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  • 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
  • Nov 21 20:22
    tinevez closed #133
  • Nov 21 20:22
    tinevez commented #133
  • Nov 21 18:16
    jeffreyEdgarYeung commented #133
  • Nov 21 17:04
    imagejan commented #90
  • Nov 21 17:01
    imagejan commented #90
  • Nov 21 16:24
    tinevez closed #83
  • Nov 21 16:24
    tinevez commented #83
  • Nov 21 16:24
    tinevez opened #110
  • Nov 21 16:23

    tinevez on start-window-2

    An icon for a help item. A Mastodon launcher JFrame that… (compare)

  • Nov 21 15:26
    tinevez commented #90
  • Nov 21 15:24
    tinevez commented #90
  • Nov 21 15:24
    tinevez commented #90
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.
SSL cert is not in place yet. Will do that within the next weeks as part of our Dockerization of everything.
As an aside: if you haven't looked at the Java 9 javadocs yet... they are pretty different! Modularized, and if you click Index there is a search bar built in now. Snazzy.
Jan Eglinger
@imagejan
:+1: :+2: :+3: :smile:
(ImageJ1 javadoc looks broken: http://javadoc.scijava.org/ImageJ1/)
Curtis Rueden
@ctrueden
ImageJ1 javadoc should be fixed now. Was a typo in the Apache config.
Jan Eglinger
@imagejan
@ctrueden yep, it's fixed, thanks! Would it be easy to switch it to Frames view by default?
Curtis Rueden
@ctrueden
@imagejan It is something weird about how Jenkins serves the javadoc. If you go to javadoc/ then there are surprisingly no frames, but javadoc/index.html has them. So the javadoc tool is doing the right thing; Jenkins is just preferring to do something weird with the directory request.
Once we switch ImageJ1 over to the same scheme as all the others, it will be moot, because it won't be served by Jenkins anymore.
The reason I didn't already switch it over is because the ImageJ1-javadoc job was part of some chain of Jenkins jobs, and I was nervous about changing it. But really, it's at the end of that chain, and wouldn't hurt anything to disable. Famous last words.
Curtis Rueden
@ctrueden
Oh, I guess the other reason I didn't set it up yet is because I haven't moved ImageJ1 over to Travis generally.
It is a workaround for the security policy crap we dealt with before. I think it is not worth grappling with in the short term.
Stefan Helfrich
@stelfrich
@ctrueden :clap: :+1:
Robert Haase
@haesleinhuepf
@ctrueden Awesome! Thanks for your efforts!