These are chat archives for fiji/fiji

15th
Jun 2017
Fevzi Kafexhiu
@fevzikafexhiu_twitter
Jun 15 2017 06:39
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
Jun 15 2017 09:28
@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
Jun 15 2017 12:31
@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
Jun 15 2017 17:11
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
Jun 15 2017 17:18

@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
Jun 15 2017 17:46
@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
Jun 15 2017 19:29
@ctrueden Thank you. Downloading the program again solved the problem.
Alex Goodman
@Alex__Goodman_twitter
Jun 15 2017 21:01
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
Jun 15 2017 21:19
@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
Jun 15 2017 21:26
Thank you!
FreyaGoetz
@FreyaGoetz
Jun 15 2017 21:30
@ctrueden Thank you for the suggestion of ImageJ Forum and who to contact. You have been very helpful today.