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

[Pearu Peterson]

Hi again,

What is the recommended way to define AOTF lines in OME-XML?

In our case the AOTF lines have three properties:

  ON/OFF flag
  AOTF frequency that defines the bandpass wavelenght
  AOTF power that defines the transmission coefficient

and currently we are specifying these properties in a Model value of
Filter element:

     <ome:Filter FilterWheel="AOTFLine1"
Model="AOTF:Line1:ON:136.14MHz:650dBm" Type="BandPass"
ID="Filter:AOTFLine1:AOTF:Line1:ON:136.14MHz:650dBm" Manufacturer="AA
Sa Opto-Electronic Division">
      <ome:TransmittanceRange Transmittance="0.96" CutIn="473"/>
    </ome:Filter>
    <ome:Filter FilterWheel="AOTFLine2"
Model="AOTF:Line2:OFF:92.525MHz:600dBm" Type="BandPass"
ID="Filter:AOTFLine2:AOTF:Line2:OFF:92.525MHz:600dBm" Manufacturer="AA
Sa Opto-Electronic Division">
      <ome:TransmittanceRange Transmittance="0.96" CutIn="632"/>
    </ome:Filter>
    <ome:Filter FilterWheel="AOTFLine3"
Model="AOTF:Line3:OFF:83.0MHz:0dBm" Type="BandPass"
ID="Filter:AOTFLine3:AOTF:Line3:OFF:83.0MHz:0dBm" Manufacturer="AA Sa
Opto-Electronic Division">
      <ome:TransmittanceRange Transmittance="0.96" CutIn="691"/>
    </ome:Filter>
    <ome:Filter FilterWheel="AOTFLine4"
Model="AOTF:Line4:OFF:92.0MHz:200dBm" Type="BandPass"
ID="Filter:AOTFLine4:AOTF:Line4:OFF:92.0MHz:200dBm" Manufacturer="AA
Sa Opto-Electronic Division">
      <ome:TransmittanceRange Transmittance="0.96" CutIn="635"/>
    </ome:Filter>

Would it be possible to add AOTF support to OME-XML specification as
well as to OMERO insight?

Thanks,
Pearu

On Tue, Nov 23, 2010 at 12:25 PM, Pearu Peterson
<pearu.peterson at gmail.com> wrote:
> Hi,
>
> I am creating ome.tif files of our custom built confocal microscope
> images and I have encountered few problems with importing such ome.tif
> files to omero. All generated ome.tif files pass ome-tif validation
> successfully and are imported to omero.
>
> 1) What sections in ome-tif xml structure correspond to a
> omero-insight table entitled "Original Metadata" under Acquisition
> tab? How to include the Original Metadata information within a ome.tif
> file?
>
> 2) Where one can specify the pixel time within OME-xml structure? The
> Exposure Time seems to refer to the total time of image acquisition
> and in confocals one should probably subtract flyback time from that.
> When using pixel time (25 microsec) in the ExposureTime of Plane
> xml-structure then in omero-insight it is shown as "0s".
>
> 3) According to
>  http://trac.openmicroscopy.org.uk/omero/ticket/2799
> omero should be able to import annotations from ome-xml files. My
> experience with omero 4.2.1 insight is that only comment annotations
> are shown in a text column that has width only 11 chars. Furthermore,
> other types of annotations like boolean, long, double, etc are not
> shown in omero-insight. Is this a bug?
>
> An example of our ome.tif file can be found in
>  http://cens.ioc.ee/~pearu/omero/
>
> Thanks,
> Pearu Peterson
> Laboratory of Systems Biology
>