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  • Sep 21 21:25
    ctrueden commented #26
  • Sep 21 13:26
    tischi commented #26
  • Sep 21 11:49
    ctrueden commented #26
  • Sep 21 11:49
    ctrueden commented #26
  • Sep 20 08:02
    erjel closed #22
  • Sep 20 08:02
    erjel commented #22
  • Sep 19 19:42
    tinevez commented #22
  • Sep 19 09:59
    erjel opened #22
  • Sep 19 08:18

    tpietzsch on master

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

  • Sep 19 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
We should get rid of that CLI hack. Johannes was fond of it, but I don't want to support it. It isn't necessary; you can use fiji --run Make_Screencast.bsh and in fact that is better anyway because SciJava will handle the parameters etc. properly.
I love the cleverness, but now it causes problems with the new #! processor, and I don't want to add a hack to SciJava just to ignore it.
Jean-Yves Tinevez
@tinevez
Hi @ctrueden. I would like to use Travis CI for another TrackMate module repo. This one: https://github.com/tinevez/TrackMate-TrackAnalysis.
Is it enough to follow the instructions of https://github.com/tinevez/TrackMate-TrackAnalysis and the copy/paste the keys we used for another repo?
Curtis Rueden
@ctrueden
@tinevez The tricky part is adding the encrypted env vars. IIRC, I pasted you the shell script I use here on gitter in the past. I cannot make it public because it has the two env var values embedded.
I could put the script in a private repo and then give trusted folks like yourself read access. The tokens/passwords in question let you 1. deploy anything to the ImageJ Maven repo; and 2. Trigger an ImageJ Jenkis job which reacts to Travis builds.
Simpler is for me to just file a PR against TrackAnalysis adding the Travis config.
Some day, perhaps everyone will deploy somewhere more general like bintray or OSS sonatype, using thr own credentials, and this problem will disappear.
Jean-Yves Tinevez
@tinevez
Ok!
Philipp Hanslovsky
@hanslovsky
@ctrueden I don't know if you remember: I recently started my own update site but wasn't able to upload anything and I didn't see any error messages. I just tried again after updating my FIJI and it worked. So that is not an issue anymore.
Curtis Rueden
@ctrueden
@hanslovsky Glad to hear it is working now.
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