[ome-users] Nikon ND2 Time information

[Sebastien Besson]

Hi Lewis,

with your variable names, you should be able to use the following to extract the timestamp of the plane iPlane for the series iSeries:

deltaT = double(omeMeta.getPlaneDeltaT(iSeries, iPlane));

As Curtis said, if this call leads to an error, you can send a sample file.

Regards,
Sebastien

On 31 May 2013, at 20:42, Curtis Rueden wrote:

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<mailto: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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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
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
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