by

Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
    Curtis Rueden
    @ctrueden
    IIRC, nothing automatically uploads new IJ1s to the ImageJ update site anymore. But I could be wrong.
    Certainly nothing updates pom-scijava automatically yet.
    We could teach the imagej/ImageJA Travis build to upload to the ImageJ core update site, after a successful build and deploy.
    Jan Eglinger
    @imagejan
    Yes, I remember you were the one uploading the latest few updates of ij.jar each time.
    Are there any issues with ij.jar and Java 6? Otherwise, uploading to the ImageJ update site is possibly fine, right?
    Curtis Rueden
    @ctrueden
    Good question!
    I forgot. Let's see what's on there now.
    Looks like ImageJA still targets 1.6 at least. But it doesn't actually build with Java 6 anymore. So in theory it should be fine, but nothing really tests it rigorously, and there could be Java-8-isms that slip in over time.
    Curtis Rueden
    @ctrueden
    Huh, it looks like 1.52p got uploaded to Java-8... but all previous ones got uploaded to ImageJ.
    It's probably for the best to always upload them to Java-8 from now on.
    Jan Eglinger
    @imagejan
    (See this forum topic for the history of 1.52p.)
    Curtis Rueden
    @ctrueden
    Thanks. It looks like I didn't comment on why I uploaded to Java-8 instead of ImageJ. Maybe I just didn't think about it. But I think using Java-8 henceforth (until Java-8 is retired) is fine.
    Jan Eglinger
    @imagejan
    In the Travis Cron Jobs settings, it says Scheduled in about 24 hours and Do not run if there has been a build in the last 24h.
    Is it fine to trigger manually? And should we change the time window to something like 23h for suppression of the build?
    (Oh, the last thing is not an option...)
    Curtis Rueden
    @ctrueden
    Sorry @imagejan, was out to lunch. I think it's fine to trigger a build manually. I'll do it now.
    Jan Eglinger
    @imagejan
    :tada: :+1:
    Phạm Đình Luân
    @LuanPham97
    Hi everyone, I'm using ImageJ to view Histogram of DICOM image. When I show Histogram for the first time, I see Min= -719, Max=1402. But when I press Alt+H to change Bins to 100. Max, Min value is change to 0 & 255.
    I think when change bins then only Bin Width should change value, I don't know why "Max", "Min", "Count" value is changed. I posted question in Stack Overflow: https://stackoverflow.com/questions/58653245/imagej-why-max-min-value-change-when-i-change-histogram-bins
    Dianne
    @djnacionales_gitlab
    Hello, I'm trying to use the worm tracking software on ImageJ but I don't know how to open it once the package is downloaded
    I already have trimmed worm videos from QuickTime Player but I don't know how to use it
    Jan Eglinger
    @imagejan
    @LuanPham97 as stated on https://imagej.net/Help, the recommended way to get support for ImageJ usage is the image.sc forum. (This Gitter chat is for discussion among developers.) When posting on the forum, make sure you tag your posts with imagej and dicom.
    @djnacionales_gitlab see above, questions like this are much better asked on the forum, where they’ll be seen by many experts.
    @djnacionales_gitlab oh, I see you posted already, thanks!
    Curtis Rueden
    @ctrueden

    For those of you using Jython scripting in ImageJ: there is a major new beta of Jython, 2.7.2b2, which improves Jython's dependency structure and also fixes many issues since 2.7.1. If you want to test it in a local Fiji installation, you can:

    git clone git://github.com/scijava/scripting-jython
    cd scripting-jython
    mvn -Dscijava.app.directory=/path/to/dev/Fiji.app
    rm /path/to/dev/Fiji.app/jars/jython-shaded*.jar

    And see how it goes. Everything I tested seems to be working, so I released scripting-jython version 0.5.0 and will include it in Fiji soon, unless I hear objections from anyone.

