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  • Dec 13 12:48
    tinevez opened #111
  • Dec 13 12:42
    tinevez closed #95
  • Dec 13 12:42
    tinevez commented #95
  • Dec 13 12:41

    tinevez on fix-feature-config

    (compare)

  • Dec 13 12:41

    tinevez on jungle

    Add a method to FeatureSpec to … A model that manages a collecti… Exploit the FeatureComputationS… and 2 more (compare)

  • Dec 10 14:41

    tinevez on colorbar

    Add a background window to the … (compare)

  • Dec 10 09:48
    tinevez synchronize #105
  • Dec 10 09:48

    tinevez on master-view-table3

    Color the table text depending … Fixed bug in Table views preven… Also close table windows when c… and 1 more (compare)

  • Dec 09 15:10

    tinevez on jungle

    Avoid keyboard clashes with BDV… Merge remote-tracking branch 'o… (compare)

  • Dec 09 14:48
    tinevez synchronize #85
  • Dec 09 14:48

    tinevez on harness-2d

    Avoid keyboard clashes with BDV… (compare)

  • Dec 09 13:30

    tinevez on jungle

    Harness 2D datasets in BDV view… Merge remote-tracking branch 'o… (compare)

  • Dec 03 12:17
    tinevez commented #90
  • Nov 28 03:30
    ctrueden commented #90
  • Nov 28 03:29
    ctrueden synchronize #90
  • Nov 27 07:59
    tinevez commented #90
  • Nov 22 09:28
    tinevez commented #90
  • Nov 22 09:26
    imagejan commented #90
  • Nov 22 09:00

    tinevez on master

    Utility to select text color ba… Select text color in the colorm… (compare)

  • Nov 22 08:40
    tinevez commented #90
Ai P. Vardhanabindu
@Aivard_twitter
Thanks @kephale . @krzysg Thanks very much. I have tried it and it works now
Curtis Rueden
@ctrueden
@StephanPreibisch You can use a different artifactId or a version suffix. Both have pros and cons. Getting Travis to build that branch requires a change to the Travis config.
I would recommend against multiple integration branches if you can avoid it.
Stephan Preibisch
@StephanPreibisch
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?
Curtis Rueden
@ctrueden
@StephanPreibisch I took a quick look at these repos. I see that the SPIM_Registration branch also depends on net.imglib2.simulation:multiview-simulation:1.0.1 which also does not exist.
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.)
Stephan Preibisch
@StephanPreibisch
Hi @ctrueden, thanks a lot for looking into this ... this does sound like a great suggestion. I'll discuss it with David Hoerl, but I am sure this is a nice way to go.
RachelLouise123
@RachelLouise123
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!
Ellen T Arena
@etarena
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! :)
RachelLouise123
@RachelLouise123
Okay thank you!
Kabouik
@Kabouik
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?
Niko Ehrenfeuchter
@ehrenfeu
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! :)
Kabouik
@Kabouik
Just for illustrating, the images look like this: https://0x0.st/dEJ.png
Niko Ehrenfeuchter
@ehrenfeu
sorry for the wrong / double name, copy-paste bug :blush:
Kabouik
@Kabouik
Oh, I see, sorry about that.
^ @ehrenfeu
Niko Ehrenfeuchter
@ehrenfeu
No problem!
Varun Sreenivasan
@kas_varun_twitter
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?
Curtis Rueden
@ctrueden
@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.
Jan Eglinger
@imagejan
@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)
Curtis Rueden
@ctrueden
Today I learned that the version of org.apache.xmlgraphics:batik-css:1.9 cached by the ImageJ Maven repository was different than the one served by Maven Central. And that the version served by Central actually has different dependencies!
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.
Curtis Rueden
@ctrueden
I fixed the JHDF5 library, releasing 14.12.6 without commons-lang or commons-io embedded. Enforcer is now happy on the fiji and fiji-javadoc projects. The next problem is from Travis: The log length has exceeded the limit of 4 MB. :dancers:
Curtis Rueden
@ctrueden
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.
Stefan Helfrich
@stelfrich
@ctrueden :+1:! I guess there is only one way to find out :smirk:
Curtis Rueden
@ctrueden
Thanks @stelfrich. Sorry for ignoring your pings lately. They are related to what we are currently doing with server+infrastructure, so I'll try to respond soon. I am also working on the generalized SIA forum now though.
I can discuss now actually, if you wish. I pinged you back.
Michelle169
@Michelle169
hello
somebody can help me with image j questions?
Niko Ehrenfeuchter
@ehrenfeu
Hello @Michelle169 , do you have development-related 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! :)
Jean-Yves Tinevez
@tinevez
@imagejan My colleagues that went to the NEUBIAS course in Gotenburg told me that 1) you rock 2) TrackMate is macro recordable.
Is 2) for real? (I knew about 1)
Jan Eglinger
@imagejan
: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:
Jean-Yves Tinevez
@tinevez
Ahhhhh!!
But this is incredibly clever! :crown:
Feels like putting it on the TrackMate scripting page?
Jean-Yves Tinevez
@tinevez
Or even include it in TrackMate code repo?
Jan Eglinger
@imagejan
Sure, put it wherever you find it useful!
Curtis Rueden
@ctrueden
Add to git repo! So awesome @imagejan! :+1: :100:
Curtis Rueden
@ctrueden
Finally finished this: http://javadoc.scijava.org/
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.
Philipp Hanslovsky
@hanslovsky
:plus1:
Curtis Rueden
@ctrueden
It still uses proxy/reverse-proxy for the 3rd party sites. We could set up Travis CI to rsync stuff daily and commit it, but... maybe that's a little aggressive, I dunno.