[ome-users] Problems to read ND2 files in FIJI with LOCI Plugins 4.4.9

[Viapiano, Mariano Sebastian,Ph.D.]

Hello,

This is my first mail to the list and I hope I am sending it to the right place (Please let me know if I need to send this somewhere else, thanks!)

For the past couple of years we have used ImageJ with a Bio-Formats importer plugin to read Nikon .ND2 files, without problems. We recently installed FIJI and found that we cannot open the same files that we were able to see before. I am attaching a zip file ("Cells_IJ versus FIJI.zip") that contains images showing an example of this.

Briefly:
*Our images are captured using Nikon NIS-Elements AR 3.22.14 (build 736), 64-bit 

* We can see the ND2 files perfectly using our "old" software:
ImageJ 1.47v, Java 1.6.0_20 (64-bit)
Plugin: LOCI_tools.jar, LOCI Plugins 4.3.3 revision ccc87b3, built 18 Oct 2011

* The ND2 files open but they are incorrect when we use this software:
FIJI (ImageJ) 1.48a, Java 1.6.0_24 (64-bit)
Plugin: LOCI_plugins.jar, LOCI Plugins 4.4.9-DEV revision 089d5ab, built 17 August 2013

Specifically, when we open the files in FIJI they have incorrect resolution and the different channels are not detected (only one channel is opened). 
 
Since ImageJ and FIJI are essentially the same software, we replaced LOCI_tools.jar in the "ImageJ/plugins" folder with "LOCI_plugins.jar" that came with FIJI. The result was that the problem was now replicated in ImageJ! However, when we replaced "LOCI_plugins.jar" in the FIJI.app/plugins folder with LOCI_tools.jar this did not fix the problem (the ND2 images still opened incorrectly). We have repeated this in several computers running Windows 7 and 8 with identical results. 

In the ZIP file I have included:
Cells.nd2 -> original ND2 file
cells_viewed with FIJI.tif -> ND2 file opened with latest distribution of FIJI and saved as TIF
cells viewed with FIJI_metadata.txt  -> self-explanatory (notice dimension C=1, which is incorrect)
cells_viewed with IJ.tif -> ND2 file opened with our older ImageJ and saved as TIF
cells viewed with IJ_metadata.txt  -> self-explanatory (notice dimension C=3, which is correct)
screencap_LOCI.jpg -> Info about the plugins when we ask for "Help->About Plugins" in ImageJ or FIJI

We will appreciate enormously any help or suggestions! (We are racking our brains trying to understand what's going on!)

Best regards,
Mariano


Mariano S. Viapiano, Ph.D.
Assistant Professor
Department of Neurosurgery
Brigham and Women's Hospital
Harvard Medical School 
4 Blackfan Circle., Harvard Institutes of Medicine, Rm 921D
Boston, MA (02115)
Tel: (617) 525-5650
Fax: (617) 713-3050
mviapiano at partners.org 




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