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Add further reading section #348

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b3f574e
added further reading section and populated it with initial content
Aug 22, 2025
945efaf
added reference to further reading page at end of capstone challenge …
Aug 25, 2025
6d8aec8
rephrased where to go next section at the end of challenge page
Aug 25, 2025
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9 changes: 9 additions & 0 deletions episodes/09-challenges.md
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Expand Up @@ -246,3 +246,12 @@ def count_colonies_enhanced(image_filename, sigma=1.0, min_colony_size=10, conne
- These methods are useful for many scientific problems, especially those involving morphometrics.

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## Where to go from here?

Take a look at our [curated list of resources](further-reading.md) for further publicly available courses, resources and scientific literature around image processing and more.

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28 changes: 28 additions & 0 deletions learners/further-reading.md
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---
title: Further Reading
permalink: /reading/
---

## Where to go from here

- [EMBL Bio-IT Python Workshop - Image Processing](https://git.embl.org/grp-bio-it-workshops/python-workshop-image-processing)
- [Introduction to Programming in the Biological Sciences Bootcamp Caltech](https://justinbois.github.io/bootcamp/2021/index.html)
- [Intro to Image Processing with scikit-image](https://justinbois.github.io/bootcamp/2023/lessons/l44_intro_to_image_processing.html)
- [Basic image quantification](https://justinbois.github.io/bootcamp/2023/lessons/l45_segmentation.html)
- [Intermediate Python Course EMBL Numpy section](https://grp-bio-it-workshops.embl-community.io/intermediate-python/02-data/index.html)
- [Scikit-image YouTube tutorials](https://www.youtube.com/playlist?list=PLBKcU7Ik-ir9Fi_hM_A6_U2UTpm7ACUtl)
- [Introduction to Bioimage Analysis by Pete Bankhead](https://bioimagebook.github.io/index.html)
- [IAFIG-RMS Python for Bioimage Analysis Course repository](https://github.com/RMS-DAIM/Python-for-Bioimage-Analysis)
- [Introduction to artificial neural networks in Python](https://carpentries-incubator.github.io/machine-learning-neural-python/index.html)

## Where to find more help

- [Image.sc Forum](https://image.sc/)
- [NFDI4BioImage Training Materials collection](https://nfdi4bioimage.github.io/training/readme.html)

## Scientific Literature

- [Checklist for publishing images and analyses ](https://www.nature.com/articles/s41592-023-01987-9)
- [REMBI: Recommended Metadata for Biological Images](https://www.nature.com/articles/s41592-021-01166-8)
- ["Twenty questions": a schema for a set of questions to guide analyses](https://www.nature.com/articles/s41592-023-01919-7)