Re: Issue with the NDi6d plugin/ Bio-Formats Importer

Posted by Herbie on
URL: http://imagej.273.s1.nabble.com/Issue-with-the-NDi6d-plugin-Bio-Formats-Importer-tp5021378p5021379.html

Good day Nathalie,

I've just opened your sample stack using BioFormats and, as far as I can
judge, it opens nicely.

If you see seemingly black slices, then please go to
   "Image >> Adjust >> Brightness/Contrast..."
and click "Reset".

Please read here
<https://forum.image.sc/t/imagej-overexposes-images/20403/2?u=herbie>
what is the cause and what the "Reset" actually does.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 30.10.18 um 21:37 schrieb Houssin, Nathalie Samantha Laetitia:

> Hello everyone,
>
> I am currently working with the ImageJ 1.52h version and I can't upload my .nd2 as a metadata document or I generate stacks with a mix or dark and grayscale images
> In brief, when I choose the NDi6d plugin --> ND to image6D, this window pops:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52h; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 114MB of 12119MB (<1%)
> java.lang.UnsatisfiedLinkError: no Nd2SdkWrapperI6D in java.library.path
>                  at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864)
>                  at java.lang.Runtime.loadLibrary0(Runtime.java:870)
>                  at java.lang.System.loadLibrary(System.java:1122)
>                  at NDi6d.ND_to_Image6D.<clinit>(ND_to_Image6D.java:44)
>                  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>                  at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>                  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
>                  at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
>                  at java.lang.Class.newInstance(Class.java:442)
>                  at ij.IJ.runUserPlugIn(IJ.java:226)
>                  at ij.IJ.runPlugIn(IJ.java:192)
>                  at ij.Executer.runCommand(Executer.java:137)
>                  at ij.Executer.run(Executer.java:66)
>                  at java.lang.Thread.run(Thread.java:745)
>
> I also tried to import an image sequence unsuccessfully (File> Import> Image Sequence) as I exported my nd2 files as .tif
> Lastly, I tried to use the Bio-Formats Importer but it seems that it is not able to recognize the amount of channels and it is generating stacks of dark images
>
> I've uploaded one of my files on dropbox if someone has any idea on why it is not working
>
> https://www.dropbox.com/s/4apvugdc649n8k9/x40o_E10%2C5_Par202--_myoIIb488_Afadin594_1.nd2?dl=0
>
> Thank you for any feedback you can provide,
>
> Bests,
>
> Nathalie
>
> Nathalie HOUSSIN
>
> Plageman's Lab
> Fry Hall room 350
> 338 W 10th avenue
> Columbus, Ohio 43210
> Tel: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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