From c7fc56daf0c87c04ad6d54e97f4d078283a2042d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 9 Sep 2025 05:48:13 +0000
Subject: [PATCH 01/28] Initial plan


From e4ce70ec6f576549e82aa86d6412f46383874f87 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 9 Sep 2025 06:02:56 +0000
Subject: [PATCH 02/28] Replace aicsimageio with bioio in imports and class
 references

Co-authored-by: pr4deepr <13831458+pr4deepr@users.noreply.github.com>
---
 core/lls_core/deconvolution.py   |  6 +++---
 core/lls_core/models/deskew.py   | 16 +++++++--------
 core/lls_core/types.py           | 34 ++++++++++++++++----------------
 core/pyproject.toml              |  4 ++--
 core/tests/test_cli.py           |  8 ++++----
 core/tests/utils.py              |  4 ++--
 plugin/napari_lattice/fields.py  |  2 +-
 plugin/napari_lattice/reader.py  | 14 ++++++-------
 plugin/pyproject.toml            |  4 ++--
 plugin/tests/test_dock_widget.py |  6 +++---
 10 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/core/lls_core/deconvolution.py b/core/lls_core/deconvolution.py
index f42863cb..4a03bf8a 100644
--- a/core/lls_core/deconvolution.py
+++ b/core/lls_core/deconvolution.py
@@ -7,7 +7,7 @@
 import logging
 import importlib.util
 from typing import Collection, Iterable,Union,Literal, Optional, TYPE_CHECKING
-from aicsimageio.aics_image import AICSImage
+from bioio import BioImage
 from skimage.io import imread
 from aicspylibczi import CziFile
 from numpy.typing import NDArray
@@ -79,8 +79,8 @@ def read_psf(psf_paths: Collection[Path],
                    if len(psf_aics_data.shape) != 3:
                        raise ValueError(f"PSF should be a 3D image (shape of 3), but got {psf_aics.shape}")
                 else:
-                    #Use AICSImageIO
-                    psf_aics = AICSImage(str(psf))
+                    #Use BioIO
+                    psf_aics = BioImage(str(psf))
                     psf_aics_data = psf_aics.data[0][0]
                     psf_aics_data = pad_image_nearest_multiple(
                         img=psf_aics_data, nearest_multiple=16)           
diff --git a/core/lls_core/models/deskew.py b/core/lls_core/models/deskew.py
index a8cb1c11..64e5563b 100644
--- a/core/lls_core/models/deskew.py
+++ b/core/lls_core/models/deskew.py
@@ -16,7 +16,7 @@
 import numpy as np
 
 if TYPE_CHECKING:
-    from aicsimageio.types import PhysicalPixelSizes
+    from bioio import PhysicalPixelSizes
 
 class DefinedPixelSizes(FieldAccessModel):
     """
@@ -161,7 +161,7 @@ def convert_skew(cls, v: Any):
 
     @validator("physical_pixel_sizes", pre=True, always=True)
     def convert_pixels(cls, v: Any, values: dict[Any, Any]):
-        from aicsimageio.types import PhysicalPixelSizes
+        from bioio import PhysicalPixelSizes
         if isinstance(v, PhysicalPixelSizes):
             v = DefinedPixelSizes.from_physical(v)
         elif isinstance(v, tuple) and len(v) == 3:
@@ -176,15 +176,15 @@ def convert_pixels(cls, v: Any, values: dict[Any, Any]):
 
     @root_validator(pre=True)
     def read_image(cls, values: dict):
-        from aicsimageio import AICSImage
+        from bioio import BioImage
         from os import fspath
 
         img = values["input_image"]
 
-        aics: AICSImage | None = None
+        aics: BioImage | None = None
         if is_pathlike(img):
-            aics = AICSImage(fspath(img))
-        elif isinstance(img, AICSImage):
+            aics = BioImage(fspath(img))
+        elif isinstance(img, BioImage):
             aics = img
         elif isinstance(img, DataArray):
             if set(img.dims) >= {"Z", "Y", "X"}:
@@ -198,9 +198,9 @@ def read_image(cls, values: dict):
             else:
                 raise ValueError("Only 3D numpy arrays are currently supported. If you have a different shape, please use a DataArray and name your dimensions C, T, Z, Y and/or Z.")
         else:
-            raise ValueError("Value of input_image was neither a path, an AICSImage, or array-like.")
+            raise ValueError("Value of input_image was neither a path, a BioImage, or array-like.")
 
-        # If the image was convertible to AICSImage, we should use the metadata from there
+        # If the image was convertible to BioImage, we should use the metadata from there
         if aics:
             values["input_image"] = aics.xarray_dask_data 
             # Take pixel sizes from the image metadata, but only if they're defined
diff --git a/core/lls_core/types.py b/core/lls_core/types.py
index 7cfe3a2e..075331c1 100644
--- a/core/lls_core/types.py
+++ b/core/lls_core/types.py
@@ -6,7 +6,7 @@
 import numpy as np
 from numpy.typing import NDArray
 from xarray import DataArray
-from aicsimageio import AICSImage
+from bioio import BioImage
 from os import fspath, PathLike as OriginalPathLike
 
 # This is a superset of os.PathLike
@@ -19,20 +19,20 @@ def is_pathlike(x: Any) -> TypeGuard[PathLike]:
 def is_arraylike(arr: Any) -> TypeGuard[ArrayLike]:
     return isinstance(arr, (DaskArray, np.ndarray, OCLArray, DataArray))
 
