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    Kyle I S Harrington
    @kephale
    i had another hacked solution that worked without using grab
    via the pomegranate library that we use for dependency fetching in clojure land
    it isn't pressing right now, as it will be a big leap to switch to RISE-based presentations/demos
    (for me)
    Curtis Rueden
    @ctrueden
    @kmader If something is missing from github.com/imagej/tutorials to make it more binder friendly, a PR would be appreciated!
    Hadrien Mary
    @hadim
    @ctrueden any thoughts about the SJJK conda release?
    Curtis Rueden
    @ctrueden
    Not at a computer today so cannot check the status. Do you think it is ready to go? I cannot remember. If you think ready then go for it.
    Kevin Mader
    @kmader
    @ctrueden no, you can move environment.yml into a binder subfolder (some people prefer this so it's less confusing or likely to get picked up by another tool) but the main thing would be tagging it on github as binder-ready so people can see it as an easy to launch script
    getting http://www.imagejfx.net/ as a one-click launch / binder project seems like it would be pretty useful as well
    Hadrien Mary
    @hadim
    @ctrueden I am not really using SJJK those days so I'll wait for you to be able to have a look. All the builds are green on the conda side.
    Curtis Rueden
    @ctrueden
    @kmader I don't think anyone is working on imagejfx anymore, nor is there any plan to continue it to my knowledge. @cmongis would be able to say for sure though.
    Kevin Mader
    @kmader
    @ctrueden ah shame, it always looked very cool, are there any working projects for ImageJ web-frontends? the binder appmode lets you have interactive notebooks with javascript widgets. It would be a cool way for packaging specific analyses or macros as web-based tools (in this example we took nvidia's latest style transfer and turned it into a little app, https://mybinder.org/v2/gh/4QuantOSS/FastPhotoStyle/master?urlpath=%2Fapps%2Fnotebooks%2Fdemo_app.ipynb)
    Jan Eglinger
    @imagejan

    :point_up: 23. Februar 2018 20:23

    the main thing would be tagging it on github as binder-ready

    @kmader what do you mean by "tagging it as binder-ready"? The "launch binder" badge was added in December with imagej/tutorials@6ea704a

    Is there something else missing?

    Kevin Mader
    @kmader
    @imagejan topics (https://github.com/topics/binder-ready)
    Jan Eglinger
    @imagejan
    @kmader @ctrueden alright, I added the binder-ready as a topic to https://github.com/imagej/tutorials
    Thanks for the pointer!
    Same for https://github.com/scijava/scijava-jupyter-kernel
    Jan Eglinger
    @imagejan
    @hadim if it's just for testing, I would be willing to have a look at the SJJK release. How can I test it before it's released via conda? On the other hand, if you think it's alright, then merge it. Then I'll test it with the tutorials notebooks on binder.
    Hadrien Mary
    @hadim
    If you want to test it you can just clone conda-forge/scijava-jupyter-kernel-feedstock#14 and then build the repo with conda build: https://conda.io/docs/user-guide/tutorials/build-pkgs.html#building-and-installing
    Alison Walter
    @awalter17

    @kkangle I’m not 100% certain if this is where the NPE you asked me about earlier came from but its a possibility.

    So ij.display().createDisplay(...) calls a DisplayService, possibly DefaultDisplayService. Which finds a matching Display and calls display(...). If the matched Display is the DefaultImageDisplay then it calls this method. And then again assuming it matches the default you get this method, which if you trace you wind up here. It creates an ImgView with a null factory, such that later in your notebook when you try to create a copy via the factory you get an NPE.

    I'm making a lot of assumptions here ... so this may not be correct, but it seems promising?

    To get around this in the meantime you could try using imagej-ops to convert your RandomAccessibleInterval to an Img in the notebook? (provided you can call Ops from your notebook, and there is a converter for RAI to Img - you may need to create an Img from the RAI and then copy the data over ... I can't remember). But then you call ij.display().createDisplay(...) on this newly created Img, which has hopefully been made with a non-null factory.

    Hopefully that kind of made sense, feel free to let me know if you have any questions.

