Pull updates from original datacarpentry/image-processing repo by marcodallavecchia · Pull Request #32 · carpentries-incubator/bioimage-analysis-python

marcodallavecchia · 2026-03-25T10:14:51Z

There has been a few important updates on the datacarpentry/image-processing repository, which is the original repo from which this work is derived.

Many of these changes are still applicable to this curriculum so I ported them over with small adaptations. The mayor updates include:

Each image included in the curriculum in the fig folder has an additional copy with -dark appended to the file name if the image needs not to be inverted in dark mode. Image color inversion is the otherwise default behavior of the varnish library used in the workbench to create the HTML page (see this Issue for more details).
Addition of an extra Further Reading section with some useful resources on image processing. This can be updated to make a more bioimage analysis specific list but for now it's a good skeleton to have.
Removed some unused image that were still in the repository but never referenced in the markdown content.
Updated some root mass calculation values in episodes/06-processing-segmentation.md that a freshly installed environment with the latest package versions computes.
Fix some inter-episode references that broke due to PR New episodes structure for new learning objectives #25 episode restructuring

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Update Workflows to Version 0.16.12

Update setup instructions

Update maintainers in readme

Expand contributing guide with specific style guidelines

…and update old link for caltech course

…ul resources

…have background, it's less legible with dark text in dark mode

…ng them inverted with dark mode does not impact the episode

…-objects-coloured-by-area.png

…irectory clean

Update Workflows to Version 1.0.0

Explicitly set dark mode images to avoid varnish image color inversion

…resource

…ction Add further reading section

…onments

… original datacarpentry/image-processing repo

Remove images present in fig folder that are not references in curriculum content

Measuring Root Mass updated results

github-actions · 2026-03-25T10:15:02Z

🆗 Pre-flight checks passed 😃

This pull request has been checked and contains no modified workflow files or spoofing.

Results of any additional workflows will appear here when they are done.

terezbelinova

Thanks @marcodallavecchia , all looks good to me.

Auto-generated via `{sandpaper}` Source : 41af219 Branch : main Author : Marco Dalla Vecchia <31376583+marcodallavecchia@users.noreply.github.com> Time : 2026-03-27 12:56:18 +0000 Message : Pull updates from original datacarpentry/image-processing repo (#32) * replace Anaconda with MiniForge * set up an environment for the workshop * Apply suggestions from code review Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Remove mention of Py3 vs Py2 Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Apply fixes from review Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org> * Link to central Python install instructions * [actions] update sandpaper workflow to version 0.16.12 * update maintainers in readme * add style guidelines to contributing guide * link to contributing file from readme * small fixes to formatting * minor changes based on reviews * added further reading section and populated it with initial content * added reference to further reading page at end of capstone challenge and update old link for caltech course * rephrased where to go next section at the end of challenge page * updated resources to remove old ones and added a few more recent useful resources * fixed quotes and added EPFL resource list * dark mode images for episodes 1 and 2 * dark mode images episode 3 * dark mode images episode 4 * dark mode image episode 5 * dark mode images episode 6 * kept automatic dark mode image for SVG vector image since it doesn't have background, it's less legible with dark text in dark mode * dark mode images episode 7 * reverted histogram images as one of them is without background. Keeping them inverted with dark mode does not impact the episode * dark mode images episode 8. Added full white background for shapes-01-objects-coloured-by-area.png * dark mode images episode 9 * dark mode images extra episode edge detection * [actions] update sandpaper workflow to version 0.18.4 * [actions] update workbench docker version to v0.2.4 (#354) Co-authored-by: uschille <7782554+uschille@users.noreply.github.com> * Update sandpaper-version.txt * [actions] update sandpaper workflow to version 0.18.4 * [actions] update sandpaper workflow to version 0.18.5 * added contributing guidelines for new images and dark mode * moved all dark images to from data to fig folder, to leave the data directory clean * Added and reordered items in further-reading.md * Change title of reference.md to Glossary to make 'More'-menu clearer * Custom order of entries on 'More'-menu * [actions] update sandpaper workflow to version 1.0.0 * removed Studies on application of image processing in various fields resource * chair images are only used in the data but not in the fig directory * colonies01.png not used, just the jpg version is used * updated root mass values based on fresh new environment * added callout block to highlight the importance of reproducible environments * fix all broken links due to restructuring of episodes structure * more updated values after re-running with fresh updated environment --------- Co-authored-by: Toby Hodges <tbyhdgs@gmail.com> Co-authored-by: Toby Hodges <tobyhodges@carpentries.org> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org> Co-authored-by: zkamvar <zkamvar@users.noreply.github.com> Co-authored-by: Ulf Schiller <uschille@users.noreply.github.com> Co-authored-by: Marco Dalla Vecchia <marco.dallavecchia@ist.ac.at> Co-authored-by: zkamvar <3639446+zkamvar@users.noreply.github.com> Co-authored-by: The Carpentries Apprentice (beta) <64428345+carpentries-bot@users.noreply.github.com> Co-authored-by: uschille <7782554+uschille@users.noreply.github.com> Co-authored-by: Ulf Schiller <uschill@udel.edu>

