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Repo info
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  • Aug 16 17:34
    acardona opened #231
  • Aug 07 13:48
    chalkie666 opened #230
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:33
    tinevez labeled #107
  • Aug 02 13:32
    tinevez opened #107
  • Aug 02 13:30
    tinevez commented #106
  • Aug 02 13:29
    tinevez synchronize #106
  • Aug 02 13:29

    tinevez on serialize-feature-model2

    Avoid feature name inflation wh… Update the MaMuT exporter examp… (compare)

  • Jul 18 11:57
    tpietzsch commented #106
  • Jul 18 11:44
    tinevez commented #106
  • Jul 18 11:41
    tpietzsch commented #106
  • Jul 18 11:32
    tinevez commented #106
  • Jul 18 11:31
    tpietzsch commented #106
  • Jul 18 11:20
    tpietzsch synchronize #106
  • Jul 18 11:20

    tpietzsch on serialize-feature-model2

    formatting Demonstrate that feature names … Add TODO and 2 more (compare)

  • Jul 10 13:08
    tinevez closed #104
  • Jul 10 13:08
    tinevez commented #104
  • Jul 10 13:08
    tinevez opened #106
  • Jul 10 10:56

    tinevez on serialize-feature-model2

    Fix weird compile error with Op… Make some static methods of MaM… JUnit test for the TrackMate im… and 5 more (compare)

  • Jul 09 11:01

    tinevez on serialize-feature-model2

    Move test data to proper packag… WIP: Junit test for MaMuT expor… (compare)

Philipp Hanslovsky
@hanslovsky

If you create a display like this:

display = ij2.display().createDisplay( name, source )

You can just call display.update() to redraw

Hadrien Mary
@hadim
Ok nice.
Last thing, I saw you have a conda package. Did you consider making a conda forge package ? It's a community driven project that use CI services (Travis, CircleCI, Appveyor) to automatically build and distribute conda packages. It's widely used in the Python community.
Philipp Hanslovsky
@hanslovsky
@hadim Eventually, I think that is a good idea. Right now, it is not in a stable enough condition for that, and there are no OSX or Windows packages. On OSX we still haven't fixed the cocoa vs awt issue but we contacted people at Janelia who might be able to help with that.
Philipp Hanslovsky
@hanslovsky
@ctrueden In case you read my previous message, that was a bug on my side and I found it now!
Curtis Rueden
@ctrueden
@hanslovsky You mean: you did fix the cocoa AWT issue now? Great!
Philipp Hanslovsky
@hanslovsky
Oh no
Sorry for the confusion :(
I had an issue with CommandInfo which seemed to be specific to one machine only. Just after I wrote a message in here, I found my bug and deleted the message afterwards.
But the good news the cocoa issue: We will have someone from scientific computing look at this problem specifically, so hopefully that will be resolved!
Curtis Rueden
@ctrueden
Cool.
Jean-Yves Tinevez
@tinevez
Hi all
Check this, might come useful if you ever need to redact long tutorials for a paper to submit, and use it as a Wiki page:
https://pandoc-scholar.github.io/
rjlubbe13
@rjlubbe13

Hello,

I am in need of assistance with using fiji on my Windows 8.1 PC. I am trying to open an image stack but cannot select all of the files at once to open them in the same window. I selected import and then image sequence, but when I tried "control+A" and "shift+down arrow" to select all of the images this did not work. Any help would be appreciated. Thank you.