-ImageLike: TypeAlias = Union[PathLike, AICSImage, ArrayLike]
-def image_like_to_image(img: ImageLike) -> DataArray:
-    """
-    Converts an image in one of many formats to a DataArray
-    """
-    # First try treating it as a path
-    try:
-        img = AICSImage(fspath(img))
-    except TypeError:
-        pass
-    if isinstance(img, AICSImage):
-        return img.xarray_dask_data
-    else:
-        for required_key in ("shape", "dtype", "ndim", "__array__", "__array_ufunc__"):
-            if not hasattr(img, required_key):
-                raise ValueError(f"The provided object {img} is not array like!")
+ImageLike: TypeAlias = Union[PathLike, BioImage, ArrayLike]
+def image_like_to_image(img: ImageLike) -> DataArray:
+    """
+    Converts an image in one of many formats to a DataArray
+    """
+    # First try treating it as a path
+    try:
+        img = BioImage(fspath(img))
+    except TypeError:
+        pass
+    if isinstance(img, BioImage):
+        return img.xarray_dask_data
+    else:
+        for required_key in ("shape", "dtype", "ndim", "__array__", "__array_ufunc__"):
+            if not hasattr(img, required_key):
+                raise ValueError(f"The provided object {img} is not array like!")
         return DataArray(img)
diff --git a/core/pyproject.toml b/core/pyproject.toml
index 1fba7b23..ad6c2b2c 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -35,8 +35,8 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"
 ]
 requires-python = ">=3.8"
-dependencies = [
-    "aicsimageio>=4.6.3",
+dependencies = [
+    "bioio>=3.0.0",
     # Earlier versions don't have Python 3.11 binaries, and the sdist
     # is misconfigured: https://github.com/AllenCellModeling/aicspylibczi/issues/90
     "aicspylibczi>=3.1.1",
diff --git a/core/tests/test_cli.py b/core/tests/test_cli.py
index 38867aba..f51096fd 100644
--- a/core/tests/test_cli.py
+++ b/core/tests/test_cli.py
@@ -2,7 +2,7 @@
 
 from typing import Callable, List
 import pytest
-from aicsimageio.aics_image import AICSImage
+from bioio import BioImage
 from npy2bdv import BdvEditor
 import numpy as np
 from pathlib import Path
@@ -15,7 +15,7 @@ def create_image(path: Path):
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
     # Save image as a tif filw in home directory
-    AICSImage(raw).save(path)
+    BioImage(raw).save(path)
     assert path.exists()
 
 
@@ -28,7 +28,7 @@ def create_data(dir: Path) -> Path:
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
     # Save image as a tif filw in home directory
-    AICSImage(raw).save(input_file)
+    BioImage(raw).save(input_file)
     assert input_file.exists()
 
     config: dict[str, str] = {
@@ -47,7 +47,7 @@ def assert_tiff(output_dir: Path):
     results = list(output_dir.glob("*.tif"))
     assert len(results) > 0
     for result in results:
-        AICSImage(result).get_image_data()
+        BioImage(result).get_image_data()
 
 def assert_h5(output_dir: Path):
     """Checks that a valid H5 was generated"""
diff --git a/core/tests/utils.py b/core/tests/utils.py
index c9744a03..daff8b4d 100644
--- a/core/tests/utils.py
+++ b/core/tests/utils.py
@@ -3,7 +3,7 @@
 from typer.testing import CliRunner
 from lls_core.cmds.__main__ import app
 import npy2bdv
-from aicsimageio import AICSImage
+from bioio import BioImage
 
 def invoke(args: Sequence[str]):
     CliRunner().invoke(app, args, catch_exceptions=False)
@@ -13,5 +13,5 @@ def valid_image_path(path: Path) -> bool:
         npy2bdv.npy2bdv.BdvEditor(str(path)).read_view()
         return True
     else:
-        AICSImage(path).get_image_data()
+        BioImage(path).get_image_data()
         return True
diff --git a/plugin/napari_lattice/fields.py b/plugin/napari_lattice/fields.py
index 862e41c2..7291e9e4 100644
--- a/plugin/napari_lattice/fields.py
+++ b/plugin/napari_lattice/fields.py
@@ -402,7 +402,7 @@ def _get_kwargs(self) -> DeskewKwargs:
         """
         Returns the LatticeData fields that the Deskew tab can provide
         """
-        from aicsimageio.types import PhysicalPixelSizes
+        from bioio import PhysicalPixelSizes
         DeskewParams.update_forward_refs()
         params = lattice_params_from_napari(
                 imgs=self.img_layer.value,
diff --git a/plugin/napari_lattice/reader.py b/plugin/napari_lattice/reader.py
index cbe90615..e271b490 100644
--- a/plugin/napari_lattice/reader.py
+++ b/plugin/napari_lattice/reader.py
@@ -13,18 +13,18 @@
 import os 
 import numpy as np
 from napari.layers import Image
-from aicsimageio.aics_image import AICSImage
+from bioio import BioImage
 
 from typing import List, Optional, Tuple, Collection, TYPE_CHECKING, TypedDict
 
-from aicsimageio.types import PhysicalPixelSizes
+from bioio import PhysicalPixelSizes
 from lls_core.models.deskew import DefinedPixelSizes
 
 from logging import getLogger
 logger = getLogger(__name__)
 
 if TYPE_CHECKING:
-    from aicsimageio.types import ImageLike
+    from bioio import ImageLike
     from xarray import DataArray
 
 class NapariImageParams(TypedDict):
@@ -74,7 +74,7 @@ def lattice_params_from_napari(
         save_names.append(save_name)
             
         if 'aicsimage' in img.metadata.keys():
-            img_data_aics: AICSImage = img.metadata['aicsimage']
+            img_data_aics: BioImage = img.metadata['aicsimage']
             # If the user has not provided pixel sizes, we extract them fro the metadata
             # Only process pixel sizes that are not none
             if physical_pixel_sizes is None and all(img_data_aics.physical_pixel_sizes):
@@ -191,13 +191,13 @@ def bdv_h5_reader(path):
     layer_type = "image"  # optional, default is "image"
     return [(images, add_kwargs, layer_type)]
 
