Unable to open .ome.tiff file : "unexpected keyword argument: is_mmstack"

[DorianKauffmannFranceBioImaging]

Describe the Bug

I'm using a lot aicsimageio and tried to move into bioio, thanks a lot for these very great work.
Following the doc, I've tried to open an image with BioImage and the bioio_ome_tiff reader (and the bioio_ome_tiled_tiff one).
However, while the image can be opened with aicsimageio, tiffile, openslide, Fiji, etc, I did not succeed to open it with bioio with a TypeError: unexpected keyword argument: is_mmstack as you can see bellow:

image_46_BF_z26.ome.tiff.gz

By information, the reading the Migration from AICSImageIO v4 to BioIO v1, the Reader Installation Instructions is showing a "Not Found" webpage.

Environment

• OS Version: Ubuntu 24
• bioio-ome-tiff Version: lastest
  (zarr version = 2.16 to be able to use aicsimageio.writers.OmeTiffWriter)

Thanks a lot for your work and I can't wait to use your new bioio library !

Best,
Dorian

[toloudis]

Thanks for this report!

Usually when we see the is_mmstack error it means you are using an older version of tifffile. As of today, the latest versions for the key bioio packages are bioio-ome-tiff 1.1.0, bioio 1.5.2, bioio-base 1.4.0.
If you can update your tifffile version I believe it might help. You might try separately pip installing tifffile and specifying a recent version. (This has come up a few times and we probably should add this to the migration guide!)

The reader installation link is indeed broken. It's supposed to point here:
https://bioio-devs.github.io/bioio/OVERVIEW.html#reader-installation
We'll get that fixed.

[DorianKauffmannFranceBioImaging]

Hello,

Thanks a lot for the quick response !

I share you what i've tried until now:
Indeed I had the '2023.2.28' version of tifffile. I tried to install the lastest but got some new errors:

So i did :
pip install "tifffile<2022.4.22" (that installs the 2022.4.8 version)
pip install "zarr<2.16.0"
pip install 'bioio-ome-tiled-tiff==1.1.0' 'aicsimageio==4.14.0' 'bioio==1.5.2' 'bioio-base 1.4.0'

However, when importing OmeTiffWriter (from aicsimageio.writers import OmeTiffWriter)
I got a little conflict,

so I tried "pip install --force-reinstall --no-cache-dir numpy"

but got a new conflict

that is in opposition with the first one, as
bioio-ome-tiff 1.1.0 requires tifffile>=2022.4.22 but bioio-ome-tiled-tiff 1.1.0 requires tifffile<2022.4.22

So I tried to create a new virtual environment following the versions of your answer:

conda create -n bio_env python=3.10
conda activate bio_env
pip install bioio=1.5.2
pip install bioio-ome-tiff==1.1.0

pip install bioio-base==1.4.0

So I installed the pip install bioio-base==1.0.7

However I got the same "TypeError: unexpected keyword argument: is_mmstack" when I tried to open my image.
So I checked the tiffile version : 2025.5.10

According to bioio-ome-tiff requirements (seen above), I installed the 2022.4.22 but got an error with scikit-image that requires the 2022.8.12 version.
No error since but still can't open my image:

Sorry for the long description,
But I hope this can help you to fix the used versions between the plug-in system of readers and between the external libraries used in bioio (the concept is really cool !)

Thanks for your support,

Best,

Dorian

[BrianWhitneyAI]

Hey Dorian!

The current dependency issue comes from a clash between these two tiff readers and our writer suite, combined with support for zarr 3+. We recently have been working to migrate our writers to each of the plugins to avoid dependency issues such as this. The work is currently out on this branch, but should make it to main shortly. In the next week or so this should all be released and most of these issue should be cleaned up.

The larger issue here is that bfio does not support zarr 3+, which will become essential to two of our biggest plugins (bioio-ome-zarr and bioio-ome-tiff). Which means you will not be able to have bioio-ome-tiled-tiff installed while one of those plugins is also installed.

If you're interested, you can install the branch and the plugin from main and hopefully this will get you up and running!