    Yang Liu
    @kkangle
    Thank you @awalter17. I have a feeling this is the problem. I’ll try to fix it, and let you know if it works, fingers crossed.😊
    Curtis Rueden
    @ctrueden
    @awalter17 Whoa, the DefaultDatasetService creates ImgView with null factory? Yuck! Gotta fix that.
    Thanks @imagejan and @hadim for testing SJJK.
    @kmader About frontends: my current thinking is that some day, there will be a JavaScript-based frontend using Electron, which ships a JVM and a Python interpreter (and whatever else the cool kids like at that point), and discovers all available functionality conforming to whatever frameworks. E.g. asks SciJava for its modules, asks Python for its modules assuming some Python-based discovery mechanism is developed by somebody, etc.
    We can do shared memory between Java and Python now, as well as between JS and Python. Presumably between JS and Java is doable. So part of this thing would be that images can be wrapped/adapted between silos.
    Curtis Rueden
    @ctrueden
    I'm going to a short hackathon in early May where we are going to start exploring JavaScript viewers that could eventually grow into something like that.
    Modular viewer components, just to start. Usable on the web, or as part of an application. And then we can build a framework around it that integrates as described above. It's a long road.
    I don't think JavaFX is the way to go, because it is still Java-centric. JavaScript UI is superior to JavaFX, wouldn't you say? Because people just keep building more and more awesome things in HTML5 + CSS + JS?
    Hadrien Mary
    @hadim
    I agree with you. Some kind of electron app that shio everything is probably the future for IJ UI.
    In that spirit I started to play with React to create a very basic tif viewer: https://github.com/hadim/tifviewer
    Curtis Rueden
    @ctrueden
    @kmader Thanks for sharing that introduction lecture. No SciJava in that one, right? At least, I didn't see any when paging through it. It's Python 3 so you'd have to use the imglyb stuff a la this notebook. This stuff is still pretty bleeding edge, unfortunately.
    As I said above, you can wrap all of ImageJ in Python now (see here) but various errors happen when digging down into various parts of ImageJ2/SciJava. We are investigating how to smooth out various rough edges.
    Anyway, that is a big honkin' introduction to the current status of biological image analysis!
    Must have been a lot of work to create.
    Curtis Rueden
    @ctrueden
    And I got sucked into reading that "Trouble at the lab" Economist article for at least 30 minutes. :-)
    Kevin Mader
    @kmader
    @ctrueden oh great it was more to just show the live coding + presentation ability, unfortunately no scijava, but we'll definitely add some in. definitely let me know what comes out of the hackathon. the js stuff does seem to be dominating the UI world and trying to keep up with react, vue, meteor, angular is a small headache, but can deliver really cool results. as my last bit of list spam, with webassembly and vue we could package some radiology ML code into entirely browser-based analysis (bit.ly/deepradnet), apparently transpiling java to webassembly doesn't work so well yet though
    Hadrien Mary
    @hadim
    @imagejan @ctrueden I just tested sjjk 0.6.0 locally on my system and it works well + all the CI builds are green so I am going to merge. If an urgent fix is needed I will be available next week to help if needed.
    CI builds started, packages should be uploaded to Anaconda within few hours.
    Curtis Rueden
    @ctrueden
    Thanks @hadim!
    (just)Tomas
    @nightdismay_twitter
    Hello everyone, could anyone help me with one simple task regarding ImageJ?
    I'm biochemist so I have really low experience with graphic/desgin, but I got one important task.. I need to know how to export all XY coordinates of an object.. not just outline, but whole object.. can anyone help with that?
    Josh Moore
    @joshmoore
    hi @nightdismay_twitter You might try asking your question on http://forum.imagej.net/ (perhaps looking for similar ones first).
    Curtis Rueden
    @ctrueden
    @imagejan It seems your logo is the winner! Congratulations. The question is: how should we proceed? There was some concern over colors. I think we should create a couple of versions with different color schemes, and with/without white outline. What do you think?
    Hadrien Mary
    @hadim
    Congrats @imagejan ! I agree with creating a couple of versions with different colors.
    Kyle I S Harrington
    @kephale
    woohoo! nice @imagejan!!
    Philipp Hanslovsky
    @hanslovsky
    Congrats @imagejan !
    Jan Eglinger
    @imagejan
    :smile: :tada: thanks all for your support!
    @ctrueden yes, color schemes that fit well to bright and dark background, as well as outlined versions would be good. Thanks a lot to @awalter17 for updating my initial script to the latest imglib-roi usage. Now we'd need to generate outlines and fill with different colors ideally from this script. Also, can we use the latest imglib-roi in Jupyter/Binder notebooks already? :)
    Jan Eglinger
    @imagejan
    And we might want something nice corresponding to Fiji_Logo_3D.js for the new logo, but displayed in BDV and SciView (of course)
    Kyle I S Harrington
    @kephale
    oo @imagejan feel free to poke us about that
    Jan Eglinger
    @imagejan
    I will try to play with different logo versions on the weekend, and then ask you for opinions/improvements, @ctrueden @kephale
    Curtis Rueden
    @ctrueden
    Sounds good, thanks @imagejan.