Auto-generated via `{sandpaper}` Source : 9f42691 Branch : md-outputs Author : GitHub Actions <actions@github.com> Time : 2026-03-27 12:58:22 +0000 Message : markdown source builds Auto-generated via `{sandpaper}` Source : 41af219 Branch : main Author : Marco Dalla Vecchia <31376583+marcodallavecchia@users.noreply.github.com> Time : 2026-03-27 12:56:18 +0000 Message : Pull updates from original datacarpentry/image-processing repo (#32) * replace Anaconda with MiniForge * set up an environment for the workshop * Apply suggestions from code review Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Remove mention of Py3 vs Py2 Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> * Apply fixes from review Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org> * Link to central Python install instructions * [actions] update sandpaper workflow to version 0.16.12 * update maintainers in readme * add style guidelines to contributing guide * link to contributing file from readme * small fixes to formatting * minor changes based on reviews * added further reading section and populated it with initial content * added reference to further reading page at end of capstone challenge and update old link for caltech course * rephrased where to go next section at the end of challenge page * updated resources to remove old ones and added a few more recent useful resources * fixed quotes and added EPFL resource list * dark mode images for episodes 1 and 2 * dark mode images episode 3 * dark mode images episode 4 * dark mode image episode 5 * dark mode images episode 6 * kept automatic dark mode image for SVG vector image since it doesn't have background, it's less legible with dark text in dark mode * dark mode images episode 7 * reverted histogram images as one of them is without background. Keeping them inverted with dark mode does not impact the episode * dark mode images episode 8. Added full white background for shapes-01-objects-coloured-by-area.png * dark mode images episode 9 * dark mode images extra episode edge detection * [actions] update sandpaper workflow to version 0.18.4 * [actions] update workbench docker version to v0.2.4 (#354) Co-authored-by: uschille <7782554+uschille@users.noreply.github.com> * Update sandpaper-version.txt * [actions] update sandpaper workflow to version 0.18.4 * [actions] update sandpaper workflow to version 0.18.5 * added contributing guidelines for new images and dark mode * moved all dark images to from data to fig folder, to leave the data directory clean * Added and reordered items in further-reading.md * Change title of reference.md to Glossary to make 'More'-menu clearer * Custom order of entries on 'More'-menu * [actions] update sandpaper workflow to version 1.0.0 * removed Studies on application of image processing in various fields resource * chair images are only used in the data but not in the fig directory * colonies01.png not used, just the jpg version is used * updated root mass values based on fresh new environment * added callout block to highlight the importance of reproducible environments * fix all broken links due to restructuring of episodes structure * more updated values after re-running with fresh updated environment --------- Co-authored-by: Toby Hodges <tbyhdgs@gmail.com> Co-authored-by: Toby Hodges <tobyhodges@carpentries.org> Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com> Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org> Co-authored-by: zkamvar <zkamvar@users.noreply.github.com> Co-authored-by: Ulf Schiller <uschille@users.noreply.github.com> Co-authored-by: Marco Dalla Vecchia <marco.dallavecchia@ist.ac.at> Co-authored-by: zkamvar <3639446+zkamvar@users.noreply.github.com> Co-authored-by: The Carpentries Apprentice (beta) <64428345+carpentries-bot@users.noreply.github.com> Co-authored-by: uschille <7782554+uschille@users.noreply.github.com> Co-authored-by: Ulf Schiller <uschill@udel.edu>

