Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Jan Eglinger
    @imagejan
    Ah, I think ListenToEvents.java is meant to be the show case.
    3 replies
    Wei Ouyang
    @oeway
    That would be great, sorry that I am rather new to this. And is it possible to implement it in Python so I can quickly test it?
    Curtis Rueden
    @ctrueden
    Just a warning: the linkage between the SciJava event system, and ImageJ1 events, is incomplete. I don't know that you'll always see a Display*Event fired in response to ImageJ1 windows and images changing state.
    That said, give it a try and see how it goes.
    Wei Ouyang
    @oeway
    I just tried it in the script editor of Fiji and it seem to work!
    Curtis Rueden
    @ctrueden
    Another warning: there are serious limitations in what you can do with ImageJ1 in headless mode, and/or with the GUI not visible. I'm actually in a meeting with @elevans at this moment troubleshooting some issues relating to that. We just found a big bug in PyImageJ relating to the run_plugin function with ImagePlus objects.
    Wei Ouyang
    @oeway
    Aha
    However, it doesn't seem to respond t imagej-1 image window
    I see a lot of events if the window is created via ij.ui().show(dataset)
    Curtis Rueden
    @ctrueden
    Yep, that's what I meant by "incomplete linkage."
    It would be great to build a more complete linkage. Or you could do what everyone else does and just hack around it forever, and cobble something together. I have mixed feelings.
    Jan Eglinger
    @imagejan
    Maybe this (fixing the IJ1<->IJ2 linkage) could be a topic for one of the upcoming mini-hackathons? At first, there needs to be a proper separation between conversion and synchronisation, and proper testing of those. There’s a meta-issue linking to the relevant places here: imagej/imagej-legacy#231
    Curtis Rueden
    @ctrueden
    @imagejan :+1:
    I do think, though, that if that's my topic, it will be my only topic. :sweat:
    Jan Eglinger
    @imagejan
    Yes, it’s quite an involved topic, I’m afraid… but I think (if I manage to reserve a few days for working on it) I’d be keen on trying to work on at least some of those issues, after maybe you can help defining the overall intended way how things should work (and therefore be tested), @ctrueden
    tina
    @xiao-ma-nong
    Jean-Yves Tinevez
    @tinevez
    超级好
    Condrej Palat
    @c_harm1_twitter
    I am currently running Fiji to analyze growing actin, I am getting to the point where i have made all the steps to skeletonize it but when I do it turns into a bubble instead of a straight line. These issues arent happening on our other computers so i was wondering if there is a setting i need to change
    Jan Eglinger
    @imagejan
    Please don’t cross-post on all channels at once. See fiji/fiji channel.
    Curtis Rueden
    @ctrueden
    @/all The new ImageJ website NEEDS YOUR HELP :muscle: to launch next Friday! Will you join our team during the virtual Fiji hackathon next week, to help review and clean up individual wiki pages? No programming experience necessary, just a few minutes of your time, any time. See here for details: https://forum.image.sc/t/53246
    Jan Eglinger
    @imagejan
    I’ll be off from June 2-11, unfortunately, but will try to help before and after that time :slight_smile:
    Curtis Rueden
    @ctrueden
    Thanks @imagejan. I have no idea how far we will actually get with the cleanup by next Friday, but unless the progress is dismal, we'll probably cut over imagej.net to the new content then. And then as needed, we can continue reviewing pages after that. I will have: A) a wiki page listing not-yet-cleaned-up pages and documenting problems to look for + how to fix them; and B) a Google spreadsheet with remaining pages to clean up, where people can claim pages so that two people don't try cleaning the same page at the same time.
    @/all If you are interested and want to chat further about it, please join the imagej/imagej.github.io Gitter channel, so we avoid spamming everyone here repeatedly. :smile:
    Jean-Yves Tinevez
    @tinevez
    :plus1: I have to rewrite all the TrackMate pages anyway. I realize it is quite some work. Ok if I focus on this first?
    Curtis Rueden
    @ctrueden
    @tinevez It's up to you! But if you feel motivated to work on TrackMate content, I fully support that. :+1:
    You could start doing that any time; all the stuff is in _pages/plugins/trackmate/*.md. And images in media/plugins/trackmate/*.
    Jean-Yves Tinevez
    @tinevez
    oki! Do you have more ideas for me?
    Curtis Rueden
    @ctrueden
    Well, like I said, there will be a spreadsheet by the end of today, listing all the pages that still need to be proof-read (a sort of "sign-up sheet"). If you want to do some of those, that would be welcome. You could cherry-pick the pages that are interesting for you personally to read anyway.
    Part of the page vetting will be converting from the old plugin infoboxes to the new Maven+JavaScript-driven one-liner in the front matter, like: artifact: sc.fiji:TrackMate_, that results in a fully populated statbox in the right-side column.
    So, if you have any plugins you want to ensure get that statbox populated, you could start there by deleting those info boxes in favor of the statbox. I'll explain all this on the "todo" page with instructions on what to look for while vetting pages.
    Jean-Yves Tinevez
    @tinevez
    oki. I will invite people from the facility too.
    Curtis Rueden
    @ctrueden
    Thank you very much! :pray: :candy: :smile_cat:
    tina
    @xiao-ma-nong
    good,厉害了
    Jan Eglinger
    @imagejan
    is there an SVG version of the image.sc forum logo somewhere?
    Curtis Rueden
    @ctrueden
    @imagejan Thanks for the heads up. I pinged the Broad Imaging folks, since they are the ones who made that logo originally.
    Michael Doube
    @mdoube

