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    Jan Eglinger
    @imagejan
    @halirutan I just edited it to improve the formatting.
    For reference: here's the forum question.
    Patrick Scheibe
    @halirutan
    In your image, what exactly are the cells you try to measure?
    Because in the second image, the regions that are marked with red seem to be the darker regions that are separated by the slightly brighter boundaries.
    However, you said you stained the cells which usually means that they should be the brightest things. @RichardKino_twitter
    Jan Eglinger
    @imagejan
    @halirutan please let's continue the discussion on the forum. It's more discoverable there, when others search for similar things...
    Richard Kino
    @RichardKino_twitter
    apologies I just saw your response @halirutan
    @halirutan I am trying to measure the endosperm cells which as you mention are the darker regions separated by the slightly brighter boundaries. These cell walls contain small amounts of mixed linkage glycans and arabinoxylan which don't stain brightly but this stain has a quick application and allows for the overall cell morphology to be viewed. The threshold tool on image J is also quite good at removing other intracellular bodies that I don't want
    Patrick Scheibe
    @halirutan
    @RichardKino_twitter You should include this information in the question as it might not be obvious for readers. Furthermore, it would be good if you included the original image and not the screenshot.
    Richard Kino
    @RichardKino_twitter
    @imagejan And thank you Jan for editing my original post, a lot easier to read!
    @halirutan Thanks for the advice, that's a good point! I will edit the post and also try to attach and upload the original image.
    Richard Kino
    @RichardKino_twitter
    @halirutan I have edited the post. Thanks!
    Richard Kino
    @RichardKino_twitter
    I think it's probably a simple issue as when I try and draw a free hand area round one of the cells after giving the scale it gives a huge area which makes me think it isn't scaled properly....
    Patrick Scheibe
    @halirutan
    @RichardKino_twitter Have you tried if you get reasonable values when you assume these areas are in pixel?
    Richard Kino
    @RichardKino_twitter
    @halirutan Well based on the scale bar the scale is 0.4775 pixels/um . Therefore for an example area measurement of 10000 which we could assume to be pixels I multiplying this value by the scale factor (10000 x 0.4775 = 4775 um (squared) which is still far too big. Unless I would then need to square root this value?
    Patrick Scheibe
    @halirutan
    @RichardKino_twitter But it's 0.4 pixel/um length of the pixel. To get the area you need to square it.
    When I understood you correctly then you need to make 0.47750.4775 to get the area of one pixel. Then you can do 100000.22800625` = 2280 um^2.
    Curtis Rueden
    @ctrueden
    Did you guys see @imagejan's request to discuss on the Forum? This chat is intended for development discussion. And it will be very confusing later when people find that forum thread and then all the discussion here in the
    Gitter channel is not visible from there.
    Richard Kino
    @RichardKino_twitter
    @ctrueden Forgive me, it's my fault. I won't post any more on this channel. I think its just that this was the only place I was getting a response! @halirutan Thanks for your help. I think I understand!
    Curtis Rueden
    @ctrueden
    @RichardKino_twitter I understand. I am glad you got some help. It is OK to post here with a link to a forum thread, to help bump it. I just think it is unfortunate when conversations get split across media because then it is hard to follow it later. The forum also lets people follow individual threads, whereas this channel is one big feed.
    Kevin Mader
    @kmader
    so was working on a few other things today and a few students complained about mixing jupyter and imagej. So we made a binder-friendly scijava kernel, so you can start ImageJ notebooks online with a single click, but mayb someone already did this https://mybinder.org/v2/gh/4QuantOSS/scijava-jupyter-kernel/master?filepath=notebooks%2FImageJ.ipynb
    @ctrueden you can do all of your presentations in ImageJ directly using Jupyter, reveal.js, RISE, scijava-jupyter-kernel (http://mybinder.org/v2/gh/kmader/quantitative-big-imaging-2018/master?filepath=Lectures/01-Introduction.ipynb)
    Kyle I S Harrington
    @kephale
    @kmader indeed you'll find that @ctrueden setup binder (https://mybinder.org/v2/gh/imagej/tutorials/master) and somewhere had some RISE stuff floating around
    Kevin Mader
    @kmader
    ah cool! you have to add the binder-ready tag to the repo so people find it
    Kyle I S Harrington
    @kephale
    i'm still curious about a version of the scijava-jupyter-kernel that uses a minimal set of dependencies, there is( or maybe was at this point? ) an issue with clashing dependencies when you start importing things like imagej-ops that are directly linked into the kernel which makes it more or less not possible to run any of my code in them at the moment
    Kevin Mader
    @kmader
    that makes things trickier, I am really curious to see how well the imglib2-numpy bridge works, there could definitely be some interesting things to come out of that
    Hadrien Mary
    @hadim
    @ctrueden I just realized the SJJK version on Anaconda is 0.5.1 instead of 0.6.0.
    Do you want me to update it?
    Hadrien Mary
    @hadim
    @ctrueden let me know conda-forge/scijava-jupyter-kernel-feedstock#14 I can push the green button whenever you want. Also I could add it to the feedstock repo so you can release new versions yourself next time.
    Curtis Rueden
    @ctrueden
    Minimal SJJK with scijava grab still not available. Still planned. But right now we are focusing on calling ij from Python via pyjnius. See https://github.com/CellProfiler/notebooks
    Curtis Rueden
    @ctrueden
    @kephale I was able to wrap an entire net.imagej.ImageJ gateway as a python object. See the imagej pyjnius demo of the above repo.
    I guess that doesn't give you clojure though :-(
    If we make the system classpath customizable somehow it could alleviate some of the grab difficulties for now.
    Kyle I S Harrington
    @kephale
    yeah, i saw the ij<->python action which is cool and certainly deserves to be a higher priority anyway.
    yes, if i can get 1 or 2 jars on the classpath then my problems pretty much go away
    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