Load nd2 (Nikon) file to image assistant / vision functions

[mzu]

Is there any easy way to open nd2 files (Nikon elments, microscopy) in NI vision assistant or to be used with any of the vision functions?

Now, I open them in ImageJ, save as a series of TIFF, and only then open them with LabVIEW. Before, I start writing my own importer, I wonder if any toolkit does that.

Search in google on "nd2 LabVIEW" produces nothing ...

(xpost: http://forums.ni.com/t5/Machine-Vision/Any-easy-way-to-load-nd2-files-Nikon-microscopy-to-Vision/td-p/1392658, http://www.labviewportal.eu/viewtopic.php?f=129&t=2803)

Edited December 20, 2010 by mzu

[Justin Goeres]

Is there any easy way to open nd2 files (Nikon elments, microscopy) in NI vision assistant or to be used with any of the vision functions?

Now, I open them in ImageJ, save as a series of TIFF, and only then open them with LabVIEW. Before, I start writing my own importer, I wonder if any toolkit does that.

You might be able to convert them with ImageMagick. I don't see ND2 on the list of supported formats, but you never know. If you want to send me a sample ND2 image, PM it to me and I'll be glad to do a quick check for you.

If ImageMagick supports ND2, you still wouldn't be able to open them directly in LabVIEW, but you could definitely automate the conversion process either by just writing a bit of System Exec.vi magic or by using my ImageMagick API from a few years ago (which I imagine still works, although I haven't looked at it in a long time ).

Good luck!

[mzu]

Justin, thank you for your reply,

I tried ImageMagick. Unfortunately, identify.exe tells me "no decode delegate for this image format" which, probably means it is not supported.

I checked inside the ImageJ ND2 reader plugin (http://rsbweb.nih.go...nd2-reader.html). It all comes down to interface with a windows DLL nd2sdkwrapperi6d.dll. This dll is written using JNI to provide some methods for one of the java classes inside the ImageJ plugin. My limited knowledge of JNI tells me that this DLL will be callable only from within the JVM (first parameter of each JNI interfaced function is a pointer to some internal JVM structure). The easiest way around all that as I see it now is to write a Java wrapper around the existing ImageJ, launch a separate JVM via System Exec and then, say, establish a TCP/IP to localhost communication to get the image data out of it. For the limited amount of images (~30) that I have it may be an overkill ...

Thank you for an offer to send you a file, but each of the files that I have is about 380MB, not an easy file to send...

Edited December 23, 2010 by mzu

[Justin Goeres]

Thank you for an offer to send you a file, but each of the files that I have is about 380MB, not an easy file to send...

No kidding . And you're right -- from your experience it sounds like it's probably not supported. Oh, well. I'm glad you were able to verify it yourself, and I'm sorry it didn't work!

[asbo]

For the limited amount of images (~30) that I have it may be an overkill ...

As in, 30 images, ever? I would just write enough code to convert them manually and be done with it

[mzu]

As in, 30 images, ever? I would just write enough code to convert them manually and be done with it

Those were 30 movies, ~1Gb each.

Actually, there is a solution. NIKON has published the SDK at http://www.nisdk.net/ (registration and verification required). They give you a dll which you can use in your projects, they also supply the manual.

[rjungmann]

Hi mzu,

Did you manage to import .nd2 files into labview? If yes: could you provide an import routine to read all images in a .nd2 file into a 3d array?

Thanks

Ralf