Issue with the NDi6d plugin/ Bio-Formats Importer

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Issue with the NDi6d plugin/ Bio-Formats Importer

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: 614-292-0636


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

Herbie
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: 614-292-0636
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Herbie
Nathalie,

I didn't check anything in the BioFormats-dialog (BioFormats-Importer).
View stack with: Hyperstack
Color mode: Default
Nothing else checked and it opens just fine with
3 color channels and 15 z-slices.

I use plain ImageJ 1.52h with Java 1.8.0_172 and the BioFormats-plugin
installed.

Please try again and be careful with the settings.

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
Am 30.10.18 um 22:17 schrieb Houssin, Nathalie Samantha Laetitia:

> Herbie,
> Thank you for checking it.
>
> I tried it again using BIoFormat and have a message :
> Warning: Data has too many channels for Default color mode
>
> I imagine that I have to change the parameters set in the dialog box of the Bioformat
> Thank you also for the tip for the color display. I have indeed stacks of black slices not corresponding to any channel. I'd probably have to reinstall the plugin
>
> Again, thank you,
>
> Nathalie
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Herbie
> Sent: Tuesday, October 30, 2018 5:02 PM
> To: [hidden email]
> Subject: Re: Issue with the NDi6d plugin/ Bio-Formats Importer
>
> 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--_myoIIb
>> 488_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: 614-292-0636
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html