[ome-users] Nikon ND2 Time information

[Curtis Rueden]

Hi Lewis,

> Where can I find this time information for each image plane in the
> .nd2 files?

It is best to extract the timestamp information from the OME metadata
(specifically: OME > Image > Pixels > Plane > DeltaT), since it has been
standardized to a format-agnostic structure. Then you won't have to worry
about whether your file is .lsm or .nd2 or etc.

If the information is not present in the OME metadata, then it means
Bio-Formats is not parsing and standardizing that information properly. In
that case, if you send us a sample file (via
http://qa.openmicroscopy.org.uk/qa/upload/), we can work on fixing the
problem.

Regards,
Curtis


On Fri, May 31, 2013 at 2:35 PM, Kraft, Lewis James <
lewis.j.kraft at vanderbilt.edu> wrote:

>  Hello,****
>
> ** **
>
> ** **
>
> I am want to read the Nikon .nd2 image file using loci_tools.jar for
> MATLAB.  I have successfully imported the image data using loci_tools.jar
> with the following MATLAB commands:****
>
> ** **
>
> imgdata=bfopen(‘fullfilepath\*.nd2’); %command for opening images using
> BioFormats MATLAB scripts****
>
> ** **
>
> img=imgdata{1,1}{1,1}; %First image in the timeseries****
>
> ** **
>
> metadata=imgdata{1,2}; %Metadata in the .nd2 file****
>
> ** **
>
> omeMeta = imgdata{1, 4}; %OME Metadata****
>
> ** **
>
> The Image data, and the OME metadata look fine.  However, the original
> metadata is missing the time information.  For example, when opening Zeiss
> .lsm files, I see the time information in metadata as,
> “*TimeStamp*,*TimeStamp*,…”.  Where can I find this time information for
> each image plane in the .nd2 files?****
>
> ** **
>
> ** **
>
> Thanks much,****
>
> Lewis Kraft****
>
> ** **
>
> ** **
>
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