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?

[github-actions]

Thank you!

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Rendered Changes

🔍 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) | 26 ++++++++++++++++++++++++++
 md5sum.txt               |  3 ++-
 3 files changed, 37 insertions(+), 1 deletion(-)

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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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⏱️ Updated at 2025-12-05 10:02:57 +0000

[K-Meech]

Thanks for putting this draft PR together @marcodallavecchia - and sorry for the long delay in reviewing 😅

I built this locally + all looked great - linking to this page from the end of the capstone challenge works well. My one concern is that some of the resources in the 'where to go from here' section are quite old now e.g. the EMBL courses which haven't been updated in ~7 years. It's probably worth us going through this list and putting the most up-to-date materials at the top (e.g. I'd vote for Pete Bankhead's book going first - as it is a great resource!)

Maybe we can go through these in our next maintainer meeting, and decide on an order / whether to remove some of the older links?

[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?

[K-Meech]

Thanks @marcodallavecchia - this looks great! I agree with the resources you removed + the new ones added.

I think you can mark this as 'ready for review' now + maybe tag @uschille for review (in case he has any comments before merging!). I think this will close the following issues: #347, #303 and #144

Opening a new issue to collect further resources sounds like a good plan. It would be nice to highlight in the description that we're particularly keen to find resources that aren't specific to bio-image analysis (as our list has a number of biology-related resources at the moment, while this aims to be a general lesson)

[K-Meech]

Suggested change

	- ["From cells to pixels: A decision tree for designing bioimage analysis pipelines"](https://onlinelibrary.wiley.com/doi/10.1111/jmi.70021)
	- [From cells to pixels: A decision tree for designing bioimage analysis pipelines](https://onlinelibrary.wiley.com/doi/10.1111/jmi.70021)

Very minor suggestion - not sure you need the quotes around this?