Mailman 3 - scikit-image

request for feedback on cross-library design proposal
by Ralf Gommers 17 Nov '21

17 Nov '21

(Apologies for the cross-posting, if you follow more than one of these lists, you may see this multiple times.) Hi all, I'd like to solicit the feedback of maintainers of NumPy, SciPy, scikit-learn, and scikit-image, and other interested community members on this blog post and proposed design to enable multiple array types in SciPy, scikit-learn, scikit-image and other libraries in this ecosystem: https://labs.quansight.org/blog/2021/11/pydata-extensibility-vision/. Because this design is meant to be shared across projects, it would be great to discuss it in a central place. The new https://discuss.scientific-python.org/ seems like a good venue for that. Here are two separate forum threads for this: - for the big picture: https://discuss.scientific-python.org/t/a-proposed-design-for-supporting-mu… - for the most tricky design decision (user-facing switch & default behavior): https://discuss.scientific-python.org/t/default-dispatching-behavior-for-su… Thanks in advance for any input! Cheers, Ralf

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Retiring the mailing list (moving to discuss.scientific-python.org)
by Stefan van der Walt 25 Oct '21

25 Oct '21

Tl;dr: *Please visit our new forum* at https://discuss.scientific-python.org/c/contributor/skimage and *click on the bell icon* to set your notification settings. Dear scikit-image community, This mailing list has been going for more than a decade, and we've had lots of good conversations here. It all started with the announcement of a new scikit <https://mail.python.org/archives/list/scikit-image@python.org/thread/3SQ4UO…> after the SciPy2009 sprints. It's been a fun journey! But, times are changing and it's not clear that email lists are still the best place for discussion: newcomers to a thread cannot see its history and it is harder to share images, highlight markup, and browse long-running conversations. Besides, the new generation of contributors prefer more modern ways of communicating. It is important that we have vibrant spaces where we can discuss (and enjoy discussing!) the project and its future. Thus, the core team has decided to switch from this mailing list to Discourse. Our communication channels will now be: - User Q&A (how to use skimage): https://forum.image.sc/tag/scikit-image *- Contribution / development discussion (previously this list!): **https://discuss.scientific-python.org/c/contributor/skimage* - Chat: https://skimage.zulipchat.com/ Egor will keep monitoring this list, and will redirect requests as necessary. Thank you for making this journey with us, and I hope to see y'all over at discuss.scientific-python.org! Next up... skimage2! Stay tuned. Best regards, Stéfan

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Contributing new algorithms to skimage
by YIMING ZHOU 05 Oct '21

05 Oct '21

Hi, I was wondering does skimage learn accept new image processing algorithms? We want to contribute Phase Stretch Transform (PST) to skimage. PST is a physics-inspired algorithm for feature detection. It's a successful algorithm which has received lots of attention since it was proposed. You can find more information on this wiki page: https://en.wikipedia.org/wiki/Phase_stretch_transform and this github page https://github.com/JalaliLabUCLA/Image-feature-detection-using-Phase-Stretc… Looking forward to your reply. Thanks Best, Yiming -- Yiming Zhou Department of Electrical and Computer Engineering University of California, Los Angeles

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Commit message guidelines
by Stefan van der Walt 14 Sep '21

14 Sep '21

Hi all, I would like to thank Marianne for updating our documentation to reflect best commit message practices. Please familiarize yourself with those changes: https://github.com/scikit-image/scikit-image/pull/5504/files Special kudos this month to Pradyumna Rahul and Fred Bunt for their stellar commit messages, even before the guidelines were published! Best regards, Stéfan

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Improving the PyData Sphinx theme
by Stefan van der Walt 24 Aug '21

24 Aug '21

Hi all, After a joint application by several projects (including scikit-image) NumFOCUS has made a grant which will fund Damián Avila to improve the PyData Sphinx theme. Proposed changes include a version switcher, better screen reader compatibility, dark mode, improved mobile support, and customized color schemes. If you have any suggestions for improvements, you can file an issue here: https://github.com/pydata/pydata-sphinx-theme/projects/1 Stéfan

