Add further reading section

[marcodallavecchia]

This draft PR partially addresses #347, #303 and #144.

Please briefly summarise the changes made in the pull request, and the reason(s) for making these changes.

This PR creates a new further-reading.md page under the More dropdown menu and adds a reference to the resource page at the end of the capstone challenge to create a where to go next? section.

I tested it locally by recompiling the material with sandpaper, I hope it will work for the final version well.

As of now I would consider this a draft because:

• We might want to review/update the list of resources mentioned
• We might want to have a standardized way of referencing things. I don't believe we make extensive use of references/citations of outside sources as of now, but we might want to create a bibliography file? Although I couldn't find relevant documentation on the workbench or sandpaper docs
• We might want to group the resources in a different way (I proposed courses, help and literature for now)
• Should we reference this section somewhere else other than the end of the capstone challenge?

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If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

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Rendered Changes

:mag: Inspect the changes: https://github.com/datacarpentry/image-processing/compare/md-outputs..md-outputs-PR-348

The following changes were observed in the rendered markdown documents:

 09-challenges.md         |  9 +++++++++
 further-reading.md (new) | 27 +++++++++++++++++++++++++++
 md5sum.txt               |  3 ++-
 3 files changed, 38 insertions(+), 1 deletion(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible.

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:stopwatch: Updated at 2025-12-09 08:22:59 +0000

[marcodallavecchia]

Thanks for the quick review @K-Meech, and no worries for the delay!

I completely agree that the resources are quite old. I tried to already go over them to at least see if they are somewhat relevant (I seem to remember of them were broken links even), but I also didn't want to add too many resources that would be too focused on bioimage analysis.

100% agree to discuss these points on the next meeting!

[marcodallavecchia]

Hello @K-Meech! As from our recent discussion, I updated the list of resources to only include a few good state-of-art resources.

I went through the carpentries incubator lessons to see if there could be other ones that could be useful to link to, but didn't find much. I did think it might be useful to add better research software and data management lessons as a potential next step in larger projects, so I included the list.

I also added a recent other publication on bioimage analysis pipelines.

Finally, I was thinking to create a new issue to track new resources to add to this list, once this PR is merged, what do you think?

[marcodallavecchia]

Thanks for the feedback @K-Meech! I also added the EPFL resource list we had discussed in the last meeting I had forgotten about.

@uschille could you take a final look? Of course if you have some non bio-image analysis specific resources we should add straight-away let me know!