    Talal Mostafa
    @TaIaI_Mostafa_twitter

    Hello everyone

    I am trying to use Batch processing using standard imageJ but I am struggling with Macros

    here is my macro

    function action(input, output, filename) {
    open(input + filename);
    run("8-bit");
    //setTool("zoom");
    //setTool("line");
    makeLine(2343, 1845, 2525, 1845);
    run("Set Scale...", "known=1 unit=mm");
    makeRectangle(0, 0, 2560, 1828);
    run("Crop");
    run("Bandpass Filter...", "filter_large=40 filter_small=1 suppress=None tolerance=50 autoscale saturate");
    setAutoThreshold("Default");
    //run("Threshold...");
    setThreshold(0, 80);
    setOption("BlackBackground", true);
    run("Convert to Mask");
    run("Analyze Particles...", "size=0.60-Infinity show=[Overlay Masks] display clear add");
    saveAs("Results", "C:/Users/Talal/Desktop/resultsall/out/filename");
    //setTool("rectangle");
    makeRectangle(0, 3, 2560, 1825);
    run("Duplicate...", " ");
    saveAs("PNG", "C:/Users/Talal/Desktop/resultsall/out/filename");
    }
    input = "C:\Users\Talal\Desktop\resultsall\enter\";
    output = C:\Users\Talal\Desktop\resultsall\out\";

    list = getFileList(input);
    for (i = 0; i < list.length; i++)
    action(input, output, list[i]);
    setBatchMode(false);

    however, it does not work. when I delete the first 2 lines it works..however, the output has the same name
    I have multiple images...my outputs is a txt sheet with the results of particle analysis and an image of the processed image
    Gabriel Selzer
    @gselzer
    @TaIaI_Mostafa_twitter this would be a great question to ask on https://forum.image.sc/, there are many knowledgable people there who would be happy to help answer your question
    Talal Mostafa
    @TaIaI_Mostafa_twitter
    Hello Gabriel
    Thank you I already did
    Deborah Schmidt
    @frauzufall

    Is this section in the wiki about adding a new template to ImageJ up to date? I'm wondering about this part:

    The templates need to be put into a subdirectory corresponding with the correct script language name.

    The examples here don't do this.

    There is also this repo: https://github.com/imagej/example-script-collection which is not mentioned in the wiki, should this still be used as a template? Then I would add a link to it.
    Jan Eglinger
    @imagejan
    I think this is outdated, the addition is from 2014: https://imagej.net/index.php?title=Script_Templates&diff=12385&oldid=12384
    Yes, it would be great if you can update the wiki page! The example-script-collection was intended to show how to manage scripts that show up in the main ImageJ menu, but not targeting script templates in the script editor.
    Still it would be good to mention it where appropriate.
    Deborah Schmidt
    @frauzufall

    Ah, ok, got it. What about this:

    This is required so that templates are made available only when the corresponding script language is available.

    Seems like this check is no longer happening and scripts are added independent of which language is available, is this correct or am I missing something in the code you linked above?

    Jan Eglinger
    @imagejan
    Hm, that's a good point. I don't know. Would also have to dig deeper...
    Deborah Schmidt
    @frauzufall
    I think this is where this check got removed: scijava/script-editor@a1d5a4a
    @ctrueden since you wrote this commit - seems like you wanted scripts without a matching available script language to still be part of the template menu, so I would just remove this paragraph from the wiki.
    Curtis Rueden
    @ctrueden
    @frauzufall Removing the paragraph sounds great. Thanks!
    The language-specific basic templates ship with the scijava/scripting-<foo> components, so the language will be available for those. The only chance of a missing language might be a component that ships scripts without an explicit Maven-side runtime dependency on the relevant scripting-<foo> component—which would then prevent automated testing of the scripts. So I think it's OK.
    Jan Eglinger
    @imagejan
    As far as I can see, this repo has a test dependency on scripting-groovy, but no runtime dependency. So it might be possible to have an ImageJ installation without Groovy support, which still shows this template in the menu...
    Curtis Rueden
    @ctrueden
    @imagejan Ah, so I guess we should add scripting-groovy as a runtime dep to imagej-legacy then, eh?
    BTW: I just purged a whole boatload of spammers from the imagej.net wiki.