tobyhodges and others added 30 commits April 1, 2025 12:31

replace Anaconda with MiniForge

349df13

set up an environment for the workshop

55346f2

Apply suggestions from code review

fb6258b

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

Remove mention of Py3 vs Py2

9ae46f2

Co-authored-by: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>

Apply fixes from review

89f5b47

Co-authored-by: Marianne Corvellec <marianne.corvellec@ens-lyon.org>

Link to central Python install instructions

9c8345e

[actions] update sandpaper workflow to version 0.16.12

c3355b7

Merge pull request #343 from datacarpentry/update/workflows

228bc8c

Update Workflows to Version 0.16.12

Merge pull request #342 from datacarpentry/update-python-setup

7597b4b

Update setup instructions

update maintainers in readme

7e87d73

Merge pull request #344 from datacarpentry/km/update-maintainers

3982f8c

Update maintainers in readme

add style guidelines to contributing guide

979c654

link to contributing file from readme

624a104

small fixes to formatting

6272d04

minor changes based on reviews

9293c50

Merge pull request #345 from datacarpentry/km/contributing-guide

72bbd95

Expand contributing guide with specific style guidelines

added further reading section and populated it with initial content

b3f574e

added reference to further reading page at end of capstone challenge …

945efaf

…and update old link for caltech course

rephrased where to go next section at the end of challenge page

6d8aec8

updated resources to remove old ones and added a few more recent usef…

d43cf5c

…ul resources

fixed quotes and added EPFL resource list

780bd07

dark mode images for episodes 1 and 2

8fc15b3

dark mode images episode 3

9a96004

dark mode images episode 4

67b8fa0

dark mode image episode 5

55a727e

dark mode images episode 6

df99ba2

kept automatic dark mode image for SVG vector image since it doesn't …

1c0cc0f

…have background, it's less legible with dark text in dark mode

dark mode images episode 7

e4dbfda

reverted histogram images as one of them is without background. Keepi…

6225e24

…ng them inverted with dark mode does not impact the episode

dark mode images episode 8. Added full white background for shapes-01…

813f2a0

…-objects-coloured-by-area.png

Marco Dalla Vecchia and others added 20 commits February 9, 2026 13:39

moved all dark images to from data to fig folder, to leave the data d…

c875bd1

…irectory clean

Added and reordered items in further-reading.md

d006c09

Change title of reference.md to Glossary to make 'More'-menu clearer

7b3be7e

Custom order of entries on 'More'-menu

82ddb66

[actions] update sandpaper workflow to version 1.0.0

b7d1991

Merge pull request #359 from datacarpentry/update/workflows

5b19786

Update Workflows to Version 1.0.0

Merge pull request #350 from marcodallavecchia/dark-mode-images

a952902

Explicitly set dark mode images to avoid varnish image color inversion

removed Studies on application of image processing in various fields …

82c4c84

…resource

Merge pull request #348 from marcodallavecchia/add_further_reading_se…

751fdea

…ction Add further reading section

chair images are only used in the data but not in the fig directory

21314ae

colonies01.png not used, just the jpg version is used

4f18430

updated root mass values based on fresh new environment

1cffe91

added callout block to highlight the importance of reproducible envir…

b958160

…onments

updated current repository status with all latest improvements on the…

f7bd410

… original datacarpentry/image-processing repo

Merge pull request #361 from marcodallavecchia/remove-unused-images

5a50ce3

Remove images present in fig folder that are not references in curriculum content

fix all broken links due to restructuring of episodes structure

df33620

Removed unused images from original datacarpentry/image-processing repo

2e23efb

more updated values after re-running with fresh updated environment

ad79637

Merge pull request #362 from marcodallavecchia/root-mass-reproducibility

4da0c08

Measuring Root Mass updated results

pulled latest updated values from fresh environment installation

600086d

marcodallavecchia self-assigned this Mar 25, 2026

terezbelinova approved these changes Mar 27, 2026

View reviewed changes

terezbelinova merged commit 41af219 into carpentries-incubator:main Mar 27, 2026
5 checks passed

marcodallavecchia deleted the update-from-original-repo branch March 27, 2026 12:59

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Pull updates from original datacarpentry/image-processing repo#32

Pull updates from original datacarpentry/image-processing repo#32
terezbelinova merged 62 commits into
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marcodallavecchia commented Mar 25, 2026

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