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Repo info
Activity
  • 09:59
    erjel opened #22
  • 08:18

    tpietzsch on master

    Create Simi/TGMM import dialogs… Add TODO (compare)

  • 05:43
    tischi commented #26
  • Sep 18 17:48
    ctrueden commented #26
  • Sep 18 12:16

    tpietzsch on serialize-feature-model2

    (compare)

  • Sep 18 12:16

    tpietzsch on master

    Implements the Contextual metho… Interface for classes that can … Feature serialization service a… and 36 more (compare)

  • Sep 18 12:16
    tpietzsch closed #106
  • Sep 18 12:16
    tpietzsch commented #106
  • Sep 18 12:12
    tpietzsch synchronize #106
  • Sep 18 12:12

    tpietzsch on serialize-feature-model2

    Make UpdateStackSerializationTe… Make TrackMateImporterTest work… Make MaMuTExporterTest work hea… (compare)

  • Sep 18 12:09
    jburel opened #237
  • Sep 18 12:08
    jburel opened #236
  • Sep 18 11:37
    tischi commented #26
  • Sep 18 11:13
    tpietzsch synchronize #106
  • Sep 18 11:13

    tpietzsch on serialize-feature-model2

    Make TrackMateImporterTest work… Make MaMuTExporterTest work hea… (compare)

  • Sep 17 21:46
    tpietzsch synchronize #106
  • Sep 17 21:46

    tpietzsch on serialize-feature-model2

    Make UpdateStackSerializationTe… (compare)

  • Sep 17 15:16
    tpietzsch synchronize #106
  • Sep 17 15:16

    tpietzsch on serialize-feature-model2

    formatting Add TODO Remove explicit array creation and 4 more (compare)

