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  • Aug 22 17:44
    ctrueden commented #205
  • 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)

Curtis Rueden
@ctrueden
Alternately, if you use MiGLayout then you do not need to hack around with min/pref/max sizes at all, because they are specified instead in the row+column layout string.
Jan Eglinger
@imagejan

normally won't wrap regardless of word-wrap setting?

I was thinking of word-wrap: break-word because I found it here: http://stackoverflow.com/a/8179481/1919049

Ellen T Arena
@etarena
Thanks both @imagejan & @ctrueden !!
I'll give it another go...
tpietzsch
@tpietzsch
Good news everyone. The correctness of BDVs cache has been formally proved. (in a way...) ;-)
@ctrueden please also take this as a lame apology why I didn't fix the imglib-algorithm mpicbg problem yet...
Florian Jug
@fjug
@tpietzsch Yeah!!! I cannot wait to hear every nasty detail about your SAT solver orgy in order to proove that!!! :beers:
(I guess this is ‘nerdish’ and directly translates to: ‘I miss you here in Dresden!’) ;)
tpietzsch
@tpietzsch
:blush:
Curtis Rueden
@ctrueden
@tpietzsch No worries. Sounds like you were focused on something deeply important, which takes precedence for sure.
Jay Tanna
@JayTanna
Hello all,
I am having a doubt about mapir pluggin of fiji. In that pericular, Calibrator.java File. I want to understand the role of scaleImage() and ScaleChannel() in that. Because of inverseRange the pixel value we are getting is < 1. So, how it works in the development of new image.
Curtis Rueden
@ctrueden
@JayTanna You mean this MAPIR plugin? That plugin is not part of Fiji. It looks like a commercial plugin. You will have to seek support from their support team.
Jan Eglinger
@imagejan
for context to the post by @JayTanna see http://stackoverflow.com/q/41954924/1919049
Curtis Rueden
@ctrueden
Thanks @imagejan. @JayTanna: if you need specific guidance, post at http://forum.imagej.net/, and post specific source code you have questions about.
Jay Tanna
@JayTanna
@imagejan
Stefan Helfrich
@stelfrich
@JayTanna As far as I can tell, your question doesn't even remotely touch on Fiji / ImageJ. Hence, you might want to reconsider pinging people in different channels on that particular topic. Also, posting a question on StackOverflow and assuming an answer within one hour is a bit optimistic..
Jay Tanna
@JayTanna
@stelfrich Sorry sir. I will take care about this next time. I will handle it more patiently.
Stefan Helfrich
@stelfrich
@stelfrich If your question were related to ImageJ, you could use the imagej tag on StackOverflow (which you should be aware of since you have already used it with you second SO account)
Curtis Rueden
@ctrueden
@iarganda It seems that bUnwarpJ 2.6.4 and 2.6.5 were never deployed to the Maven repository. I am taking care of that now. There was also a problem with the 2.6.4 tag pointing to the wrong commit; I have also fixed that.
Curtis Rueden
@ctrueden
@tpietzsch @fjug I noticed that bigdataviewer-vistoolswas uploaded to Fiji, but not added to pom-scijava and not added to fiji/fiji either. I am now doing so. It is necessary that all components of Fiji be properly managed at the Maven level.
On a more positive note: VisTools looks quite awesome. @tischi was wishing to show things in ImageJ via BDV easily, so I am starting to play with BDVFunctions.show.
.Kenneth
@Kennott_twitter
Hello. I am studying pelage color variation among populations of a species of rodents. My problem is that I am not good with eye color judgement and would like to quantify the color intensities from photos (RGB, or any other) and comparatively quantitatively check for any groupings. Is this possible in ImageJ? Any other software? Someone kindly assist. Thank you.
Curtis Rueden
@ctrueden
@Kennott_twitter Definitely possible. Did you post on forum.imagej.net? Many image processing experts hang out there. This chat consists of lots of programmers. I can give you several naive ways to measure that (e.g. Coloc 2 plugin?), but all of which might be wrong somehow for your use case. ;-)
tpietzsch
@tpietzsch
@ctrueden I'm sorry for that. I didn't consider bigdataviewer-vistools ready for a bigger audience yet, and I still wouldn't consider it stable. I'm not sure how it ended up in Fiji updater, probably that was an oversight. Anyway, I'm happy that people find it useful and start using it! Thanks @fjug for the guerilla promotion action :+1:
@ctrueden thank you for adding it to the proper poms!
Curtis Rueden
@ctrueden
@tpietzsch You're welcome—thanks for implementing it. In future if you have something not ready for larger audience, but desired to go in Fiji, we can still add it to POMs and update site—just not advertise it.
tpietzsch
@tpietzsch
:+1:
David Walker
@djw23_MOB_twitter
Hi there, I'm new room. I need help with a macro I've written in FIJI. It works fine but I want to be able to save the results table for each image processed. The problem is that for each image, the dialog window for from the getdirectory window opens up for each image...and I don't want that as I want to be automatic. Apologies if this the incorrect place to post this. Thanks in advance
Jan Eglinger
@imagejan
@djw23_MOB_twitter best ask this on http://forum.imagej.net and also include the macro code.
David Walker
@djw23_MOB_twitter
ok thanks Jan
Curtis Rueden
@ctrueden
@djw23_MOB_twitter Did you look at the Batch page's "Flexible option"? It has code that does what you want, essentially.
Philipp Hanslovsky
@hanslovsky
@iarganda I trained a random forest classifier with the weka segmentation plugin. Is there a way of applying the classifier to a whole series of images without loading them into memory all at once? Also, how much effort would it be to port the feature calculation into the imglib2 realm? I have an InstanceView that extends AbstractConvertedRandomAccessible< RealComposite< R >, Instance > and a CompositeInstance that wraps around RealComposite that I can use for predictions using an existing classifier. I do not know, however, how to fill the RandomAccessibleInterval< R > with features that are required for an existing classifier before passing it to my InstanceView.
Philipp Hanslovsky
@hanslovsky

