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    Kilian
    @Kilianjoex_twitter
    Oh okay, sorry and thank you :)
    Jan Eglinger
    @imagejan
    For the record, here’s the forum post. Thanks!
    Nic Barandun
    @nbara93_gitlab
    Hey guys :)
    I came across a weird and to me new problem in Fiji/ImageJ: When I open several images (.nd format) they all get the same name which gets quite confusing… Anyone of you ever experienced the same issue?
    Jan Eglinger
    @imagejan
    @nbara93_gitlab this is a known issue with bio-formats and the Metamorph (nd) format. I reported it in 2018 here: ome/bioformats#3216, and it’s tracked on the bio-formats trello board: https://trello.com/c/823WSGPH/247-metamorph-incorrect-image-name-in-title-bar
    Please comment on these issues, so that the developers know there’s some interest in getting this fixed. I submitted sample data and there was a pull request (ome/bioformats#3032) already that should be fixing that format, but it was never merged because apparently it breaks some legacy datasets… It’s a pity that backwards-compatibility to (non-standard?) legacy files weighs more than actual support for the standard format here 🙁
    Jan Eglinger
    @imagejan
    As a workaround: avoid any underscores in your file names, and if that doesn’t help: isolate each dataset into its own subfolder.
    Nic Barandun
    @nbara93_gitlab
    @imagejan Thank you for your quick reply! Indeed, getting rid of underscores in my file names worked very well :)
    I will comment on these issues in order to make the developers (once more) aware of this issue.
    Cheers!
    albid852
    @albid852
    Hey guys! I'm trying to convert 16-bit dicoms to 8-bit png images, but I can't get the same effect as ImageJ does when doing my conversion processes. Does anyone know what algorithm ImageJ uses for normalization?
    Ellen TA Dobson
    @etadobson
    @albid852 A great place to ask this question is on the forum: https://forum.image.sc/ This channel is more for developers... We can better help you on the forum - just post there. :smile:
    albid852
    @albid852
    Oh okay, thanks!
    Curtis Rueden
    @ctrueden
    I made a poll where you can vote on what I work on next. Feel free to vote if you have opinions.
    Bram van den Broek
    @bramvdbroek:matrix.org
    [m]
    Hi all, I'd like to loosely follow the development chatter, if that's ok.
    Jan Eglinger
    @imagejan
    :+1: welcome @bramvdbroek:matrix.org !
    (I suppose you know of the other channels: fiji, scijava-common, scifio, imglib2, … ?!)
    Bram van den Broek
    @bramvdbroek:matrix.org
    [m]
    I do now. :-)
    There must be a large amount of crosstalk between some of those channels, right?
    Curtis Rueden
    @ctrueden
    @bramvdbroek:matrix.org We make an effort to talk about the topically relevant thing in each channel. But don't always succeed. And occasionally there are cross-posts—but for the most part, the chat in each room is unique.
    Bram van den Broek
    @bramvdbroek:matrix.org
    [m]
    Thanks Curtis.
    I'll try to 'listen' silently unless I think I can say something useful. 👍️
    Michael Doube
    @mdoube
    I have just somehow pushed to imagej-ops master, did not realise I had permissions to do that!
    It should be a PR instead imagej/imagej-ops@d6074eb
    Michael Doube
    @mdoube
    Hmmm. Maybe not. Getting different results running the same code on two different machines.
    Francisco Javier Valero Moreno
    @JavierValeroMoreno
    hello there
    Francisco Javier Valero Moreno
    @JavierValeroMoreno
    i have a little question, im building a plugin (Well in fact i only change one param from an existent plugin) i build the jar file and when i put it in the plugin folder imageJ dont detect it and i dont know if it is because i use a incorrect jdk or if i am not doing in the correct way (im using jdk 1.8.0_201)
    Jean-Yves Tinevez
    @tinevez
    Do you have an error message?
    Francisco Javier Valero Moreno
    @JavierValeroMoreno
    nope, imageJ just dont see the plugin, when i compile and generate the jar file it go well
    maybe its because i use other java version?
    Jean-Yves Tinevez
    @tinevez
    hmm I would not bet on this.
    Ok first: You say that you modify an existing plugin. Did you remove the previous version in the Fiji folders before copying yours?
    Francisco Javier Valero Moreno
    @JavierValeroMoreno
    i renamed
    the new plugin i mean
    Jan Eglinger
    @imagejan
    You renamed the jar file? the class? both? Is it an ImageJ1-style plugin (in that case the name is required to contain an underscore, and the jar file needs to be in plugins, not jars)? Or an IJ2/SciJava command?
    (probably better to discuss this in a topic on https://forum.image.sc/c/development/5 if it gets more involved…)
    pointing to your source code always helps.
    Francisco Javier Valero Moreno
    @JavierValeroMoreno
    thanks every one, i just solved, as you say, it was for renamed
    i named as the original plugin and it works :D
    Jean-Yves Tinevez
    @tinevez
    :plus1:
    Jan Eglinger
    @imagejan
    @hinerm it seems that ij version 1.53h (released three weeks ago) wasn’t deployed to the maven repo. The travis build failed with error: release version 1.6 not supported.
    If you have a minute, can you have a look?
    (might be imagej/imagej1@dd51b56 that switched back to Java 1.6 compatibility…)
    Mark Hiner
    @hinerm
    Gotta love claiming Java 6 compatibility while containing Java 6-incompatible code
    @ctrueden what is our procedure when ImageJ1 creates a paradox?
    Mark Hiner
    @hinerm
    nvm, PR created: imagej/imagej1#109
    Jan Eglinger
    @imagejan
    :+1: :blue_heart:
    Jan Eglinger
    @imagejan

    :worried: The real paradox is that Java-6 “compatibility” was re-introduced to avoid Fiji blocking on startup. From the commit linked above:

    Fixed a 1.53h17 regression, caused by building ij.jar for Java 8,
    that prevented Fiji from launching.

    see also this forum topic, this thread on the mailing list, and imagej/ij1-patcher#50

    NicoKiaru
    @NicoKiaru
    ij1 is supposed to be Java 6 compatible ?
    Mark Hiner
    @hinerm
    thanks @imagejan. It also revealed a weakness in the way we're setting -source, -target and -release flags
    Mark Hiner
    @hinerm
    well, not a weakness.. I guess it was a known thing, just a breakage introduced in pom scijava 30
    Curtis Rueden
    @ctrueden

    @hinerm I'm trying to deploy 1.53h from my local machine as discussed. Here is the command (taken from the .travis/build.sh):

    mvn clean && mvn -Dmaven.compiler.target=6 -Dmaven.compiler.source=7 -Dmaven.compiler.release= -Psonatype-oss-release deploy

    Using Java 11 to build. This successfully builds a JAR targeting Java 6 (and sidestepping the Java-7-specific use of JList with generic parameter). However, there is now a new problem building the javadoc:

    Execution attach-javadocs of goal org.apache.maven.plugins:maven-javadoc-plugin:3.2.0:jar failed: String index out of range: 0

    I'm on it, but just wanted to give a status update here. I'll post again with any progress.

    Mark Hiner
    @hinerm
    :+1:
    @ctrueden do you want to move the scijava.jvm.build.version flag to the default-compile execution while you're looking at it?