I would recommend against multiple integration branches if you can avoid it.
Thanks a lot @ctrueden .. we could wait transforming the BigStitcher into a pom-scijava child until we finally release it. Could we maybe already set it up as travis job that crashes for now due to the pom-fiji, but so we can quickly change the state? Does that make sense?
Maybe it makes more sense to use your own groupId like
de.mdc-berlin.preibischlab for all your stuff?
Then you can have
de.mdc-berlin.preibischlab:multiview-simulation and de.mdc-berlin.preibischlab:SPIM_Registration and de.mdc-berlin.preibischlab:BigStitcher?
And you can use master branch for all of those (fork SPIM_Registration from fiji into the
PreibischLab org).
I'm happy to file the PRs needed so that Travis can build and deploy the respective master branches of those to the ImageJ Maven repository for you.
This would also be nice because the
SPIM_Registration fork, even though the groupId is changed, would still make a JAR with the same name, and thus be overridden when you replace SPIM_Registration on your update site. (For some definition of "nice"—alternately it might make more sense to change the package prefix and artifactId so that both can coexist without conflict.)
Hi, I'm having some issues using the 3D viewer and volume viewer plugins. I'm trying to create a 3D model from micro ct scan data however it keeps telling me that it is running out of memory. I've tried increasing the virtual memory but that hasn't had any effect. I've also tried reducing the number of scan slices being used but that hasn't done anything either. I keep getting the same error message is there any way I can resolve this? Any help will be much appreciated!
Hey @RachelLouise123 - it would be best if you can post this on the Forum... that is the best place to ask these types of questions to get you the best help! :)
Hi. I would like to analyze colour (or maybe just average brightness, since I'm interested in dark pigmentation) in 8 samples per image, in a series of images. All samples are on a white background that should be relatively easy to extract with a threshold filter. How should I proceed to get Fiji to automatically select the 8 distinct areas in each image, and then what would be the best way to get a color (or value along a lightness-darkness relative scale) measurement?
Hi @Kabouik - Hey @RachelLouise123 - it would be best if you can post this on the Forum... that is the best place to ask these types of questions to get you the best help! :)
^ @ehrenfeu
Hi there, I have a problem with Image J and Fiji on Surface Pro 4, running Windows 10. When I try to adjust brightness/contrast of an image, the window "B&C" does not show up. I can see that the window opens as a taskbar item, but I cannot see the window. Can someone help me fix this?
@kas_varun_twitter I'm not 100% sure whether this still works on Windows 10, but in many cases it's possible to pull a window from off-screen using an approach like this. You could try doing that for the B&C window.
@kas_varun_twitter I've seen this happening on multi-screen setups. If the approach suggested by @ctrueden doesn't work for some reason, you can also run a script like this from the script editor (e.g. Groovy):
import ij.WindowManager
WindowManager.getWindow("B&C").setLocation(50, 50)
I have now resynced the ImageJ Maven repository's proxy to match what is on Maven Central. However, this means that Fiji now no longer builds, due to an enforcer violation.
It is a legitimate issue with the cisd:jhdf5 artifact being an unshaded uber-JAR which includes commons-lang and commons-io.
The fix is for me to create a version of the CISD JHDF5 library which does not include those libraries internally, but instead depends on them appropriately.
For anyone remotely interested in my babblings from yesterday: I changed the Javadoc generator script to reduce the verbosity of the output on the log (scijava/scijava-scripts@9fb63d8). Unfortunately, it now shows no output whatsoever while building the javadocs—although it should still show errors if something goes wrong.
Anyway, the
javadoc.scijava.org site is coming along now. LOCI just needs to set up the server/Apache side of things, which we'll do as part of our server Dockerization project, ongoing.
I can discuss now actually, if you wish. I pinged you back.
somebody can help me with image j questions?
Otherwise, you'll probably be better off using the Forum... that is the best place to ask image-processing related questions to get you the best help! :)
:laughing: seems like I failed transmitting the information: that the macro language is too limited to work with such awesome things as TrackMate, but that you can do everything with a more powerful scripting language.
So when using a 64-line script to call it, it actually is macro recordable :smile:
So when using a 64-line script to call it, it actually is macro recordable :smile:
Feels like putting it on the TrackMate scripting page?
Same thing as javadoc.imagej.net, except that the ImageJ software stack layers are not proxied to jenkins.imagej.net anymore, but rather served by GitHub Pages. So now the old javadoc.imagej.net redirects to it.
And Travis CI keeps those Javadocs up to date.
