.data, axis_pos, 0)
+decimals = math.ceil(math.log10(1 + arr.shape[0]))
+output_filename_pattern = f'{args.output}/%0{decimals}d.tiff'
+for img_idx, img in enumerate(arr):
+    img = np.moveaxis(img[None], 0, axis_pos)
+
+    # Optionally, squeeze the image
+    if args.squeeze:
+        s = [axis_pos for axis_pos in range(len(img_in.axes)) if img.shape[axis_pos] == 1 and img_in.axes[axis_pos] not in 'YX']
+        img = np.squeeze(img, axis=tuple(s))
+        img_axes = giatools.util.str_without_positions(img_in.axes, s)
+    else:
+        img_axes = img_in.axes
+
+    # Save the result
+    filename = output_filename_pattern % (img_idx + 1)
+    tifffile.imwrite(filename, img, metadata=dict(axes=img_axes))