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New logo
by Stefan van der Walt 09 Aug '21

09 Aug '21

Hi everyone, If you are interested in discussing a new logo for scikit-image, please join us on Zulip chat under #development, topic "logo design". https://skimage.zulipchat.com/login/#narrow/stream/181448-development/topic… Thanks! Stéfan

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ValueError with skimage.filters.threshold_local
by Fang CAO 06 Aug '21

06 Aug '21

Hello, thank you for the great scikit-image library. I have encountered an error when using the function skimage.filters.threshold_local: threshold = skimage.filters.threshold_local(data, 7, method='gaussian', offset=0, mode='nearest') File "/mnt/depot64/NPsoftware/simnibs/charm_dev/charm_env/lib/python3.8/site-packages/skimage/filters/thresholding.py", line 209, in threshold_local check_nD(image, 2) File "/mnt/depot64/NPsoftware/simnibs/charm_dev/charm_env/lib/python3.8/site-packages/skimage/_shared/utils.py", line 320, in check_nD raise ValueError(msg_incorrect_dim % (arg_name, '-or-'.join([str(n) for n in ndim]))) ValueError: The parameter `image` must be a 2-dimensional array For my understanding, the 'image' can be N-dimensional, but why does it give me the error? Do I misunderstand something? In my case, the 'data' is a 3D image with dtype of 'float32', and the element values range from '-2000' to '+2000'. Thank you in advance. Kind regards, Fang

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Commit messages
by Stefan van der Walt 05 Aug '21

05 Aug '21

Dear team, I notice that we've become a bit lax at writing proper commit messages. Especially with squash merges, it is now common to see in the long list of items like "polish things up a bit" and "more verbose". What do you think is the best way of handling this? Perhaps we should copy the PR description into the commit message, instead of having a list of random gibberish? Or maybe the first commit should have a detailed description, and then we simply cut the rest of the items from that list? Stéfan

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Request for comments: plans for breaking changes in scikit-image 1.0
by Juan Nunez-Iglesias 27 Jul '21

27 Jul '21

Dear skimagers, We are aiming to release scikit-image 1.0 near the end of the year. We are, however, planning to make a number of breaking changes in the API that will affect downstream libraries. We have published a proposal for how we plan to do this at https://bit.ly/skip-3. The gist of it is: - we'll release 0.19 in the coming weeks. - we'll release 0.20 immediately after, which will be exactly the same but with a warning to pin scikit-image to `<0.20` (for those that want to stay in 0.x land indefinitely) or `!=0.20.*` (for those that want to be "on the ball" when 1.0 is released and update their code as soon as possible). - we'll publish a transition guide along with 1.0rc0, and maintain 0.19.x with bug fixes for another year to give users time to transition. The document describes alternative approaches ("change the wheels on the bus while still driving it" or "make a new bus with a new name") and why the core team ultimately chose to promote the current approach. Nonetheless, scikit-image is committed to being a community-led project, so we are still gathering feedback and can make substantive modifications to the plan going forward. Please don't hesitate to voice your concerns so we can make the best choice for our entire community going forward! Thank you, Juan.

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Contributing to Scikit-Image and Mentorship
by BRANDON READ 17 Jul '21

17 Jul '21

Hi all, I'm interested in contributing to scikit-image but I am new to scientific programming. I studied physics in undergrad and have a minor in bioinformatics. As a result, I'm familiar with oop, data structures, and algorithms. I'd like some mentorship to get started on actually developing / contributing code. I'm interested in image processing for structural biology applications, and sometimes in my spare time I write scripts for my current company. However, it is not production-grade, and it is quite hacky. I'm hoping that through contributing to scikit-image, in whatever way possible, I can gain some skills and give back in parallel. According to the scikit-image website, mentoring is available and it seems like contributing to open source is encouraged. Would anyone be interested in mentoring me? Thank you for your time, Brandon Read

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