Open Microscopy Environment

Dear sirs, in my new computer, Windows 8.1, I installed ImageJ plus LOCI plugin/bioformats but I am still unable to open .nd2 files. (exception in image 1).


I don’t have problem if I open this files with IMAGE J under WIN NT and Win7.
The ImageJ Version is 1.48v, downloaded at 64bit. As well as Java, which I updated on my PC (image 2).


I also tried to download ImageJ without Java, but the results is the same (image 3)


Moreover, I tried to install 32bit version (as I did on Win NT and Win 7), but it still didn’t work.
Can you have any suggestion to solve this problem?

Thank you very much.

Chiara Fresia

Dear Chiara

Which version of Bio-Formats are using?


Regards

Jmarie

Bioformats 5.1.1

Thank you

Dear Chiara,

Please could you upload a sample image using http://qa.openmicroscopy.org.uk/qa/upload/ so that we can try to reproduce the problem locally -- I have a 64-bit Windows7 system with the same 64-bit Java version. This will let us determine if it's a bug in Bio-Formats or something specific to the software versions you are using.


Thanks,
Roger

Thank you Roger. I hope I uploaded it well.
I confirm that this is one of the files I open on computers/ImageJ other than my last one.

Thank you very much

Chiara

Hi,

I have tried it with 64-bit Java 8u45 on 64-bit Windows 7 but it works without giving this error. (That said, I'm not sure the pixel data is necessarily correct; could you possibly add a screenshot of what it's supposed to look like?)

I'll try on 64-bit Windows 8.1 which I have on my home PC later on today.

Dear Chiara,

I have now also tested on Windows with the Bio-Formats 5.1.1 release (bftools standalone and with Fiji), and in both cases I can read the file without problem and the image matches what NIS Elements shows. This is Windows 8.1 x64 with Java 8u45 x64.

I would next suggest double-checking that you are definitely using the 5.1.1 release and not an older version. You can do this by going to "Help > About Plugins > Bio-Formats Plugins" and checking the version displayed.

Also note the last point in https://www.openmicroscopy.org/site/sup ... usage-tips which can result in a broken Bio-Formats installation. It might be worth looking at what's in the jars/ and plugins/ directories of your ImageJ installation to double-check that this isn't happening in your case.


Kind regards,
Roger Leigh

Dear Roger, you are very kind and my only hope in this situation. Moreover, please consider that I don’t understand but little of computers.
As you may see in the first screenshot, the Bioformat version is the right one.


I checked the jar and plugin folder too, as you may see.
I tried to uninstall all version/s of Java, in order to be sure to have the ultimate copy.
I noticed one thing: given that my version of Explorer (the suggested one) is a 32 bit version, automatically the Java installed is a 32 bit one (in folder “program files 86X”, which, I suppose for you is the same, hosts the 32 bit programs); then, I manually added the 64 bit version too (in the different folder “programmi”, for 64 bit programmes).
After restarting, I launched ImageJ, and it show the windows I attached here as second Image.


???
How do you interpret this? May it be connected to my inability to open .nd2 files?

Thank you very much indeed,
Hope to read you soon.

Chiara

I think it would make sense to try to see if it works with Fiji:

If you download
http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip and http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-win64.zip this will give you a current ImageJ with Bio-Formats 5.1.1. The first will use the system JRE; the second includes a 64-bit JRE. If you unpack each and then start each in turn and run the updater, you'll get a current setup after restarting. Testing the image import with each will then hopefully show us whether the problem is with the system Java or your ImageJ installation.


Thanks,
Roger

Dear Roger, here me are.
I downloaded the two folders, as you said. I extracted them, obtaining these two folder (order of launch)

which, opened, gave me the followed possibilities (ordered by action):

1_ I launched ImageJ-win64 from the “Fiji nojre” folder. It asked me to update, which I allowed, and the following exceptions were: 1-Fiji nojre-ImageJ64, updater done

2_ I launched ImageJ-win32 from the “Fiji nojre” folder. It didn’t ask me to update, and the following exceptions were: 2-Fiji nojre-ImageJ32


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