- read metadata from first file in ome tiff sequence

ndbioimage/readers/tifread.py

@@ -1,3 +1,5 @@
+import re
+import warnings
 from abc import ABC
 from functools import cached_property
 from itertools import product
@@ -6,8 +8,8 @@ from pathlib import Path
 import numpy as np
 import tifffile
 import yaml
-import warnings
+from lfdfiles import TiffFile
-from ome_types import model, from_xml
+from ome_types import from_xml, model
 
 from .. import AbstractReader, try_default
 
@@ -31,10 +33,16 @@ class Reader(AbstractReader, ABC):
 
     def get_ome(self):
         if self.reader.is_ome:
+            match = re.match(r'^(.*)(pos.*)$', self.path.stem, flags=re.IGNORECASE)
+            if match is not None and len(match.groups()) == 2:
+                a, b = match.groups()
+                file0 = TiffFile(self.path.with_stem(a + re.sub(r'\d', '0', b)))
                 with warnings.catch_warnings():
                     warnings.simplefilter('ignore', category=UserWarning)
-                return from_xml(self.reader.ome_metadata)
+                    ome = from_xml(file0.ome_metadata)
-        else:
+                    ome.images = [image for image in ome.images if self.path.stem[:len(image.name)] == image.name]
+                    return ome
+
         page = self.reader.pages[0]
         size_y = page.imagelength
         size_x = page.imagewidth

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ndbioimage"
-version = "2025.3.0"
+version = "2025.3.1"
 description = "Bio image reading, metadata and some affine registration."
 authors = [
     { name = "W. Pomp", email = "w.pomp@nki.nl" }