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

[Roger Leigh]

On 19/08/2013 21:38, Viapiano, Mariano Sebastian,Ph.D. wrote:

> 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!)

This is definitely the right place, welcome!

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

I have done testing with various Bio-Formats (loci_tools) versions, and
found that this appears to not be directly related to ImageJ/FIJI; this
is a regression in Bio-Formats dating back to a year last April.  This
was working correctly in 4.3.3, but does not work in 4.4.0 onwards.
Performing a "git bisect" on the bioformats.git sources, it looks like
this was introduced in revision ed0e55daf in between the 4.4.3 and 4.4.0
releases.  This fits in with your observations above.

We perform extensive automated testing for all file formats for all
changes (http://hudson.openmicroscopy.org.uk/view/Bio-Formats/).
However, in this case we did not have a suitable test file which
demonstrated the issue (such as the one you uploaded), so that this
wasn't picked up by testing.  With the file you uploaded, we can add
this to our collection of test ND2 images so that once fixed, we can
ensure that this will not reoccur.

I have opened ticket #11386 for this issue
(https://trac.openmicroscopy.org.uk/ome/ticket/11386), and you should
get notified on any changes as we work on the problem.

Many thanks for letting us know about the problem, and providing the
sample file demonstrating the problem.  If you find any other problems
then please do let us know.

I would suggest using 4.3.3 until we have addressed the problem; you
should be able to use the 4.3.3 loci_tools.jar
(http://cvs.openmicroscopy.org.uk/snapshots/bioformats/4.3.3/loci_tools.jar)
with newer ImageJ versions and also with FIJI (though FIJI will require
a number of jars removing including all the loci*/scifio*/ome* jars in
plugins and jars, and possibly others as well).


Kind regards,
Roger Leigh

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096