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  • 15:59

    ctrueden on jfreesvg

    WIP: Add JFreeSVG library to th… (compare)

  • Oct 18 08:46

    tinevez on fix-no-tags-crash

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  • Oct 17 13:19
    yifnzhao commented #82
  • Oct 17 12:23

    tpietzsch on master

    Fix crash: assigning tags when … Merge pull request #108 from fi… (compare)

  • Oct 17 12:23
    tpietzsch closed #108
  • Oct 17 11:24
    tinevez opened #108
  • Oct 17 11:24

    tinevez on fix-no-tags-crash

    Fix crash: assigning tags when … (compare)

  • 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
Curtis Rueden
@ctrueden
I also like the forum better because it is "more public"—easily searchable from https://search.imagej.net/, whereas searching the gitter history is spotty at best. It seems somehow random which conversations are indexed...
@Alex__Goodman_twitter The best person to answer your question is @tinevez. But you are better off posting on the ImageJ Forum, as I mentioned just now. He will answer you there too. :-)
Alex Goodman
@Alex__Goodman_twitter
Thank you!
FreyaGoetz
@FreyaGoetz
@ctrueden Thank you for the suggestion of ImageJ Forum and who to contact. You have been very helpful today.
Fevzi Kafexhiu
@fevzikafexhiu_twitter
@ctrueden Thanks a bunch. It worked when I saved the table as .tsv file.
Ai P. Vardhanabindu
@Aivard_twitter
Hi. After the recent update, I am not able to detect particles using Mosaic. Is there any way I can fix this please?
Kyle I S Harrington
@kephale
@Aivard_twitter I suggest posting this on http://forum.imagej.net/ not many MOSAIC folks are here on gitter @skalarproduktraum
Krzysztof Gonciarz
@krzysg
@Aivard_twitter We have normalized cutoff parameter in range 0-1, please play with it a little and it will work for you (0 - means no discrimination at all so all detected particles will be taken into account and 1-all will be filtered out).
Ulrik Günther
@skalarproduktraum
thanks for dropping by, @krzysg :+1:
FreyaGoetz
@FreyaGoetz
Good afternoon @axtimwalde @acardona ! I have aligned a stack of 1684 slices and would like to export as a tiff stack. I followed the suggestion I got on the ImageJ forum to" right-click in the canvas, then Export > Create flat image..." which turned my 3.4 GB stack into 104GB of individual images. My end goal is to make an .avi of the stack so my boss can scroll through the stack. I'm fine with exporting individual slices as long as they remain registered when I open them as a tiff series in ImageJ
Oops, hit send too soon. I think the size increase is due to all of the black space that was added around the slices. I tried to crop to the ROI but cropping is apparently not available in TrakEM2. Any suggestions will be much appreciated!
Stephan Saalfeld
@axtimwalde
@FreyaGoetz "Export > Create flat image..." exports the currently selected rectangle
you can also "DIsplay > Change Layer Size..." (or something like this)
also, if you convert the series of tiffs into a series of say PNGs, the black padding does not cost you anything
FreyaGoetz
@FreyaGoetz
@axtimwalde Thank you. That export worked differently when I was zoomed in and I finally got the result I was looking for.
Marius
@quantentunnels
Hi everyone, I am experiencing segfaults when starting ImageJ on my two Debian Jessie machines. Used to work several weeks ago. Starting with --system flag however works. Is anybody else experiencing this?
Marius
@quantentunnels
Ah, just found the relevant forum post for that issue :smile:
Hadrien Mary
@hadim
@ctrueden one of the student in my lab has a segfault issue trying to launch Fiji on Ubuntu 17.04. We tried many Fiji versions (life line, with/without JRE, Java6/8) . Any idea? It happens when he recentrly updated his Fiji but the weird thing is that it happens now with all the Fiji version we are trying...
Alison Walter
@awalter17
@hadim There's a forum post regarding this issue. For now, the work around seems to be launching Fiji/Imagej with --system option
Hadrien Mary
@hadim
@awalter17 thank I'll try that.
Hadrien Mary
@hadim
We still have an issue:
Warning: falling back to system Java
Unrecognized option: -Xincgc
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Jan Eglinger
@imagejan
Please let's collect all relevant information on the forum thread mentioned by @awalter17
Hadrien Mary
@hadim
Working now after switching to Java 8. Thanks guy.
Curtis Rueden
@ctrueden
Pure-Java library for netCDF and HDF5: https://github.com/NCAR/nujan
Stephan Saalfeld
@axtimwalde
'The Nujan writer only writes new files. It does not update existing files.'
that sounds like one step back compared to 'does not support parallel writing' (HDF5)
Curtis Rueden
@ctrueden
Dealbreaker for your use case, eh?
@axtimwalde Are you saying there is a different pure-Java HDF5 writer?
Stephan Saalfeld
@axtimwalde
good for compact small files, I guess but it means that you always have to save the complete image or stack or time-series
I don't know of other pure Java HDF5 writers
Curtis Rueden
@ctrueden
I don't understand your comments, then.
What are you comparing Nujan against, if it's the only pure-Java implementation? The JNI-based ones? Of course they are better—they call the reference C implementation, no? But they will be fundamentally limited to the platforms for which they've been compiled.
Kyle I S Harrington
@kephale
N5 :P
Stephan Saalfeld
@axtimwalde
I just tried to understand what it does
and whether it is interesting for me
saving only new HDF5 files is a step back compared to existing JNI based libraries available for Java, and it is not necessary that JNI based implementations are better only because they are written in C
Stephan Saalfeld
@axtimwalde
@kephale, I am pretty happy with N5 currently, but there is no support for it beyond the very limited number of platforms for which a JVM with java.nio exists
Kyle I S Harrington
@kephale
but it should be pretty easy to port, right? its mostly channels + compression libraries
Curtis Rueden
@ctrueden

it is not necessary that JNI based implementations are better only because they are written in C

Agreed. My point is that in this case, the complete (and only) HDF5 reference implementation is written in C, so the Java libraries which simply interface with that are indeed likely to work much better, at least on supported platforms.

very limited number of platforms for which a JVM with java.nio exists

Is java.nio not available on the JVM on some platforms? I would expect it is there for Windows, macOS, Linux x86/x64, Linux ARM/ppc, Linux s390x (what is that?), Solaris, Solaris SPARC, AIX, z/OS, IBM i. That does not strike me as particularly limited?

Curtis Rueden
@ctrueden
I am glad that N5 is working well though. ^_^
Kyle I S Harrington
@kephale
it seems like a good idea, but presumably it will need a proper C/C++ port to get the python audience
Kyle I S Harrington
@kephale
@ctrueden do you have an opinion about default jekyll sites for hosting imagej projects on github pages (sp. i'm figuring out where to redirect imagej.fun)? open to better ideas, like if the suggestion is to redirect to the IJ wiki or something...
Curtis Rueden
@ctrueden
@kephale My opinion is: either put a simple splash/intro page there, or just simply redirect to https://imagej.net/FunImageJ.
Kyle I S Harrington
@kephale
cool, i may swap to a splash in the future, for now i'm just redirecting
Curtis Rueden
@ctrueden
For examples of the former, see http://scif.io/, http://scijava.org/ and http://fiji.sc/. For an example of the latter (sort of), see http://imglib2.net/
I think the redirect is fine, and easiest, and allows everyone to edit the content in a consistent way.
We did a splash for fiji.sc because everyone is so picky about exactly how it gets presented on the top-level page.
Kyle I S Harrington
@kephale
but the splash would be tempting for https://xkcd.com/297/
thanks!