-def tiff_reader(path: ImageLike) -> List[Tuple[AICSImage, dict, str]]:
+def tiff_reader(path: ImageLike) -> List[Tuple[BioImage, dict, str]]:
     """Take path to tiff image and returns a list of LayerData tuples.
-    Specifying tiff_reader to have better control over tifffile related errors when using AICSImage
+    Specifying tiff_reader to have better control over tifffile related errors when using BioImage
     """
     
     try:
-        image = AICSImage(path)
+        image = BioImage(path)
     except Exception as e:
         raise Exception("Error reading TIFF. Try upgrading tifffile library: pip install tifffile --upgrade.") from e
 
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 07e5a259..5974059f 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -35,8 +35,8 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"
 ]
 requires-python = ">=3.8"
-dependencies = [
-    "aicsimageio>=4.6.3",
+dependencies = [
+    "bioio>=3.0.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
     "fsspec>=2022.8.2",
diff --git a/plugin/tests/test_dock_widget.py b/plugin/tests/test_dock_widget.py
index 6fde3b6a..d8a058ec 100644
--- a/plugin/tests/test_dock_widget.py
+++ b/plugin/tests/test_dock_widget.py
@@ -9,7 +9,7 @@
 from magicclass._gui._gui_modes import ErrorMode
 import pytest
 from lls_core.sample import resources
-from aicsimageio.aics_image import AICSImage
+from bioio import BioImage
 from napari_lattice.fields import PixelSizeSource
 from tempfile import TemporaryDirectory
 
@@ -35,7 +35,7 @@ def image_data(request: pytest.FixtureRequest):
     Fixture function that yields test images as file paths
     """
     with as_file(resources / request.param) as image_path:
-        yield AICSImage(image_path, )
+        yield BioImage(image_path, )
 
 def set_debug(cls: MagicTemplate):
     """
@@ -48,7 +48,7 @@ def _handler(e: Exception, parent: Widget):
     for child in cls.__magicclass_children__:
         set_debug(child)
 
-def test_dock_widget(make_napari_viewer: Callable[[], Viewer], image_data: AICSImage):
+def test_dock_widget(make_napari_viewer: Callable[[], Viewer], image_data: BioImage):
     # make viewer and add an image layer using our fixture
     viewer = make_napari_viewer()
 

From be54c3ba1e94e54612a72d3d756b701bf33b291f Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Fri, 14 Nov 2025 16:45:45 +1100
Subject: [PATCH 03/28] Add default physical pixel sizes to BioImage obj

Without this, writing by the bioio-ome-tiff writer fails.
---
 core/tests/test_cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/core/tests/test_cli.py b/core/tests/test_cli.py
index f51096fd..cadd279a 100644
--- a/core/tests/test_cli.py
+++ b/core/tests/test_cli.py
@@ -15,7 +15,8 @@ def create_image(path: Path):
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
     # Save image as a tif filw in home directory
-    BioImage(raw).save(path)
+    b = BioImage(raw, physical_pixel_sizes={ax: 1. for ax in 'ZYX'})
+    b.save(path)
     assert path.exists()
 
 

From ebfc88cc7da12d74e4c7e982326fcf3963135e90 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Fri, 14 Nov 2025 16:46:13 +1100
Subject: [PATCH 04/28] typo: filw -> file

---
 core/tests/test_cli.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/core/tests/test_cli.py b/core/tests/test_cli.py
index cadd279a..0347c2da 100644
--- a/core/tests/test_cli.py
+++ b/core/tests/test_cli.py
@@ -14,7 +14,7 @@ def create_image(path: Path):
     # Create a zero array of shape 5x5x5 with a value of 10 at (2,4,2)
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
-    # Save image as a tif filw in home directory
+    # Save image as a tif file in home directory
     b = BioImage(raw, physical_pixel_sizes={ax: 1. for ax in 'ZYX'})
     b.save(path)
     assert path.exists()
@@ -28,7 +28,7 @@ def create_data(dir: Path) -> Path:
     # Create a zero array of shape 5x5x5 with a value of 10 at (2,4,2)
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
-    # Save image as a tif filw in home directory
+    # Save image as a tif file in home directory
     BioImage(raw).save(input_file)
     assert input_file.exists()
 

From df1990a1b67602611c7a422f3907e4f5e2128435 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Fri, 14 Nov 2025 17:04:22 +1100
Subject: [PATCH 05/28] Add physical pixel size to BioImage in create_data

---
 core/tests/test_cli.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/core/tests/test_cli.py b/core/tests/test_cli.py
index 0347c2da..aed29f1f 100644
--- a/core/tests/test_cli.py
+++ b/core/tests/test_cli.py
@@ -29,7 +29,8 @@ def create_data(dir: Path) -> Path:
     raw = np.zeros((5, 5, 5))
     raw[2, 4, 2] = 10
     # Save image as a tif file in home directory
-    BioImage(raw).save(input_file)
+    b = BioImage(raw, physical_pixel_sizes={ax: 1. for ax in 'ZYX'})
+    b.save(input_file)
     assert input_file.exists()
 
     config: dict[str, str] = {

From d31ab66ab6f10a0f2fddf2fa74acd95de49e0fb5 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Fri, 14 Nov 2025 17:04:37 +1100
Subject: [PATCH 06/28] Add bioio plugin dependencies