Jean-Yves Tinevez
@tinevez
Hi @rjlubbe13 .
Can you post this issue on the imagej forum forum.imagej.net?
Curtis Rueden
@ctrueden
@rjlubbe13 The File > Import > Image Sequence command wants you to select a folder, not files. Choose the folder containing the files, click OK, and then it will scan that folder. If you need further assistance, I second @tinevez's advice to make a forum post.
Ellen T Arena
@etarena
where is the best place to search for @Parameter properties? (especially for a new user to Script Parameters)
Jean-Yves Tinevez
@tinevez
@etarena Here: https://github.com/scijava/scijava-common/blob/master/src/main/java/org/scijava/plugin/Parameter.java
In Eclipse you still get them via autocompletion and friends ;)
Ellen T Arena
@etarena
thanks @tinevez ... :)
Curtis Rueden
@ctrueden
You can also browse them easily in the javadoc for org.scijava.plugin.Parameter.
Ellen T Arena
@etarena
:thumbsup: @ctrueden
Samantha Rae
@smantharae14_twitter
Hi, I'm looking for some help with an error message I'm receiving when attempting to run TurboReg
Curtis Rueden
@ctrueden
@smantharae14_twitter Hopefully your forum thread here helps you overcome your troubles. (I cross-link it here, for the benefit of other members of this chat.)
smrak815
@smrak815
Recently, after an update to FIJI, importing of .lif files results in the wrong scale being presented in the window, which is a pain since a correct scale is required for accurate sholl analysis. Is this a bug?
Curtis Rueden
@ctrueden
@smrak815 It is almost certainly related to the Bio-Formats plugin, which is what handles your LIF files.
Bio-Formats has regular updates and bug-fixes, so perhaps one of these fixes caused your trouble.
You could try asking in the Bio-Formats Gitter channel. They will almost certainly ask you to send a sample non-working file.
smrak815
@smrak815
thanks for the quick response! I'll look into Bio-Formats' Gitter Channel
olcl
@olcl
Hi, i'm having some issues with fiji. I can load my pics but i can't open the color balance nor the brightness/contrast control panel with the latest version of fiji. The panel is opened in the back with viewing issues, and i can't change anything. My computer runs win10. Is it due to Fiji? ImageJ? Java? thanks a lot!
Curtis Rueden
@ctrueden
@olcl To find out, try testing with: older Life-Line versons of Fiji; older versions of ImageJ1 (Help / Update ImageJ... menu); different machines.
Jean-Yves Tinevez
@tinevez
Hi all.
I just activated a Travis build: https://travis-ci.org/tinevez/TrackMate-extras following instructions from @ctrueden .
How to trigger the build now? Do I have to release a non-snapshot version?
Jean-Yves Tinevez
@tinevez
Ok its wrokgin now
Jean-Yves Tinevez
@tinevez
I failed the build with an error Return code is: 400
Do I have to right to upload to ImageJ nexus?
Bon apparently if I push a SNAPSHOT version then all is fine.
Yeeeeeeah http://maven.imagej.net/service/local/repositories/releases/content/org/scijava/TrackMate_extras/0.0.4/TrackMate_extras-0.0.4.jar
Thanks @ctrueden
Curtis Rueden
@ctrueden
@tinevez Yeah, you can only deploy each release version once. That is a fundamental rule of Maven.
Very glad you got it working! :-)
Curtis Rueden
@ctrueden
@bogovicj I just released pom-scijava 15.0.0, and am on the cusp of releasing fiji 2.0.0-pre-1. However, I hit a problem:
  Found in:
    sc.fiji:trakem2_tps:jar:1.1.2:runtime
    sc.fiji:trakem2-transform:jar:1.0.0:runtime
  Duplicate classes:
    mpicbg/trakem2/transform/ThinPlateSplineTransform.class
I checked, and both of those components do indeed have that class on the current master. Where is it supposed to live?
I guess that trakem2_tps needs updating to the latest TrakEM2, no? I can file a PR.
tpietzsch
@tpietzsch
@ctrueden :+1: wow, that was fast!
(pom-scijava 15.0.0)
Curtis Rueden
@ctrueden
@tpietzsch I decided to leave out a couple of the notebook-related updates. So there will probably be a 15.1.0 end of next week.
John Bogovic
@bogovicj
@ctrueden , just merged your PR, thanks!
Curtis Rueden
@ctrueden
@bogovicj I'd like to get the opencsv update into the relevant components, and then cut new releases today. Would you be willing to give me push access so I can cut the releases directly? Or have time to take care of it yourself today?
Curtis Rueden
@ctrueden
@bogovicj I am doing the PRs for opencsv now, for the three affected components.
Curtis Rueden
@ctrueden
@bogovicj It is a little tricky because we need to update jitk-tps first, release it, then update bigwarp_fiji to use that new release.
Curtis Rueden
@ctrueden
@bogovicj PRs filed. saalfeldlab/jitk-tps#3, saalfeldlab/bigwarp#34, saalfeldlab/trakem2-tps#5. The first one needs to be merged, and then jitk-tps 2.1.1 needs to be released, before the latter two will work correctly.
John Bogovic
@bogovicj
Thanks @ctrueden . I'll take care of these, but I'm happy to give you push access as well, for the future (provided @axtimwalde agrees)
Curtis Rueden
@ctrueden
@bogovicj Thanks. I have meetings for the next couple of hours; if you are able to make releases of these three components soon, I'll update pom-scijava accordingly after my meetings, and I'll be able to get the new Fiji out the door! :-)