@iarganda I am trying to load a trained classifier, what am I doing wrong? Minimum working (or failing) example:

final WekaSegmentation seg = new WekaSegmentation();
final String cp = "/data/hanslovskyp/hk-test/ds-8/2017-02-21-7_40.model";
seg.loadClassifier( cp );

Output (stdout & error):

Field of view: max sigma = 16.0, min sigma = 0.0
Membrane thickness: 1, patch size: 19
Read class name: class 1
Read class name: class 2
Error while adjusting data!
java.lang.NullPointerException
    trainableSegmentation.WekaSegmentation.adjustSegmentationStateToData(WekaSegmentation.java:4141)
    trainableSegmentation.WekaSegmentation.loadClassifier(WekaSegmentation.java:712)
    de.hanslovsky.zspacing.spark.experiments.mask.weka.Dummy.main(Dummy.java:12)

    at trainableSegmentation.WekaSegmentation.adjustSegmentationStateToData(WekaSegmentation.java:4141)
    at trainableSegmentation.WekaSegmentation.loadClassifier(WekaSegmentation.java:712)
    at de.hanslovsky.zspacing.spark.experiments.mask.weka.Dummy.main(Dummy.java:12)
Stefan Helfrich
@stelfrich
@hanslovsky 3D data?
Philipp Hanslovsky
@hanslovsky
No, 2D
Stefan Helfrich
@stelfrich
Model as well as image to which you want to apply it?
Philipp Hanslovsky
@hanslovsky
Yes. I trained the model using the Trainable Weka Segmentation plugin
So that should be 2D, right?
The images to which I want to apply the classifier are 2D as well.
But loading fails already when loading the classifier with the example above.
The exception happens in this.featureStackArray.getEnabledFeatures() and this.featureStackArray is null.
at WekaSegmentation.java:4141
Stefan Helfrich
@stelfrich
WekaSegmentation() doesn't initialize featureStackArray
Stumbled over that before but never reported that behavior ( :-1: for me)
I switched to using the WekaSegmentation(ImagePlus) constructor
Philipp Hanslovsky
@hanslovsky
Cool, thanks for the hint! Will that calculate features that I potentially might not need?
Stefan Helfrich
@stelfrich
That's actually a good question..