  • Sep 17 02:58
    ctrueden commented #235
KaraokeMary
@KaraokeMary
I can't seem to make the XYZ global among all three planes. There must be a way to do this, right?
Curtis Rueden
@ctrueden
@KaraokeMary Could you describe what you mean by "XYZ global among all three planes"? Isn't each plane its own Z plane?
Curtis Rueden
@ctrueden
@KaraokeMary I see you also posted to the ImageJ mailing list. That is a better place to solve your issue than here in Gitter. (Although best would be http://forum.imagej.net/ rather than the mailing list.)
KaraokeMary
@KaraokeMary
I did, but so far no luck. The XYZ coordinates in the selection tools is different depending on if I am in sagittal, coronal, or transverse. The X is always on the left and the Y is always at the top, regardless of plane. I need them to make them correspond somehow though all three.
KaraokeMary
@KaraokeMary
I posted on the forum a few days ago, but no luck.
Ellen T Arena
@etarena
@KaraokeMary - I saw your post on the forum... Perhaps it's worth adding a bit more detail in your post? Change the title to be more specific for what you need? Which tools specifically are you using? Write out your current workflow and where you find it's 'breaking' down... if you can include an original dataset - that is also super helpful for us all to help you. :)
@KaraokeMary - I just updated the title of your post on the Forum... feel free to edit it again. Let's see if we can get you the help you need.
Varun Kapoor
@kapoorlab
Hi did somebody notice that if I do this : https://imagej.net/File:MavenRunConfig.png for a maven based Java project and try to open Fiji it quits during opening always?
Curtis Rueden
@ctrueden
@kapoorlab Nope, I don't use Eclipse that way. If you have time to troubleshoot and report back more details (or better: find a fix and update the wiki to reflect that fix), it would be much appreciated.
irsasho
@IrsaShoukat_twitter
Hello everyone. I am new to image j and need some guidance. I have a time lapse where each time point has multiple stacks (7 per time point). Is there a plug in that will automatically detect the best stack for me (instead of me having to do this manually) ?
Ellen T Arena
@etarena
@IrsaShoukat_twitter - the best place to post this type of question is on the ImageJ Forum ... it's easier to get more detailed, searchable feedback there. :) Just include as much detail (and example image?) as you can... we'll get you help!
irsasho
@IrsaShoukat_twitter
ok! thank you :)
Ellen T Arena
@etarena
:)
Varun Kapoor
@kapoorlab
@ctrueden ok I will try this tomorrow by doing a local fiji install and then hopefully be able to find a fix.
Varun Kapoor
@kapoorlab
Ok I know why it is acting like this, to fix this I need to know this: If my maven based main java project depends on other local maven based java projects, how do I generate the jars of those to be compiled when generating the main jar file? This would fix the issue I had with Fiji quitting on opening after following the wiki instructions above, plus including the libraries on the java build path of the main project did not help.
Jan Eglinger
@imagejan
@kapoorlab mvn -Dimagej.app.directory=/path/to/your/Fiji.app should take care of copying all dependencies of your maven project, no?
Stefan Helfrich
@stelfrich
@imagejan @kapoorlab I might be wrong here, but that doesn't actually trigger a build of an artifact but "only" retrieves an artifact from your local Maven repository
Varun Kapoor
@kapoorlab
@stelfrich @imagejan Yeah this does not goes in to build a jar for the referenced dependent project, it would be nice to build a jar for the master project which triggers the compilation of dependent maven projects and includes those jars in the Fiji.app/plugins/jars folder and the jar for the main plugin in Fiji.app/plugins folder , is that possible somehow?
Curtis Rueden
@ctrueden
@kapoorlab Does your project depend on snapshot versions of other libraries? Ideally it should not. If it does not, then it does not matter whether you rebuild, or fetch the existing dependency from the Maven repository. That's a major advantage of reproducible builds: modularity of builds.
If you do depend on snapshot versions of other libraries, then things become a lot more complicated. It is your responsibility to generate the JARs from the "bottom up" of your dependency tree. The imagej-maven-plugin does not (and probably will never) support this use case.
Varun Kapoor
@kapoorlab
@ctrueden Ok i get it, i am working with three snapshot versions of slave projects that the master needs and right now I do physically put them in the plugins/jar, when they become non-snapshots then I will try again by putting them in the java build path of the master.
Curtis Rueden
@ctrueden
@kapoorlab One thing I like to do to ease development in that scenario is to use symlinks from the target/foo-x.y.z.jar file to the Fiji.app installation. Then, while you still need to rebuild each with mvn package, at least you do not need to copy them every time.
This assumes you need to test in a full-blown Fiji.app installation, though. Do you really need to do that?
Varun Kapoor
@kapoorlab
@ctrueden Do not need this so urgently, just wanted to know if i am missing some automated way of doing it in the wiki imageJ way of doing things. But I can live with moving jars to their correct location for now, thanks for letting me know about this.
Curtis Rueden
@ctrueden
@kapoorlab If you do not need a full-blown Fiji.app installation for testing, then the much simpler thing to do is to run your code via a main method from inside the IDE.
amirffff
@amirffff
@amirffff
Hi guys
can I ask a general question?
How do you work with imageJ in order to write scripts (Jython, Macro, Java) and why?
thanks in advance
Ellen T Arena
@etarena
@amirffff posted on the forum this same question - so all responses can be addressed there. ^^^ The link is pasted here for others to follow.
amirffff
@amirffff
@etarena Thnaks I have already done it
Ellen T Arena
@etarena
:thumbsup:
Varun Kapoor
@kapoorlab
@ctrueden , yeah thats how i am doing it now, when it is done then a direct integration of maven based eclipse project having master-slave relation into Fiji would be convenient. Thanks.
amirffff
@amirffff
there is anyone in this forum now?
Jan Eglinger
@imagejan
Interesting discussion on the mailing list about Fiji vs. plain ImageJ1.x performance on multithreaded systems: http://imagej.1557.x6.nabble.com/very-very-very-slow-process-tp5020053p5020144.html
Any opinions/experience from the Fiji experts?
Curtis Rueden
@ctrueden
@imagejan I'm sorry, I don't have much insight into the problem, nor any time to investigate it. I agree with @axtimwalde that the parameters used to launch the JVM are paramount. I did not see any details from Michael Schmid about the exact invocations to java that were used. If I were to investigate I would definitely want to do the benchmarks after invoking java directly, rather than via the ImageJ launcher. The goal being to ensure we are comparing apples to apples.
The next step is then to profile the code to see where the bottlenecks are, comparing plain IJ1 with IJ2.
I will respond to the mail now with these suggestions.
Varun Kapoor
@kapoorlab
Hi, quick question, need to draw 3d line from (x, y, z)A to (x, y, z)B on a canvas of imageplus without having to write a drawing routine myself, can i find one where this is already there?
Curtis Rueden
@ctrueden
@kapoorlab bresenham style? Or antialiased? Or...?
You can render it with imglib2-roi + BDV now data structure wise. @awalter17
Varun Kapoor
@kapoorlab
Just for visualizing tracks which I extract out of a graph, any style would be ok for this, is there a method that I can call for such a rendering?
Curtis Rueden
@ctrueden
@kapoorlab You want to make a 3D display then, it sounds like? TrackMate does it using the 3D Viewer, but the 3D Viewer is on its way out unfortunately.
Varun Kapoor
@kapoorlab
@ctrueden Ok then if I could link my program to trackmate visualization utilities that would be great, I want to come in with a graph or a model made from a graph and then call trackmate utilities to visualize, is that possible @tinevez, anz example on how an external java program can call trackmate visualization part of the library?
Jean-Yves Tinevez
@tinevez
@kapoorlab The best is to check the https://imagej.net/Scripting_TrackMate page.
Here I use a Model object programmatically to create some spots and links and then to show them.
matrixbot
@matrixbot
superusercode test
superusercode Does Fiji have an IRC room?
Varun Kapoor
@kapoorlab
@tinevez Merci beaucoup, it looks exactly what I was looking for, I will try to use this and let you know if I faced any issues.
Kabouik
@Kabouik
Hi, is there a way to reorder ROI according to y AND x coordinates ? Or manually with clicks? The Sort button seems to work only on y coordinates.
Kabouik
@Kabouik
Nevermind, my sample was not so big so I just worked around by exporting the measurement results one by one in the order I needed.
Curtis Rueden
@ctrueden
@matrixbot It does! But it's not very active. I usually see posts there after a few days, long after whoever asked the question has given up and left. -_- So I would not recommend using it.
You should use http://forum.imagej.net/, or here if you want to discuss code.