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Repo info
    Sonia Jain
    Hello all. I need to count nuclei and gamma H2AX foci inside nuclei. I have about 120 images to do so. I would highly appreciate a faster method which can be applied to all the images reliably. Please help. It would save a lot of my time, and analysis can be done in unbiased and timely manner.
    I used analyze particles to count nuclei and find maxima to get foci inside nuclei. But how to apply this to all the images, I need to learn?
    Ellen TA Dobson
    @soniajain1:matrix.org The best place for you to get this type of image analysis help is on the image.sc forum - post your question there. And include a sample image - as well as the exact steps you've tried thus far... We can help you get started with scripting to batch process your images.
    Curtis Rueden
    There is some dormant code on the imagej.net front page for a plugin highlight carousel, lifted from the fiji.sc Bootstrap site. I could get it working, but I'm wondering: do y'all think it would be nice to have a plugin carousel on imagej.net, with a broader community-driven set of highlighted plugins? And if so, should it live on imagej.net front page, or imagej.net/plugins, or imagej.net/list-of-extensions, or...? Or should we not bother? Opinions?
    Curtis Rueden
    Maybe I should just ask this question on the Image.sc Forum.
    Matthias Arzt

    Hello everyone, I'm a member of the tomancak lab now. Since one and a halve weeks now!

    @ctrueden / @hinerm Could you please create a new update site https://sites.imagej.net/TomancakLab/ and give access rights to me "Maarzt" and @xulman "xulman"

    2 replies
    Vladimír Ulman
    (yes, pls... and thanks)
    Jean-Yves Tinevez
    (Congratulations guys!)
    I think this belongs here? Is the radius in pixels?
    Michael Doube
    Some users and I have run into a problem calling BoneJ's ImageJ2-style 'wrapper' plugins from ImageJ macros in batch mode setBatchMode(true): the output images are never created or made available to the user in a way they can be readily accessed in macro code. My guess is that the output parameter processing is not occurring, or is occurring but the data are not 'presented' in a macro accessible way. In a batch mode macro images can normally be accessed with selectImage(), but no images are available to be selected. Macros run fine with setBatchMode(false).
    One workaround is to use Python instead:
    Michael Doube
    wrapper = commandService.run("org.bonej.wrapperPlugins.ThicknessWrapper",False,["inputImage", input_image_ij1, "showMaps", True, "maskArtefacts", True])
    wrapperInstance = wrapper.get()
    trabecular_map = wrapperInstance.getOutput("trabecularMap");
    Is this a known / intended behaviour? Or a side effect of mixing IJ1 and IJ2 worlds that is unlikely to be fixed?
    Curtis Rueden

    @mdoube Thanks for the report, and sorry to hear of the trouble. I would call this a bug. Regarding whether it's "known": maybe years ago I could have said yes, there is some quirk of the IJ<->IJ2 synchronization with batch mode, but in 2022 I cannot recall, so I'll say no, it's not known. Whether it can be fixed: would need to dig to see whether it's easily fixable, or more systemic. Sorry I can't shed more light on it off the top of my head.

    I tried reading the thread you linked, but it's >70 posts long and the last discussion is in Jython, which has diverged from the macro issue. I scanned the entire thread searching for setBatchMode but couldn't find any post with that command. Is there a particular post number you can link me to that would illustrate the issue?

    If you file an issue in imagej-legacy I can probably spend some time digging on Friday, May 27.

    Michael Doube
    but it's >70 posts long
    Yeah... that one was a beast. Sorry you waded through it. I only diagnosed it properly while trying to do my own macros in the last couple of days.
    Michael Doube
    The clue is in CommandService.run().get() I think. If you don't call get() from the Jython code there is no instance of the plugin and no outputs to get with getOutput(). But there is no similar way to get the output from a macro.
    If you file an issue in imagej-legacy I can probably spend some time digging on Friday, May 27
    Yes OK will do, thanks for the pointer for the correct location, I have a feeling someone else has reported this bug somewhere unexpected.
    Michael Doube
    Done: imagej/imagej-legacy#277 thanks @ctrueden !
    Adriana PGS

