Potential Community Contribution to the knowledge base: Bio-image Analysis Notebooks

[haesleinhuepf]

Hi all,

I am considering making a community contribution to your project if you are interested. I maintain the Bio-image Analysis Notebooks, a collection of Jupyter notebooks demonstrating how to analyse microscopy images using Python. These notebooks serve as knowledge base for the BioImage Analysis GPT. If you are interested, I could serve this knowledge base to you (in whatever format you require) and you could make it part of the BioImage-IO ChatBot knowledge base. The only thing I would kindly ask you to is to respect the CC-BY license under which the notebooks are licensed:

• "Attribution — You must give appropriate credit , provide a link to the license, and indicate if changes were made . You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use."

Let me know if this sounds interesting to you!

Best,
Robert

[oeway]

Thank you for the offer—we'd be happy to include your Bio-image Analysis Notebooks in the BioImage-IO ChatBot knowledge base. Of course, we'll provide proper attribution as required by the CC-BY license. As you can see in our recent PR, we're actively improving reference and author attribution in the chat interface based on your previous comments.

The easiest is to send a PR to add a new entry to the manifest file pointing to a Github folder with the notebooks rendered in markdown (if that's possible), the content will be injected once we rebuild the knowledge base. Maybe wait a bit on #149 so you know how to add author license information.

[haesleinhuepf]

Awesome!

notebooks rendered in markdown (if that's possible)

I think I have seen others converting ipynb files into myst markdown files... But before I start researching how to do this: Have you done this before? If there's a conversion script I could reuse, that would be great. Otherwise, I'll write it.

Thanks again!

[oeway]

I think I have seen others converting ipynb files into myst markdown files... But before I start researching how to do this: Have you done this before? If there's a conversion script I could reuse, that would be great. Otherwise, I'll write it.

Thanks!

No, we don't have it yet, but i believe you can do it with something like nbconvert.

I guess the best is to add a CI script so we can publish markdown content automatically to a github branch, then we just need to point to it.