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.
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 :)
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.
@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. :-)
@Aivard_twitter I suggest posting this on http://forum.imagej.net/ not many MOSAIC folks are here on gitter @skalarproduktraum
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!
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
@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...
@hadim There's a forum post regarding this issue. For now, the work around seems to be launching Fiji/Imagej with
--system option
that sounds like one step back compared to 'does not support parallel writing' (HDF5)
@axtimwalde Are you saying there is a different pure-Java HDF5 writer?
I don't know of other pure Java HDF5 writers
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.
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
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?