Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Hadrien Mary
    @hadim
    Hello amirffff. Please try to search for a question before asking here as this chat is primarly dedicated to ImageJ development. Here two ressources that can help you understand the differences between Ij1, IJ2 and Fiji: https://imagej.net/Frequently_Asked_Questions http://forum.imagej.net/t/fiji-versus-imagej2-or-imagej/4380
    Feel free to post a question on the forum if you need more information.
    docnathandice
    @docnathandice
    i have a image of cells with scars that we have marked with a florescent stain. i need a way to count them. i am trying to tag them with the point marker set to white. can someone help me do this. i am new to this program.
    Curtis Rueden
    @ctrueden
    @docnathandice Can you please post your question on the ImageJ Forum?
    If you post a sample image, perhaps someone can advise on whether/how they can be counted automatically, as well.
    Richard Kino
    @RichardKino_twitter
    hello I am currently counting wheat endosperm cells using the cell magic wand counter tool, however after setting the scale and measurements, image j is measuring the cells and giving me area values for each cells that cannot be accurate, does anyone have any ideas how I might correct this?
    Gabriel Einsdorf
    @gab1one
    @RichardKino_twitter Can you please post your question on the ImageJ Forum?
    If you post a sample image, perhaps someone can advise on whether/how they can be counted automatically, as well. :)
    Richard Kino
    @RichardKino_twitter
    Thanks I've posted it on the forum. Any idea how long typically it takes for someone to reply? Or whether their replied to at all?
    Jan Eglinger
    @imagejan
    @RichardKino_twitter anything between 30 sec and several months, depending on how well you formulated your question and whether you include a catching example image ;-)
    Patrick Scheibe
    @halirutan
    @RichardKino_twitter Putting description-text as a code-block is the first this that makes a question hard to read.
    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)