[ome-users] Trouble with LOCI reader and Nikon Elements 4.10.01

[Roger Leigh]

On 24/07/2013 02:04, Melissa Linkert wrote:
>> We have recently updated to Nikon Element 4.10.01. The headers of
>> images saved with this version are not correctly recognized by LOCI
>> readers v 4.4.4, 4.4.6, or yesterday's daily build. It feels as if
>> there was possibly a different offset of some sort that e.g. makes
>> only one of the two pixel sizes in a 2D image appear properly. What
>> is worse is that the movie dimensions are completely wrong, for
>> example z/t/c 1/29/3 instead of 8/20/1.
>
> Do you see the same behavior with the most recent stable version (4.4.8)?

I can definitely see the problem with current dev_4_4 with the sample
you provided.

>> Can I upload a sample movie for you? Is there any additional
>> information I can provide you with?

Thanks for uploading the sample image.  It would be useful to know the
exact dimensionality of the data in this image, i.e. sizes for x/y/z/c/t

Using current bioformats, I get:


Series count = 22
Series #0 :
         Image count = 87
         RGB = false (1)
         Interleaved = false
         Indexed = false (false color)
         Width = 304
         Height = 232
         SizeZ = 1
         SizeT = 29
         SizeC = 3
         Thumbnail size = 128 x 97
         Endianness = intel (little)
         Dimension order = XYCZT (certain)
         Pixel type = uint16
         Valid bits per pixel = 16
         Metadata complete = true
         Thumbnail series = false
         -----
(repeated for another 21 series)

However, it would be useful to know which of these values are "real";
which of the x/y/c/z/t values here are actually correct?

Putting some debugging statements in NativeND2Reader around the
conditional at line ~848:
       if (planeCount < imageOffsets.size() && planeCount > 0 &&
         (imageOffsets.size() % (planeCount / core.length)) == 0)

I get
   imageOffsets.size() == 644
   planeCount == 1914 (== 29 * 22 * 3)
The conditional is false, i.e. core[] was set earlier on; I'll check
further where exactly it's being assigned.  I'm not yet sure how the
value 644 bears any relation to the actual image dimensionality; knowing
what the correct values are will definitely help to understand this.


Regards,
Roger

--
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