[ome-users] Metadata from FLEX

[Melissa Linkert]

Hi Anatole,

Thank you very much for your feedback.

>   We seem to have a problem with the metadata of imported plates
> from FLEX files (from an OPERA microscope). Only the first image of
> the first well (usually A-1, but whichever it is) seems to have any
> metadata, the other wells have 'microscope' metadata set, but not
> 'image' nor the specific channels.

Each .flex file is a single well; Bio-Formats does try to group together
.flex files that belong to the same plate, but if it fails to do so then
the behavior you describe is expected.

> Even in that first well, the channel metadata are off, all three
> channel (in our case) being labeled with the same laser and the
> exposure time is missing (even though it seems to have been read OK,
> as clicking on the small colored dot at the bottom show the right
> value; it's just not showing on the right panel).

Do you see the correct channel/laser links and exposure times in Fiji?

In order to fix both problems, it would be very helpful if you could send a
small dataset that demonstrates the problems; for the latter, it would
be helpful to know what the expected laser and exposure time values are for
each channel.  I will send you information on how to send files to the
Bio-Formats/OMERO developers off-list.

Regards,
-Melissa

On Fri, Jan 14, 2011 at 01:52:47PM +0000, Anatole Chessel wrote:
> 
> Hi all,
> 
> 
>   We seem to have a problem with the metadata of imported plates
> from FLEX files (from an OPERA microscope). Only the first image of
> the first well (usually A-1, but whichever it is) seems to have any
> metadata, the other wells have 'microscope' metadata set, but not
> 'image' nor the specific channels.
> 
> Even in that first well, the channel metadata are off, all three
> channel (in our case) being labeled with the same laser and the
> exposure time is missing (even though it seems to have been read OK,
> as clicking on the small colored dot at the bottom show the right
> value; it's just not showing on the right panel).
> 
> Loading the FLEX with bioformat under FIJI show the same behavior:
> if the 'OME-XML metadata' are asked for, they correspond to what is
> happening in Insight (complete meta-data only for the first well).
> 
> Any thoughts?
> 
> Many thanks,
> 
> A.
> 
> -- 
> Anatole Chessel
> Research associate
> The Gurdon Institute
> University of Cambridge
> Tennis Court Road, Cambridge CB2 1QN
> tel: +44 (0)1223 767197
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users