    Hello, i am having problems opening my images. They do not appear as merged, and the following text opens each time with them:

    (Fiji Is Just) ImageJ 2.1.0/1.52v; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 90MB of 49027MB (<1%)
    java.lang.NoClassDefFoundError: Could not initialize class com.jgoodies.forms.layout.FormSpecs
    ETC.... (see image)

    Does anyone know how i can fix this? Thank you

    John Bogovic
    Hi @AdrianaPerezgr2_twitter . I replied to you on the forum
    Jan Eglinger
    I have a strange issue with tests passing locally (on Windows) but failing in CI , maybe someone here give me a quick hint (before I ask on the forum)...
    I tried to wrap ImageJ's "Subtract background" headlessly: https://github.com/fmi-basel/faim-ij2-ij/blob/main/src/main/java/ch/fmi/ij/BackgroundSubtraction.java
    and wrote a small test here: https://github.com/fmi-basel/faim-ij2-ij/blob/main/src/test/java/ch/fmi/ij/BackgroundSubtractionTest.java

    Interestingly, I get a HeadlessException in only one of the two tests, and the other one is failing:

      Error:  Failures: 
      Error:    BackgroundSubtractionTest.testEqualParameters:75 Pixel values differ on coordinate (0, 0, 0, 0, 0), expected: 1904 actual: 158
      Error:  Errors: 
      Error:    BackgroundSubtractionTest.testUnequalParameters:82 » Headless


    6 replies
    I put this on the forum but maybe somebody knows how to access the origin value from properties?
    When I scale an image, the origin doesn't change. It seems like it should though.
    9 replies
    Gabriel Selzer

    What is the best way to resolve the fact that

    int myInt = 4
    ij.convert().supports(myInt, IntegerType.class)

    returns false? Is it to add a new Converter in imagej-common?

    Curtis Rueden
    New converter in SciJava Common.
    I'm surprised that returns false.
    Oh wait.
    You said IntegerType! I misread as Integer.
    Yes, imagej-common is the right place, then.
    And there is an issue for it already.
    Which is closed and merged. @gselzer You actually reviewed that PR! imagej/imagej-common#82
    Should be part of imagej-common 0.35.0, not yet part of an imagej2 release unfortunately.
    Curtis Rueden
    @gselzer Getting closer now: scijava/pom-scijava@d58ce8a.
    Gabriel Selzer

    Which is closed and merged. @gselzer You actually reviewed that PR! imagej/imagej-common#82

    Yeah, I thought it was fixed already. I just couldn't find the PR... :sweat_smile:

    But, with another look, I'm not sure that PR does enough
    We'd want to ensure that the IntegerToIntType converter could handle that conversion above
    Curtis Rueden
    Feel free to make additional converters!
    You have to be careful to set the priorities correctly.
    Gabriel Selzer
    I'd actually think what is best is to make a converter that calls the others based on a switch
    That could then be HIGH priority
    Hi there,I'm opening an RGB tiff image on imageJ with data in three separate channels -RBG, but when I open it the channels tool shows up both the blue and green in the green channel and I'm unable to separate the green only in a separate channel. Can anyone please help, much appreciate it !!

    Hey Everyone, Can someone advise or give any lead to this problem?
    I want to extract the geometry of the crystals and matrix as can be seen in the image. I would like to import the crystal structure and matrix data in Abaqus software for doing FEM analysis. Can anybody please provide me an idea, of how to do that? Because this software accepts geometries only such as
    . dwg. dxg, .step. .stl, .iges, AutoCAD file, not an image file.

    I have posted on forum two weeks before but still not answers received. Here is the complete link to problem at the forum -


    Curtis Rueden
    @hinerm Just wanted to draw your attention to this forum post about ImageJ-OMERO sessions I made a couple of weeks ago. Check out Josh's answer. We probably don't need to change anything right now, but it's good to be aware of our design limitation of one session per server. Now isn't a bad time to think about if we can/should do better.