Explicitly set all direct dependencies

[imagejan]

Running pixi x pipreqs ./src gives:

defusedxml==0.7.1
matplotlib==3.10.0
numcodecs==0.15.1
numpy==2.2.3
ome_zarr==0.10.3
pandas==2.2.3
pint==0.24.4
pydantic==2.10.6
python_dateutil==2.9.0.post0
PyYAML==6.0.2
questionary==2.1.0
scipy==1.15.2
skimage==0.0
tifffile==2025.2.18
tqdm==4.67.1
zarr==3.0.4

Some of those currently aren't listed explicitly in our pyproject.toml but inherited as transient dependencies. Let's list explicit dependencies for all packages we directly import.

(Note: python_dateutil should be removed as datetime.fromisoformat does all we need, but this is obsolete once we remove the eicm subpackage, see also #202.)

Can be addressed together with #221.