---
 core/pyproject.toml   | 8 ++++----
 plugin/pyproject.toml | 6 ++++--
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index ad6c2b2c..f7c9e575 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -35,11 +35,11 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"
 ]
 requires-python = ">=3.8"
-dependencies = [
+dependencies = [
     "bioio>=3.0.0",
-    # Earlier versions don't have Python 3.11 binaries, and the sdist
-    # is misconfigured: https://github.com/AllenCellModeling/aicspylibczi/issues/90
-    "aicspylibczi>=3.1.1",
+    "bioio-bioformats>=1.3.0",
+    "bioio-czi>=2.4.0",
+    "bioio-ome-tiff>=1.4.0",
     "click",
     "dask",
     "dask[distributed]",
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 5974059f..1d74b55a 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -35,8 +35,11 @@ classifiers = [
     "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"
 ]
 requires-python = ">=3.8"
-dependencies = [
+dependencies = [
     "bioio>=3.0.0",
+    "bioio-bioformats>=1.3.0",
+    "bioio-czi>=2.4.0",
+    "bioio-ome-tiff>=1.4.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
     "fsspec>=2022.8.2",
@@ -45,7 +48,6 @@ dependencies = [
     # The lower bound is because we need this Python 3.8 fix: https://github.com/hanjinliu/magic-class/pull/108
     "magic-class>=0.7.5",
     "magicgui<0.8.0",
-    "napari-aicsimageio>=0.7.2",
     "napari-workflow-inspector",
     "napari-workflows>=0.2.8",
     "napari[all]>=0.4.11",

From 8998f42f10b82f6ff5e83e237b9f095bfac5e07d Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Fri, 14 Nov 2025 17:04:55 +1100
Subject: [PATCH 07/28] Use separate resolutionunit for tifffile write

---
 core/lls_core/writers.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/core/lls_core/writers.py b/core/lls_core/writers.py
index 8fdcb9ed..0ca55d0b 100644
--- a/core/lls_core/writers.py
+++ b/core/lls_core/writers.py
@@ -118,7 +118,8 @@ def flush(self):
                 str(path),
                 data = images_array,
                 bigtiff=True,
-                resolution=(1./self.lattice.dx, 1./self.lattice.dy, "MICROMETER"),
+                resolution=(1./self.lattice.dx, 1./self.lattice.dy),
+                resolutionunit="MICROMETER",
                 metadata={'spacing': self.lattice.new_dz, 'unit': 'um', 'axes': 'TZCYX'},
                 imagej=True
             )

From 337a6990642b7f2f41021932ac59413ef2928005 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Sat, 15 Nov 2025 13:12:00 +1100
Subject: [PATCH 08/28] Use bioio-tifffile to read raw.tif

bioio-bioformats fails with dask use:

https://github.com/bioio-devs/bioio-bioformats/issues/40

After fixing reading, I got a validationerror
when save_dir was not set, so I set
save_dir to a temporary directory as in
other tests.
---
 core/tests/test_process.py | 42 +++++++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 16 deletions(-)

diff --git a/core/tests/test_process.py b/core/tests/test_process.py
index f3a19f78..e7142b0a 100644
--- a/core/tests/test_process.py
+++ b/core/tests/test_process.py
@@ -9,6 +9,8 @@
 from pathlib import Path
 from napari_workflows import Workflow
 from pytest import FixtureRequest
+from bioio_tifffile import reader as tiffreader
+from bioio import BioImage
 
 
 from .params import parameterized
@@ -51,22 +53,30 @@ def test_save(minimal_image_path: str, args: dict):
 
 
 def test_process_deconv_crop():
-    for slice in (
-        LatticeData.parse_obj(
-            {
-                "input_image": root / "raw.tif",
-                "deconvolution": {
-                    "psf": [root / "psf.tif"],
-                },
-                "crop": CropParams(
-                    roi_list=[[[0, 0], [0, 110], [95, 0], [95, 110]]]
-                ),
-            }
-        )
-        .process()
-        .slices
-    ):
-        assert slice.data.ndim == 3
+    with tempfile.TemporaryDirectory() as tempdir:
+        for slice in (
+            LatticeData.parse_obj(
+                {
+                    # use BioImage rather than just Path to ensure tifffile
+                    # is used instead of bioformats, which prevents dask use
+                    # due to a bug:
+                    # https://github.com/bioio-devs/bioio-bioformats/issues/40
+                    "input_image": BioImage(
+                        root / "raw.tif", reader=tiffreader.Reader
+                    ),
+                    "deconvolution": {
+                        "psf": [root / "psf.tif"],
+                    },
+                    "crop": CropParams(
+                        roi_list=[[[0, 0], [0, 110], [95, 0], [95, 110]]]
+                    ),
+                    "save_dir": tempdir,
+                }
+            )
+            .process()
+            .slices
+        ):
+            assert slice.data.ndim == 3
 
 
 def test_process_time_range(multi_channel_time: Path):

From 8a616e53847a10fff2ca46be85f34051c7160dd8 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Sat, 15 Nov 2025 13:14:52 +1100
Subject: [PATCH 09/28] Fix patch to patch bioio instead of aicsimageio

