Built a bioio reader for imzML files

[DBP008]

Hi bioio team!
I'm not sure if this is the right place to reach-out, please redirect me otherwise 😄

I've created a bioio plugin for imzML mass spectrometry imaging (MSI) data and published it on PyPI: bioio-imzml.

It handles both continuous and processed-mode MSI files and integrates cleanly with BioIO's reader plugin architecture, which I particularly enjoy for its reliance on dask / xarray
This should be useful for anyone working with mass spec imaging data in Python
It heavily relies on pyimzml to do the parsing from .imzml to numpy

I'm not sure if this even aligns with how you envision plugins extending bioio
Would this be worth listing?

Of course, I'm always happy to adjust the API or implementation based on feedback

Thanks for building such a clean framework!

Have a nice day!

Davide

Repo: https://github.com/DBP008/bioio-imzml
PyPI: https://pypi.org/project/bioio-imzml/

PS: @BrianWhitneyAI I'm the same guy who opened the ome-zarr-zip issue 😂

[toloudis]

Beautiful! This is exactly the kind of thing we have had in mind for bioio.

Are you advertising your reader anywhere else, such as image.sc? (I'm not sure how many bioio + imzML users there could be.)
There isn't a catalog of third-party bioio readers anywhere yet. We could definitely add it to our central bioio docs.

[DBP008]

Thank you so much!
I did not advertise this anywhere (because I didn't know which was the proper way to contribute to bioio)
But maybe as soon as this is more tested (I'm using it more and more in another parallel project) I will for sure post it in image.sc

[BrianWhitneyAI]

Hey @DBP008 thank you this is awesome!!!!

[DBP008]

Thank you @BrianWhitneyAI :)

[BrianWhitneyAI]

@DBP008 out of curiosity did you use the cookiecutter for this repo? Im wondering how useful it is to have given the rise of gen ai

[DBP008]

No, I'm sorry I didn't use the cookiecutter, should I have?
I tried building it from scratch / grouping different convenience scripts I was using
Ofc, Claude helped me a lot for testing / docs

[BrianWhitneyAI]

No we included it when we set up the org to help external users make their own plugins. AFAIK no one other than me has ever used it. Wondering if we can just depreciate it.

[BrianWhitneyAI]

Actually @rtubelleza just recently used the cookiecutter!

[BrianWhitneyAI]

@DBP008 Two updates for ya. 1) The zipped zarr support has been merged and released (v3.8.0). 2) We added your plugin to the registry in the bioio readme!

[DBP008]

Thank you so much for this @BrianWhitneyAI !
I really appreciate it :)
I think you and your team are doing something really amazing and worth using 💪
I'll try to help out again if I can (and if you want to)