[ome-users] Nikon nd2 files and bfopen

[Melissa Linkert]

Hi Sarah,

If possible, could you please send one of the ND2 files that you are
working with?  Nikon ND2 files are quite complex, and it's possible
that your files store pinhole size and stage position data differently
than the files that we have here.

Files smaller than 10 MB can be sent as an email attachment; larger
files can be placed on our FTP server.  I will send you our FTP server
details off-list.

Regards,
-Melissa

On Mon, Jan 25, 2010 at 5:27 AM, Sarah Chacko
<sarah.chacko at lincoln.ox.ac.uk> wrote:
> Hi Melissa,
>
> I have replaced the loci_tools.jar and restarted MATLAB, but the code you suggest still gives me pinhole sizes 0 or -1 and empty 0x0 double for the positionX and so on. The same loci_tools.jar (latest trunk build) doesn't find the values in ImageJ either.
>
> Is there something else I should do?
>
> Thank you very much for your help with this,
>
> Sarah
> ________________________________________
> From: melissa.linkert at gmail.com [melissa.linkert at gmail.com] On Behalf Of Melissa Linkert [melissa at glencoesoftware.com]
> Sent: 20 January 2010 17:43
> To: Sarah Chacko
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Nikon nd2 files and bfopen
>
> Hi Sarah,
>
> My apologies for not getting back to you sooner.  You are correct, the
> stage position and pinhole metadata is stored in the file -
> Bio-Formats just wasn't parsing it correctly.
>
> Stage position and pinhole size metadata should be recorded if you
> update your copy of loci_tools.jar to the latest trunk build (see
> http://loci.wisc.edu/bio-formats/downloads).  You can then retrieve
> the metadata as follows:
>
> data = bfopen('/path/to/ND2/file')
> % positionNumber can be set to anything in the range [1, size(data, 1)]
> positionNumber = 1
> pinhole = data{positionNumber, 2}.get('Pinhole size')
> positionX = data{positionNumber, 2}.get(sprintf('X position for
> position #%d', positionNumber))
> positionY = data{positionNumber, 2}.get(sprintf('Y position for
> position #%d', positionNumber))
> positionZ = data{positionNumber, 2}.get(sprintf('Z position for
> position #%d', positionNumber))
>
> Regards,
> -Melissa
>
> On Wed, Jan 13, 2010 at 3:30 PM, Sarah Chacko
> <sarah.chacko at lincoln.ox.ac.uk> wrote:
>> Hello,
>>
>> I am using the bfopen.m program in MATLAB to open Nikon .nd2 files; timeseries and z stacks.They are the newer version of nd2, I think the format was changed in the last few years.
>>
>> The data looks good, but I can't find a lot of the metadata. I am not completely comfortable with cell arrays so I wondered whether I'm not extracting it right, or whether some of it is not converted. For example I could find the filters, but not the pinhole size, and I couldn't find the lists of XY and Z and offset positions for each frame, though they must be in the file because they appear in the metadata in Nikon's viewer.
>>
>> Thanks,
>>
>> Sarah
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>