[ome-devel] ome.tif creation and omero-insight

[Pearu Peterson]

Hi,

On Tue, Nov 23, 2010 at 7:36 PM, Jean-Marie Burel <j.burel at dundee.ac.uk> wrote:

> We are currently reworking on the OME-TIFF export.
>
> As you have noticed not all metadata are exported, this is a limitation of
> the current system.

Yes. In the first instance when we considered using OMERO for
organizing our microscopy data we liked very much the idea of OME and
we were considering saving all our data as ome.tif files and perhaps
using OMERO as a definite database of our experimental data. Our
current experience, however, is that keeping the experimental data in
its original form is still the safest approach. OMERO is great for
getting a quick overview of the data but it is still too unstable as
the omero-insight occasionally crashes. To be specific, we are
experiencing the following problems:

- exporting large data sets (a timeseries of more than two thousand
640x480 images) to OME-TIFF produces ome.tif file with 0 size. Smaller
data sets are exported successfully. I can provide the problematic
ome.tif files on request. Also, after the failure of exporting large
data sets to OME-TIFF exporting smaller data sets stops working as
well and a restart of omero-server is required.

- trying to read annotations of another users data when annotations
are long and under More button, crashes omero-insight.

> Q2) I will check what's going on with the exposure time

That would be great. I also noticed that exporting the data to ome-tif
will preserve the original values. So, perhaps this issue is due to
rounding in displaying the values.
While the exposure time for CCD cameras may be in the order of seconds
then the exposure time for confocal scanning microscopes is in the
order of microseconds.

> Q3) We have noticed a problem with XML-annotations, we should be able to
> release a fix soon.

Are you saying that we should provide the original metadata of our
microscope data as XML-annotations? We can certainly generate them as
XML-annotations provided that its support is planned for future
releases of OMERO.

> Our clients currently only display annotations internally created. This is
> obviously a limitation.

I see. If OMERO could preserve the annotations in the OME-TIFF
import-export process then that would be already satisfactory.

Could you also consider including internal annotations to the OME-TIFF export?
We have Zeiss microscope data in lsm files that we are importing to
OMERO and it would be very nice if our analysis software could get all
the metadata from exported OME-TIFF files. Currently we have to keep
the original lsm files and use our custom software for extracting the
microscope metadata in the analysis software.

> I will create a ticket to address the problem
>
> The problem related to microscope fields not displayed has now been fixed

Thanks!

Best regards,
Pearu