---
 core/tests/test_validation.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/core/tests/test_validation.py b/core/tests/test_validation.py
index d4cb50cb..b0e455a9 100644
--- a/core/tests/test_validation.py
+++ b/core/tests/test_validation.py
@@ -48,7 +48,7 @@ def test_allow_trailing_slash():
 
 def test_infer_czi_pixel_sizes(rbc_tiny: Path):
     mock = PropertyMock()
-    with patch("aicsimageio.AICSImage.physical_pixel_sizes", new=mock):
+    with patch("bioio.BioImage.physical_pixel_sizes", new=mock):
         DeskewParams(input_image=rbc_tiny)
-        # The AICSImage should be queried for the pixel sizes
+        # The BioImage should be queried for the pixel sizes
         assert mock.called

From 692e4298ecb5fbf385e0928a513427fffce83463 Mon Sep 17 00:00:00 2001
From: Pradeep Rajasekhar <pradeep.rajasekhar@gmail.com>
Date: Wed, 26 Nov 2025 16:55:17 +1100
Subject: [PATCH 10/28] fix dependency issues

---
 plugin/pyproject.toml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 1d74b55a..e6a9d510 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -40,6 +40,7 @@ dependencies = [
     "bioio-bioformats>=1.3.0",
     "bioio-czi>=2.4.0",
     "bioio-ome-tiff>=1.4.0",
+    "bioio-tifffile==1.3.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
     "fsspec>=2022.8.2",
@@ -102,6 +103,11 @@ ignore_unused = [
     "fsspec",
     "imageio",
     "ome-types"
+
+    #bioio packages are needed but not directly imported
+    "bioio-bioformats",
+    "bioio-czi",
+    "bioio-ome-tiff"
 ]
 output_format = "human_detailed"  
 

From f0c666966eda041b529ebc645b0f893121046f65 Mon Sep 17 00:00:00 2001
From: Pradeep Rajasekhar <pradeep.rajasekhar@gmail.com>
Date: Wed, 26 Nov 2025 16:55:38 +1100
Subject: [PATCH 11/28] use bioio for reading psf with czi extension

---
 core/lls_core/deconvolution.py | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/core/lls_core/deconvolution.py b/core/lls_core/deconvolution.py
index 4a03bf8a..c6144aaa 100644
--- a/core/lls_core/deconvolution.py
+++ b/core/lls_core/deconvolution.py
@@ -8,8 +8,8 @@
 import importlib.util
 from typing import Collection, Iterable,Union,Literal, Optional, TYPE_CHECKING
 from bioio import BioImage
+import bioio_czi
 from skimage.io import imread
-from aicspylibczi import CziFile
 from numpy.typing import NDArray
 import os
 import numpy as np
@@ -62,12 +62,10 @@ def read_psf(psf_paths: Collection[Path],
     for psf in psf_paths:
         if psf.exists() and psf.is_file():
             if psf.suffix == ".czi":
-                psf_czi = CziFile(psf.__str__())
-                psf_aics = psf_czi.read_image()
+                psf_czi = BioImage(psf.__str__(), reader=bioio_czi.Reader)
+                psf_aics = psf_czi.data
                 # make sure shape is 3D
-                psf_aics = psf_aics[0][0]  # np.expand_dims(psf_aics[0],axis=0)
-                # if len(psf_aics[0])>=1:
-                #psf_channels = len(psf_aics[0])
+                psf_aics = psf_aics[0][0]  
                 assert len(
                     psf_aics.shape) == 3, f"PSF should be a 3D image (shape of 3), but got {psf_aics.shape}"
                 # pad psf to multiple of 16 for decon
@@ -79,7 +77,7 @@ def read_psf(psf_paths: Collection[Path],
                    if len(psf_aics_data.shape) != 3:
                        raise ValueError(f"PSF should be a 3D image (shape of 3), but got {psf_aics.shape}")
                 else:
-                    #Use BioIO
+                    #Use BioIO
                     psf_aics = BioImage(str(psf))
                     psf_aics_data = psf_aics.data[0][0]
                     psf_aics_data = pad_image_nearest_multiple(

From dc3e6eee19f25f2e95fddfe742794ccd22dfcbc5 Mon Sep 17 00:00:00 2001
From: Pradeep Rajasekhar <pradeep.rajasekhar@gmail.com>
Date: Wed, 26 Nov 2025 17:02:32 +1100
Subject: [PATCH 12/28] update dependencies

---
 core/pyproject.toml   | 8 +++++++-
 plugin/pyproject.toml | 2 +-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index f7c9e575..4128d174 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -40,6 +40,7 @@ dependencies = [
     "bioio-bioformats>=1.3.0",
     "bioio-czi>=2.4.0",
     "bioio-ome-tiff>=1.4.0",
+    "bioio-tifffile==1.3.0",
     "click",
     "dask",
     "dask[distributed]",
@@ -158,7 +159,12 @@ ignore_unused = [
 
     # Used for the deployment, but never imported
     "build",
-    "twine"
+    "twine",
+
+    #bioio packages are needed but not directly imported
+    "bioio-bioformats",
+    "bioio-czi",
+    "bioio-ome-tiff"
 ]
 output_format = "human_detailed"  
 
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index e6a9d510..b9a73f80 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -102,7 +102,7 @@ ignore_unused = [
     # This is pinned but unused
     "fsspec",
     "imageio",
-    "ome-types"
+    "ome-types",
 
