Migrate from aicsimageio to bioio

[Copilot]

This PR migrates napari_lattice from the deprecated aicsimageio library to bioio following the migration guide. AICSImageio is being deprecated and bioio provides improved dependency management and continued support.

Changes Made

Dependencies:

• Updated both core/pyproject.toml and plugin/pyproject.toml to use bioio>=3.0.0 instead of aicsimageio>=4.6.3

Import replacements:

• from aicsimageio import AICSImage → from bioio import BioImage
• from aicsimageio.aics_image import AICSImage → from bioio import BioImage
• from aicsimageio.types import PhysicalPixelSizes → from bioio import PhysicalPixelSizes
• from aicsimageio.types import ImageLike → from bioio import ImageLike

Class references:

• All AICSImage class references updated to BioImage
• Type annotations and error messages updated accordingly

API Compatibility

BioImage provides an identical interface to AICSImage, making this a seamless drop-in replacement:

• Same constructor parameters
• Same attributes: data, dims, physical_pixel_sizes, xarray_dask_data
• Same PhysicalPixelSizes class interface

Files Modified

• plugin/napari_lattice/fields.py
• plugin/napari_lattice/reader.py
• plugin/tests/test_dock_widget.py
• core/lls_core/types.py
• core/lls_core/deconvolution.py
• core/lls_core/models/deskew.py
• core/tests/utils.py
• core/tests/test_cli.py

The migration follows the minimal change principle - only the necessary imports and class names were changed. The napari-aicsimageio dependency remains unchanged as napari-bioio doesn't exist yet.

Fixes #100.

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[jni]

@pr4deepr the aicsimageio dependency is keeping napari-lattice pinned to an ancient napari version. Do you want me to take over from copilot? 😂

Are there any other reasons the installation instructions specify old napari and old numpy?

[pr4deepr]

Thanks @jni . Been meaning to get to this, but struggling with time.
That would be super helpful.
I think some of the dependency problem is to do with napari-aicsimageio and depending on aicsimageio.
As there is no napari plugin for bioio (AFAIK), we'll have to create a reader for the czi file atleast, similar to this:

napari_lattice/plugin/napari_lattice/reader.py

Line 139 in 145576e

def bdv_h5_reader(path):

pyclesperanto_prototype depends on older version of numpy.