Updated tifffile for Zarr V3 support (#360)

updated tifffile for zarr v3 support

Author: srivarra

iohub/_deprecated/singlepagetiff.py

@@ -3,15 +3,13 @@
 import json
 import logging
 import os
-from pathlib import Path
 
 import natsort
 import numpy as np
 import tifffile as tiff
 import zarr
 
 from iohub._deprecated.reader_base import ReaderBase
-from iohub.mmstack import _tiff_to_fsspec_store
 
 
 class MicromanagerSequenceReader(ReaderBase):
@@ -210,14 +208,10 @@ def _create_stores(self, p):
         for c, fn in self.coord_to_filename.items():
             if c[0] == p:
                 self.log.info(f"reading coord = {c} from filename = {fn}")
+                # tifffile.zarr.ZarrTiffStore is a native zarr v3 store
                 with tiff.imread(fn, aszarr=True) as store:
                     try:
-                        array = zarr.open(
-                            _tiff_to_fsspec_store(
-                                store, root_uri=Path(fn).parent.as_uri()
-                            ),
-                            mode="r",
-                        )[:]
+                        array = zarr.open(store, mode="r")[:]
                         z[c[1], c[2], c[3]] = array
                     except Exception:
                         self.log.error(

iohub/mmstack.py

@@ -1,21 +1,17 @@
 from __future__ import annotations
 
-import io
-import json
 import logging
 from copy import copy
 from pathlib import Path
 from typing import TYPE_CHECKING, Iterable
 from warnings import catch_warnings, filterwarnings
 
 import dask.array as da
-import fsspec
 import numpy as np
 import zarr
-import zarr.storage
 from natsort import natsorted
 from numpy.typing import ArrayLike
-from tifffile import TiffFile, ZarrTiffStore
+from tifffile import TiffFile
 from xarray import DataArray
 
 from iohub.mm_fov import MicroManagerFOV, MicroManagerFOVMapping
@@ -35,34 +31,6 @@ def _normalize_mm_pos_key(key: str | int) -> int:
         raise TypeError("Micro-Manager position keys must be integers.")
 
 
-def _tiff_to_fsspec_store(
-    zarr_tiff_store: ZarrTiffStore, root_uri: str
-) -> zarr.storage.FsspecStore:
-    """Bridge tifffile (zarr-python v2 interface) with zarr-python v3.
-
-    Parameters
-    ----------
-    zarr_tiff_store : ZarrTiffStore
-        Zarr (v2) wrapper for a TIFF series
-    root_uri : str
-        `file://` URI to the directory containing the TIFF files
-
-    Returns
-    -------
-    zarr.storage.FsspecStore
-        Zarr (v3) wrapper for a TIFF series
-    """
-    spec_container = io.StringIO()
-    zarr_tiff_store.write_fsspec(spec_container, url=root_uri)
-    fs, _ = fsspec.url_to_fs(
-        "reference://",
-        fo=json.loads(spec_container.getvalue()),
-        target_protocol="file",
-        asynchronous=True,
-    )
-    return zarr.storage.FsspecStore(fs=fs)
-
-
 def find_first_ome_tiff_in_mmstack(data_path: Path) -> Path:
     if data_path.is_file():
         if "ome.tif" in data_path.name:
@@ -152,10 +120,8 @@ def _parse_data(self):
             self.width,
         ) = dims.values()
         self._set_mm_meta(self._first_tif.micromanager_metadata)
-        zarr_tiff_store = series.aszarr(multiscales=True)
-        self._store = _tiff_to_fsspec_store(
-            zarr_tiff_store, root_uri=self._root.as_uri()
-        )
+        # tifffile.zarr.ZarrTiffStore is a native zarr v3 store
+        self._store = series.aszarr(multiscales=True)
         _logger.debug(f"Opened {self._store}.")
         data = da.from_zarr(zarr.open(self._store, mode="r")["0"])
         self.dtype = data.dtype

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
     "pandas>=1.5.2",
     "pydantic>=2.8.2",
     "pydantic_extra_types>=2.9.0",
-    "tifffile>=2024.1.30, <2025.5.21",
+    "tifffile>=2025.5.21",
     "natsort>=7.1.1",
     "ndtiff>=2.2.1",
     "zarr>=3.0.8",