     #bioio packages are needed but not directly imported
     "bioio-bioformats",

From f453a3e12dbffde706de4972254e924e4a5fa361 Mon Sep 17 00:00:00 2001
From: Pradeep Rajasekhar <pradeep.rajasekhar@gmail.com>
Date: Wed, 26 Nov 2025 17:29:17 +1100
Subject: [PATCH 13/28] update fawltydeps

---
 .github/lint/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/lint/action.yml b/.github/lint/action.yml
index 46648d71..05e47479 100644
--- a/.github/lint/action.yml
+++ b/.github/lint/action.yml
@@ -10,7 +10,7 @@ runs:
   using: "composite"
   steps:
     - run: |
-        pip install fawltydeps==0.12.0
+        pip install fawltydeps
         fawltydeps --check --detailed --verbose
       shell: bash -l {0}
       working-directory: ${{ inputs.directory }}

From 077e8475a9b804e514543d02bae456aadef49170 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Tue, 2 Dec 2025 14:20:00 +1100
Subject: [PATCH 14/28] Update test matrix to 3.10 3.13

---
 .github/workflows/test_and_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index e176f86f..1e637c81 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8","3.9","3.10"] #not compatible with py 3.10 and 3.12 yet
+        python-version: ["3.10", "3.13"]
 
     env:
       DISPLAY: ":99.0"

From 7aad4d1b4bb41f5a4545e0b221c3f3246e126f37 Mon Sep 17 00:00:00 2001
From: Juan Nunez-Iglesias <jni@fastmail.com>
Date: Tue, 2 Dec 2025 14:22:38 +1100
Subject: [PATCH 15/28] Remove white space

---
 .github/workflows/test_and_deploy.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 1e637c81..bdc7c372 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -46,7 +46,7 @@ jobs:
         with:
           # Install a specific version of uv.
           version: "0.6.17"
-        
+
       - name: Install core
         timeout-minutes: 10
         run: |
@@ -94,9 +94,9 @@ jobs:
     # github secrets (see readme for details)
     needs: [test]
     runs-on: ubuntu-latest
-    environment: 
+    environment:
       name: github-pages
-    permissions: 
+    permissions:
       id-token: write
       pages: write
       contents: write
@@ -136,7 +136,7 @@ jobs:
         uses: actions/deploy-pages@v4
 
       - uses: ncipollo/release-action@v1.18.0
-        name: Create GitHub release 
+        name: Create GitHub release
         if: contains(github.ref, 'tags')
         with:
           skipIfReleaseExists: true

From d865bd9e0ae5f3d48922dccf6fe26a45132adb50 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Tue, 2 Dec 2025 17:30:11 +1100
Subject: [PATCH 16/28] fix issues with workflow_path when running tests
 locally in windows

---
 core/tests/test_workflows.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/core/tests/test_workflows.py b/core/tests/test_workflows.py
index 28b1edb1..b8d617da 100644
--- a/core/tests/test_workflows.py
+++ b/core/tests/test_workflows.py
@@ -97,9 +97,11 @@ def test_table_workflow(lls7_t1_ch1: Path, table_workflow: Workflow):
 def test_argument_order(rbc_tiny: Path):
     # Tests that only the first unfilled argument is passed an array
     with tempfile.TemporaryDirectory() as tmpdir:
+        # Get the path relative to this test file
+        workflow_path = Path(__file__).parent / "workflows" / "argument_order" / "test_workflow.yml"
         params = LatticeData(
             input_image = rbc_tiny,
-            workflow = "core/tests/workflows/argument_order/test_workflow.yml",
+            workflow = str(workflow_path),
             save_dir = tmpdir
         )
         for output in params.process_workflow().process():
@@ -109,9 +111,11 @@ def test_sum_preview(rbc_tiny: Path):
     import numpy as np
     # Tests that we can sum the preview result. This is required for the plugin
     with tempfile.TemporaryDirectory() as tmpdir:
+        # Get the path relative to this test file
+        workflow_path = Path(__file__).parent / "workflows" / "binarisation" / "workflow.yml"
         params = LatticeData(
             input_image = rbc_tiny,
-            workflow = "core/tests/workflows/binarisation/workflow.yml",
+            workflow = str(workflow_path),
             save_dir = tmpdir
         )
         previews = list(params.process_workflow().roi_previews())
@@ -122,9 +126,10 @@ def test_crop_workflow(lls7_t1_ch1: Path):
     # Tests that crop workflows only process each ROI lazily
 
     with tempfile.TemporaryDirectory() as tmpdir:
+        workflow_path = Path(__file__).parent / "workflows" / "binarisation" / "workflow.yml"
         params = LatticeData(
             input_image = lls7_t1_ch1,
-            workflow = "core/tests/workflows/binarisation/workflow.yml",
+            workflow = str(workflow_path),
             save_dir = tmpdir,
             crop=CropParams(
                 roi_list=[

From 79203792596161237cf70dde17991b069062e2f9 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 11:05:13 +1100
Subject: [PATCH 17/28] remove bioio_bioformats

---
 core/pyproject.toml   | 4 ++--
 plugin/pyproject.toml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 4128d174..f42733c0 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -37,7 +37,7 @@ classifiers = [
 requires-python = ">=3.8"
 dependencies = [
     "bioio>=3.0.0",
-    "bioio-bioformats>=1.3.0",
+    #"bioio-bioformats>=1.3.0",
     "bioio-czi>=2.4.0",
     "bioio-ome-tiff>=1.4.0",
     "bioio-tifffile==1.3.0",
@@ -162,7 +162,7 @@ ignore_unused = [
     "twine",
 
