[ome-users] Nikon nd2 files and bfopen

[Sarah Chacko]

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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