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    Gabriel Selzer
    @gselzer
    @dfperrault that would be a good question to ask on forum.image.sc (if it hasn't been asked already :sweat_smile:)
    A quick search for 'raspberry pi' shows many different results
    dfperrault
    @dfperrault
    Thanks!
    Gabriel Selzer
    @gselzer
    :+1:
    Mallow24
    @Mallow24
    Hello everyone I am sorry I am really a beginner in using Image but I would have a question about the timestamp in imageJ i would like to plot the %area vs the time in order to analyze cell migration.
    I also created a macro code but I am not able to include the known time interval and starting time. Maybe you have time to help me thank you in andvanced! :)
    Gabriel Selzer
    @gselzer
    @Mallow24 this would be a great question for the image.sc forum
    Sonia Jain
    @soniajain1:matrix.org
    [m]
    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
    @etadobson
    @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
    @ctrueden
    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
    @ctrueden
    Maybe I should just ask this question on the Image.sc Forum.
    Matthias Arzt
    @maarzt

    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
    @xulman
    (yes, pls... and thanks)
    Jean-Yves Tinevez
    @tinevez
    (Congratulations guys!)
    odinsbane
    @odinsbane
    https://imagej.cit.nih.gov/ij/developer/api/ij/ij/process/ImageProcessor.html#blurGaussian(double)
    I think this belongs here? Is the radius in pixels?
    Michael Doube
    @mdoube
    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
    @mdoube
    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?
    More here: https://forum.image.sc/t/save-tiff-stack-from-ellipsoid-factor-in-headless-mode/58811
    Curtis Rueden
    @ctrueden

    @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
    @mdoube
    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
    @mdoube
    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
    @mdoube
    Done: imagej/imagej-legacy#277 thanks @ctrueden !
    Adriana PGS
    @AdrianaPerezgr2_twitter

    @AdrianaPerezgr2_twitter
    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

    image.png
    John Bogovic
    @bogovicj
    Hi @AdrianaPerezgr2_twitter . I replied to you on the forum
    Jan Eglinger
    @imagejan
    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

    https://github.com/fmi-basel/faim-ij2-ij/runs/6423053171?check_suite_focus=true#step:5:101

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

    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
    @ctrueden
    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
    @ctrueden
    @gselzer Getting closer now: scijava/pom-scijava@d58ce8a.
    Gabriel Selzer
    @gselzer

    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
    @ctrueden
    Feel free to make additional converters!
    You have to be careful to set the priorities correctly.