     #bioio packages are needed but not directly imported
-    "bioio-bioformats",
+    #"bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff"
 ]
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index b9a73f80..2cdb8ad6 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -37,7 +37,7 @@ classifiers = [
 requires-python = ">=3.8"
 dependencies = [
     "bioio>=3.0.0",
-    "bioio-bioformats>=1.3.0",
+    #"bioio-bioformats>=1.3.0",
     "bioio-czi>=2.4.0",
     "bioio-ome-tiff>=1.4.0",
     "bioio-tifffile==1.3.0",
@@ -105,7 +105,7 @@ ignore_unused = [
     "ome-types",
 
     #bioio packages are needed but not directly imported
-    "bioio-bioformats",
+    #"bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff"
 ]

From f0d6bfa9b9730ee44b8010399bcb8e00746d2329 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 12:34:52 +1100
Subject: [PATCH 18/28] testing if modifying install order fixes tiff reading
 issues

---
 core/pyproject.toml   | 6 +++---
 plugin/pyproject.toml | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index f42733c0..2bdfaccf 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -37,10 +37,10 @@ classifiers = [
 requires-python = ">=3.8"
 dependencies = [
     "bioio>=3.0.0",
-    #"bioio-bioformats>=1.3.0",
     "bioio-czi>=2.4.0",
-    "bioio-ome-tiff>=1.4.0",
     "bioio-tifffile==1.3.0",
+    "bioio-ome-tiff>=1.4.0",
+    "bioio-bioformats>=1.3.0",
     "click",
     "dask",
     "dask[distributed]",
@@ -62,7 +62,7 @@ dependencies = [
     "resource-backed-dask-array>=0.1.0",
     "scikit-image",
     "StrEnum",
-    "tifffile>=2023.3.15,<2025.2.18", #>=2022.8.12
+    #"tifffile>=2023.3.15,<2025.2.18", #>=2022.8.12
     "toolz",
     "tqdm",
     "typer<0.17.0",
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 2cdb8ad6..b4db3f7a 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -37,10 +37,10 @@ classifiers = [
 requires-python = ">=3.8"
 dependencies = [
     "bioio>=3.0.0",
-    #"bioio-bioformats>=1.3.0",
+    "bioio-tifffile==1.3.0",
     "bioio-czi>=2.4.0",
     "bioio-ome-tiff>=1.4.0",
-    "bioio-tifffile==1.3.0",
+    #"bioio-bioformats>=1.3.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
     "fsspec>=2022.8.2",

From d7d77ccfcb75765f5389a5e27e874d71081c8fb2 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 12:37:50 +1100
Subject: [PATCH 19/28] enable bioformats in fawltydeps

---
 core/pyproject.toml   | 2 +-
 plugin/pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 2bdfaccf..93d75a74 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -162,7 +162,7 @@ ignore_unused = [
     "twine",
 
     #bioio packages are needed but not directly imported
-    #"bioio-bioformats",
+    "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff"
 ]
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index b4db3f7a..7d9153c5 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -105,7 +105,7 @@ ignore_unused = [
     "ome-types",
 
     #bioio packages are needed but not directly imported
-    #"bioio-bioformats",
+    "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff"
 ]

From cd01a8d4bce363359d7face17c4116153b43d37e Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 12:50:59 +1100
Subject: [PATCH 20/28] tifffile to fawltydeps

---
 core/pyproject.toml   | 3 ++-
 plugin/pyproject.toml | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 93d75a74..48e92dc0 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -164,7 +164,8 @@ ignore_unused = [
     #bioio packages are needed but not directly imported
     "bioio-bioformats",
     "bioio-czi",
-    "bioio-ome-tiff"
+    "bioio-ome-tiff",
+    "tifffile"
 ]
 output_format = "human_detailed"  
 
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 7d9153c5..b5fb6f40 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -107,7 +107,8 @@ ignore_unused = [
     #bioio packages are needed but not directly imported
     "bioio-bioformats",
     "bioio-czi",
-    "bioio-ome-tiff"
+    "bioio-ome-tiff",
+    "tifffile"
 ]
 output_format = "human_detailed"  
 

From 4179fb8f362d5bf711620c3832bb429906002fd9 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 13:29:23 +1100
Subject: [PATCH 21/28] fix tifffile in pyproject

---
 core/pyproject.toml   | 4 +---
 plugin/pyproject.toml | 2 --
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 48e92dc0..379dc4c9 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -39,7 +39,6 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-czi>=2.4.0",
     "bioio-tifffile==1.3.0",
-    "bioio-ome-tiff>=1.4.0",
     "bioio-bioformats>=1.3.0",
     "click",
     "dask",
@@ -62,7 +61,7 @@ dependencies = [
     "resource-backed-dask-array>=0.1.0",
     "scikit-image",
     "StrEnum",
-    #"tifffile>=2023.3.15,<2025.2.18", #>=2022.8.12
+    "tifffile", #>=2023.3.15,<2025.2.18", #>=2022.8.12
     "toolz",
     "tqdm",
     "typer<0.17.0",
@@ -165,7 +164,6 @@ ignore_unused = [
     "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff",
-    "tifffile"
 ]
 output_format = "human_detailed"  
 
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index b5fb6f40..ce2b8445 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -39,7 +39,6 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-tifffile==1.3.0",
     "bioio-czi>=2.4.0",
-    "bioio-ome-tiff>=1.4.0",
     #"bioio-bioformats>=1.3.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
@@ -108,7 +107,6 @@ ignore_unused = [
     "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff",
-    "tifffile"
 ]
 output_format = "human_detailed"  
 

