From b3f574ed1eb62442df39f76c5bc8aaa32378fff3 Mon Sep 17 00:00:00 2001 From: Marco Dalla Vecchia Date: Fri, 22 Aug 2025 22:36:08 +0200 Subject: [PATCH 1/3] added further reading section and populated it with initial content --- learners/further-reading.md | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 learners/further-reading.md diff --git a/learners/further-reading.md b/learners/further-reading.md new file mode 100644 index 00000000..057c7941 --- /dev/null +++ b/learners/further-reading.md @@ -0,0 +1,28 @@ +--- +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](http://justinbois.github.io/bootcamp/2021/index.html) + - [Intro to Image Processing with scikit-image](https://justinbois.github.io/bootcamp/2021/lessons/l38_intro_to_image_processing.html) + - [Basic image quantification](http://justinbois.github.io/bootcamp/2021/lessons/l39_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) + From 945efafb008e542dcbe0e0ed5c422f4f4567bd42 Mon Sep 17 00:00:00 2001 From: Marco Dalla Vecchia Date: Mon, 25 Aug 2025 06:39:32 +0200 Subject: [PATCH 2/3] added reference to further reading page at end of capstone challenge and update old link for caltech course --- episodes/09-challenges.md | 11 +++++++++++ learners/further-reading.md | 6 +++--- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/episodes/09-challenges.md b/episodes/09-challenges.md index 4d934944..06f078fb 100644 --- a/episodes/09-challenges.md +++ b/episodes/09-challenges.md @@ -246,3 +246,14 @@ 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. :::::::::::::::::::::::::::::::::::::::::::::::::: + + +:::::::::::::::::::::::::::::::::::::::: discussion + +## Further Reading + +Wondering where to go from here? + +Take a look at our [curated list of resources for further learning](further-reading.md). + +:::::::::::::::::::::::::::::::::::::::::::::::::: \ No newline at end of file diff --git a/learners/further-reading.md b/learners/further-reading.md index 057c7941..dd889fc7 100644 --- a/learners/further-reading.md +++ b/learners/further-reading.md @@ -6,9 +6,9 @@ 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](http://justinbois.github.io/bootcamp/2021/index.html) - - [Intro to Image Processing with scikit-image](https://justinbois.github.io/bootcamp/2021/lessons/l38_intro_to_image_processing.html) - - [Basic image quantification](http://justinbois.github.io/bootcamp/2021/lessons/l39_segmentation.html) +- [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) From 6d8aec8be8b63e19434c8992219042362c1fcff9 Mon Sep 17 00:00:00 2001 From: Marco Dalla Vecchia Date: Mon, 25 Aug 2025 06:52:14 +0200 Subject: [PATCH 3/3] rephrased where to go next section at the end of challenge page --- episodes/09-challenges.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/episodes/09-challenges.md b/episodes/09-challenges.md index 06f078fb..26496d49 100644 --- a/episodes/09-challenges.md +++ b/episodes/09-challenges.md @@ -250,10 +250,8 @@ def count_colonies_enhanced(image_filename, sigma=1.0, min_colony_size=10, conne :::::::::::::::::::::::::::::::::::::::: discussion -## Further Reading +## Where to go from here? -Wondering where to go from here? - -Take a look at our [curated list of resources for further learning](further-reading.md). +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. :::::::::::::::::::::::::::::::::::::::::::::::::: \ No newline at end of file