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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
Curtis Rueden
@ctrueden
@tinevez tinevez/TrackMate-TrackAnalysis#1
Jean-Yves Tinevez
@tinevez
Success! Thanks @ctrueden
Curtis Rueden
@ctrueden
:+1:
Fevzi Kafexhiu
@fevzikafexhiu_twitter
Hello there, I kindly as anyone who can tell me how to save my table results in form of tab-delimited csv file. It used to be like that before I updated the FIJI, now it saves the tables in form of comma-delimited csv file!
Thanks in advance!
Ignacio Arganda-Carreras
@iarganda
@ctrueden I have just read your message about MorphoLibJ and Travis. I have followed your instructions, so I hope everything is OK now.
Curtis Rueden
@ctrueden
@fevzikafexhiu_twitter This changed in ImageJ 1.x. There is a setting in the options now IIRC.
Or try putting tsv for extension.
FreyaGoetz
@FreyaGoetz
Hi all, I hope this is the right place to get some help. I'm working on aligning slices in a tiff stack using TrakEM2 and I hadn't restarted Fiji for a while. I just restarted Fiji and accepted all updates. Now when I try to start a new(blank) trakEM2 project I get a bunch of erros. I'm not sure how to paste screen shots but I'll try.
image.png
image.png
image.png
If there is a more preferred way to share these errors, I'm happy to try that.
Curtis Rueden
@ctrueden

@FreyaGoetz

If there is a more preferred way to share these errors, I'm happy to try that.

It would be great if you could post on the ImageJ Forum: http://forum.imagej.net/

Before you do that... to troubleshoot very quickly here:
If you are using the Java-6 version of Fiji, try enabling the Fiji-Legacy update site.
Otherwise, try switching to the Java-8 version. You can do that easily by simply downloading Fiji again.
More information available at: https://imagej.net/Java_8
I suspect you are using the Java-6 version of Fiji, and so enabling Fiji-Legacy will solve it for you.
FreyaGoetz
@FreyaGoetz
@ctrueden Thank you for getting back to me so quickly! I will use your suggestion of posting erros if I need to again. For now I'm downloading Fiji again.
On another note, is this the room I would use to ask for advice on using TrakEM2? I have individually photographed 1682 individual serial sections and I have watched all the videos on alignments. At this point I'm paying around with settings to try and get better alignments but so far they haven't been very good. Who knows! Maybe the newest version of Fiji will be better :)
FreyaGoetz
@FreyaGoetz
@ctrueden Thank you. Downloading the program again solved the problem.
Alex Goodman
@Alex__Goodman_twitter
Screen Shot 2017-06-15 at 2.01.04 PM.png
Hello and I'm having trouble using TrackMate within Fiji. To begin, I'm attempting to track the linear motion of particles (different shapes and speeds) using the Linear Motion LAP Tracker. However, the software traces a jagged line rather than a smooth curve of the path. I'm measuring the average speed of the particles and it's crucial the software calculates the distance traveled accurately. Thanks in advance. P.S. the picture I just posted is representative of the problem.
Curtis Rueden
@ctrueden
@FreyaGoetz This is the best Gitter room for questions about TrakEM2, yes. You might need to mention @axtimwalde to have any hope of a helpful answer though, and the main TrakEM2 author @acardona does not use Gitter I don't think. You would be much better off posting in the ImageJ Forum.
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.'