From 76c9ed00c03db8257670dd6b91beb52502baae0e Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 13:37:26 +1100
Subject: [PATCH 22/28] remove bioformats due to instability

---
 core/pyproject.toml   | 2 --
 plugin/pyproject.toml | 2 --
 2 files changed, 4 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 379dc4c9..bf5f38a1 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -39,7 +39,6 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-czi>=2.4.0",
     "bioio-tifffile==1.3.0",
-    "bioio-bioformats>=1.3.0",
     "click",
     "dask",
     "dask[distributed]",
@@ -161,7 +160,6 @@ ignore_unused = [
     "twine",
 
     #bioio packages are needed but not directly imported
-    "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff",
 ]
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index ce2b8445..da7603c0 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -39,7 +39,6 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-tifffile==1.3.0",
     "bioio-czi>=2.4.0",
-    #"bioio-bioformats>=1.3.0",
     "dask[distributed]",
     # This isn't used directly, but we need to pin this version
     "fsspec>=2022.8.2",
@@ -104,7 +103,6 @@ ignore_unused = [
     "ome-types",
 
     #bioio packages are needed but not directly imported
-    "bioio-bioformats",
     "bioio-czi",
     "bioio-ome-tiff",
 ]

From b825398308128bb8ae0bb7f0d84c34bcc615a84e Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 14:52:53 +1100
Subject: [PATCH 23/28] add omet-tiff for tif writing

---
 core/pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index bf5f38a1..c10c6125 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -39,6 +39,7 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-czi>=2.4.0",
     "bioio-tifffile==1.3.0",
+    "bioio-ome-tiff",
     "click",
     "dask",
     "dask[distributed]",

From 154b592013638877988bb5ff39bc196fc65be37b Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 15:08:06 +1100
Subject: [PATCH 24/28] add tifffile constraints back

---
 core/pyproject.toml   | 2 +-
 plugin/pyproject.toml | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index c10c6125..178dffba 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -61,7 +61,7 @@ dependencies = [
     "resource-backed-dask-array>=0.1.0",
     "scikit-image",
     "StrEnum",
-    "tifffile", #>=2023.3.15,<2025.2.18", #>=2022.8.12
+    "tifffile>=2023.3.15,<2025.2.18", #>=2022.8.12
     "toolz",
     "tqdm",
     "typer<0.17.0",
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index da7603c0..32a93b95 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -60,6 +60,7 @@ dependencies = [
     "typing_extensions>=4.7.0",
     "rich",
     "StrEnum",
+    "tifffile>=2023.3.15,<2025.2.18", #tiff
     "xarray"
 ]
 

From e82bbb6616f88336c85473694449d6e94cdbe407 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 15:17:08 +1100
Subject: [PATCH 25/28] specify min bioio-ome tif version

---
 core/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 178dffba..351ffeeb 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -39,7 +39,7 @@ dependencies = [
     "bioio>=3.0.0",
     "bioio-czi>=2.4.0",
     "bioio-tifffile==1.3.0",
-    "bioio-ome-tiff",
+    "bioio-ome-tiff>=1.4.0",
     "click",
     "dask",
     "dask[distributed]",

From f03f86f73343df61298ec4aa74e00af37b44036c Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 15:24:39 +1100
Subject: [PATCH 26/28] add to fawltydeps

---
 plugin/pyproject.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index 32a93b95..beefa96e 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -106,6 +106,8 @@ ignore_unused = [
     #bioio packages are needed but not directly imported
     "bioio-czi",
     "bioio-ome-tiff",
+    "bioio-tifffile",
+    "tifffile"
 ]
 output_format = "human_detailed"  
 

From 21f17f530fef3e7066fd4c6275a148c72be023ce Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 15:43:22 +1100
Subject: [PATCH 27/28] loosen tifffile version restriction

---
 core/pyproject.toml   | 2 +-
 plugin/pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/core/pyproject.toml b/core/pyproject.toml
index 351ffeeb..a54dd676 100644
--- a/core/pyproject.toml
+++ b/core/pyproject.toml
@@ -61,7 +61,7 @@ dependencies = [
     "resource-backed-dask-array>=0.1.0",
     "scikit-image",
     "StrEnum",
-    "tifffile>=2023.3.15,<2025.2.18", #>=2022.8.12
+    "tifffile>=2023.3.15",#<2025.2.18", #>=2022.8.12
     "toolz",
     "tqdm",
     "typer<0.17.0",
diff --git a/plugin/pyproject.toml b/plugin/pyproject.toml
index beefa96e..55cd159c 100644
--- a/plugin/pyproject.toml
+++ b/plugin/pyproject.toml
@@ -60,7 +60,7 @@ dependencies = [
     "typing_extensions>=4.7.0",
     "rich",
     "StrEnum",
-    "tifffile>=2023.3.15,<2025.2.18", #tiff
+    "tifffile>=2023.3.15",#,<2025.2.18", #tiff
     "xarray"
 ]
 

From 556ad201a36e9abaed5e388c9258a7de9ed801b8 Mon Sep 17 00:00:00 2001
From: Pradeep <pradeep.rajasekhar@gmail.com>
Date: Wed, 3 Dec 2025 16:12:49 +1100
Subject: [PATCH 28/28] add testing for 3.11 3.12

---
 .github/workflows/test_and_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index bdc7c372..3165a9d6 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.13"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     env:
       DISPLAY: ":99.0"