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  • Oct 15 10:36
    DeboraOlivier closed #138
  • Oct 15 09:03
    DeboraOlivier opened #138
  • Oct 07 20:13
    ctrueden commented #7
  • Oct 07 20:11
    ctrueden closed #7
  • Oct 07 20:11

    ctrueden on master

    Fix packaging of "F div F0" scr… (compare)

  • Oct 07 15:52

    tinevez on master

    Make the SparseLAPFrameToFrameT… (compare)

  • Oct 02 12:55
    ctrueden closed #226
  • Oct 02 12:55
    ctrueden commented #226
  • Oct 02 11:28
    ctrueden commented #211
  • Sep 30 13:45

    ctrueden on master

    POM: update Kota Miura GitHub ID Comment out plugins.dir assignm… Remove the IJ_Alt_Key_Listener … (compare)

  • Sep 27 12:27
    ctrueden commented #234
  • Sep 26 19:17
    imagejan commented #234
  • Sep 26 19:17
    imagejan commented #234
  • Sep 25 17:11
    antipa opened #7
  • Sep 23 11:40
    frauzufall closed #233
  • Sep 23 10:25

    tinevez on master

    Make the LAP tracker more exten… (compare)

  • Sep 22 10:05
    tischi commented #26
  • Sep 21 21:25
    ctrueden commented #26
  • Sep 21 13:26
    tischi commented #26
  • Sep 21 11:49
    ctrueden commented #26
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.
matrixbot
@matrixbot
superusercode I'll just keep accessing gitter through matrix then.
Kabouik
@Kabouik
Last year I used a folder batch .ijm script that I wrote based on that: https://imagej.net/Batch_Processing
Now I am trying to run it again, on the same folders, and I get an error because my script starts with "@" (the three lines defining input folder, output folder and suffix). I tried commenting them out with either "//" or "#", but of course then the following lines don't work because they do not know input.
Was there an update breaking this syntax, or is it possible that I edited the script in a wrong text editor that removed some important symbols due to wrong syntax highlighting?
Jan Eglinger
@imagejan
@Kabouik the syntax is explained here: https://imagej.net/Script_Parameters
// @ is legacy and works
#@ is current recommendation
independent of the script language you choose
Kabouik
@Kabouik
None of them work, I suppose there are other changes to apply to my script then
Jan Eglinger
@imagejan
If in doubt, please open a topic on the forum with some example code and your installation details
Kabouik
@Kabouik
But it that something that changed since last year? I wonder why my script was even starting with @ and not // if it didn't work back then (probably did a mistake with some alternate versions of the script)
For instance, with the current recommendation, I get an error from line 1: Statement cannot begin with "#" in line 1.
Curtis Rueden
@ctrueden
@Kabouik The script syntax was enhanced, but it is supposed to be backwards compatible. If not, it is a bug. If you post the first 10 lines of your script, it would be helpful for analysis.
Kabouik
@Kabouik

@ctrueden The script is short so it pasted it full here: https://hastebin.com/iwexirecox.php
This is with the #@, but it doesn't work here. Last time I used it successfully was last year so I don't quite remember the details. When I opened it today, there was no // or # before the "@". Perhaps that was an error, this was my first ImageJ script so I am not familiar with the syntax, but is that possible that it worked like that anyway last year?

In any case, it doesn't work now, fails right from these parameters at the top.

I can open a thread on the forum if that is easier, but it looks like I just got the syntax wrong somwhere, might not be worth cluttering the forum for a simple typo in a script.
Kabouik
@Kabouik
Also, I get the same error if I do File/New/Script and Templates/ImageJ 1.x/Examples/Process folder (IJ1 macro), save the script, and execute it. FiJi says that the line 5 cannot start with #.
Kabouik
@Kabouik
Alright it seems to work with the button "RUN" from the script editor (and "#@"), but not from Plugins/Macros/Run (weird, because I have another script that works from there). And I needed to edit the first lines to replace "style" with "value" to prefill the window asking for input and output paths.
Kabouik
@Kabouik
Thanks @imagejan, @ctrueden, for pointing into the right direction.
amirffff
@amirffff
Hi everyone
does someone programming with imageJ/Jthon and can help me please?
Curtis Rueden
@ctrueden
@Kabouik The Plugins/Macros/Run is an ImageJ 1.x command, which has not been tested with ImageJ2 scripts. Sorry for the confusion there.
@Kabouik The syntax looks correct, apart from the style attribute being used incorrectly, yeah.
The script should work if you press Run in script editor, and it should work if you place it into $IMAGEJ_DIR/scripts/Foo/Bar. Then it will appear in the Foo > Bar menu and should work from the menus, as well.
Curtis Rueden
@ctrueden
NOTICE: The ImageJ server infrastructure will be going down within the next few minutes. Downtime should be short (less than 10 minutes).
Curtis Rueden
@ctrueden
Servers should all be back online; please ping if you notice otherwise.
li8
@liberium_li8_twitter
I have taken several microscopy images through a camera but I can't upload then to Image J unless I use bio-format importing. The problem is that in this way I can't apply the color threshold, as it doesn't work properly, with all 3 items (Hue, saturation and brightness) appearing blank. Any ideas?
Jan Eglinger
@imagejan
@liberium_li8_twitter bio-formats will import as multi-channel hyperstack. Try converting to RGB first before using color threshold.
li8
@liberium_li8_twitter
It worked! Thank you very much! Have a nice day!