    Part of the page vetting will be converting from the old plugin infoboxes to the new Maven+JavaScript-driven one-liner in the front matter, like: artifact: sc.fiji:TrackMate_, that results in a fully populated statbox in the right-side column.

    BoneJ has 5 artifacts, which I think may be breaking the statbox

    - org.bonej:bonej-plugins
    - org.bonej:bonej-utilities
    - org.bonej:bonej-ops
    - org.bonej:bonej-legacy-plugins_
    - org.bonej:bonej-legacy-util_
    @alessandrofelder might take a look at it later today
    Curtis Rueden
    @ctrueden
    @mdoube I'm not sure there's much @alessandrofelder is going to be able to do. The statbox simply does not support lists of artifacts yet. But we could make it do so! I just don't know what you'd expect to actually have happen in this case. How should the statbox look?
    Since all the BoneJ artifacts are monoversioned, the release versions and release dates will align. But what about the developers and contributors? Those could differ, no? So which ones do we show? All of them unioned?
    By the way, I found a bug in the statbox while updating the BoneJ page: I tried to set the name explicitly as name: BoneJ while setting also artifact: org.bonej:bonej-utilities, with the idea that the statbox title should still be "BoneJ" even though it was being keyed off the metadata from the bonej-utilities artifact. But the statbox erroneously overwrites the statbox title upon loading the POM. I thought I had coded it not to do that.
    Maybe bonej-plugins would be the best thing to key the statbox off of, at least for now. Would that be satisfactory? The metadata should look reasonable then, I think?
    Michael Doube
    @mdoube

    Since all the BoneJ artifacts are monoversioned, the release versions and release dates will align. But what about the developers and contributors? Those could differ, no? So which ones do we show? All of them unioned?

    Yes - union all the devs and contributors

    Maybe bonej-plugins would be the best thing to key the statbox off of, at least for now. Would that be satisfactory? The metadata should look reasonable then, I think?

    Yes that would be fine for now. I tried setting a logo following the syntax in TrackMate's statbox but it didn't show up.

    Michael Doube
    @mdoube
    the statbox also seems to break if there are multiple citation DOIs, perhaps only if the list of DOIs are the last statbox entry.
    Michael Doube
    @mdoube
    I tried to set the name explicitly as name: BoneJ while setting also artifact: org.bonej:bonej-utilities, with the idea that the statbox title should still be "BoneJ" even though it was being keyed off the metadata from the bonej-utilities artifact.
    That seems like a sensible behaviour, and needed in BoneJ's case.
    Curtis Rueden
    @ctrueden
    @mdoube Thanks, I filed imagej/imagej.github.io#146 to track the multi-artifact statbox enhancement.
    Curtis Rueden
    @ctrueden
    @/all The new ImageJ wiki has launched! https://forum.image.sc/t/53641