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Collecting existing resources #144

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Collecting existing resources#144
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uschillequist00tobyhodgesK-Meechmarcodallavecchiabobturneruk
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help wantedLooking for Contributorstype:discussionDiscussion or feedback about the lesson

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@tobyhodges
tobyhodges
opened on Aug 13, 2021

Use this thread to collect links to existing resources that could be useful for inspiration, resusing content, suggesting to learners as further reading after the lesson, images that might make good examples, etc.

Activity

  1. tobyhodges
    assigned
    uschille
    ,
    quist00
    ,
    tobyhodges
    ,
    K-Meech
    and
    bobturneruk
    on Aug 13, 2021

  2. bobturneruk commented on Aug 13, 2021

    @bobturneruk
    bobturneruk
    on Aug 13, 2021
    Contributor

    Good idea, @tobyhodges!

  3. tobyhodges commented on Aug 13, 2021

    @tobyhodges
    tobyhodges
    on Aug 13, 2021
    MemberAuthor

    EMBL Bio-IT Python Workshop - Image Processing by Jonas Hartmann (@WhoIsJack), Karin Sasaki (@karinsasaki), and me. MIT licensed, so we can reuse anything here that seems like it could help. However, the material is tailored towards a molecular biology audience, and was not designed for The Carpentries approach, so this may be more in the "inspiration" than "reuse" category.

  4. tobyhodges commented on Aug 13, 2021

    @tobyhodges
    tobyhodges
    on Aug 13, 2021
    MemberAuthor

    We should point learners to https://forum.image.sc/ as a source of support as they continue to learn image processing beyond the workshop.

  5. quist00 commented on Aug 13, 2021

    @quist00
    quist00
    on Aug 13, 2021
    Contributor

    Introduction to image processing with scikit-image
    http://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

  6. K-Meech commented on Oct 1, 2021

    @K-Meech
    K-Meech
    on Oct 1, 2021
    Contributor

    This was an intermediate python course we ran internally at EMBL - the numpy section I wrote might be helpful for examples on pros/cons of numpy: https://grp-bio-it-workshops.embl-community.io/intermediate-python/02-data/index.html Repo here: https://git.embl.de/grp-bio-it-workshops/intermediate-python

  7. tobyhodges
    added
    help wantedLooking for Contributors
    type:enhancementPropose enhancement to the lesson
    on May 17, 2022

  8. tobyhodges commented on May 17, 2022

    @tobyhodges
    tobyhodges
    on May 17, 2022
    MemberAuthor

    These links should be converted to a list in a section to be presented to the learner at the end of the lesson (appending to the last episode), pointing them to resources where they can learn more. Once that section exists, we can close this issue.

    I think that will be a good place to mention napari and other image viewers too.

    To anyone who wants to make a pull request to tackle this: feel free to tag me for a review!

  9. mkcor commented on Nov 5, 2022

    @mkcor
    mkcor
    on Nov 5, 2022
    Contributor

    For further exploring after the lesson, learners might be interested in scikit-image tutorials that @alexdesiqueira and I recently presented to the Data Umbrella community. The videos for the two webinars are available under a “scikit-image” playlist on their YouTube channel: https://www.youtube.com/playlist?list=PLBKcU7Ik-ir9Fi_hM_A6_U2UTpm7ACUtl

  10. erickmartins commented on Nov 29, 2023

    @erickmartins
    erickmartins
    on Nov 29, 2023
    Contributor

    Resources that came to mind immediately:

    1. Mentioned in the curriculum advisory committee: Checklist for publishing images and analyses https://www.nature.com/articles/s41592-023-01987-9
    2. REMBI: Recommended Metadata for Biological Images https://www.nature.com/articles/s41592-021-01166-8
    3. "Twenty questions": a schema for a set of questions to guide analyses https://www.nature.com/articles/s41592-023-01919-7
    4. Pete Bankhead's outstanding gitbook on image analysis https://bioimagebook.github.io/index.html
    5. The "Python for Bioimage Analysis" materials from the RMS-DAIM group https://github.com/RMS-DAIM/Python-for-Bioimage-Analysis
  11. marcodallavecchia
    self-assigned this
    on Jun 6, 2025

  12. marcodallavecchia commented on Jun 6, 2025

    @marcodallavecchia
    marcodallavecchia
    on Jun 6, 2025
    Contributor

    I will try to pick up on this issue and create a Further Reading page in the deployed material soon. I will also add to this list the publication mentioned in #303.

    Thanks everyone for all the good suggestions!
    I will leave one of mine here for now: Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis notebooks collection https://nfdi4bioimage.github.io/training/readme.html

  13. uschille
    added
    type:discussionDiscussion or feedback about the lesson
    and removed
    type:enhancementPropose enhancement to the lesson
    on Jun 20, 2025

  14. marcodallavecchia commented on Mar 25, 2026

    @marcodallavecchia
    marcodallavecchia
    on Mar 25, 2026
    Contributor

    Closed by #348

  15. marcodallavecchia
    closed this as completedon Mar 25, 2026
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