[ome-devel] Beginners help

[Josh Moore]

On Wed, Jul 1, 2015 at 8:29 AM, Ashoka Bantumilli <AshokaB at optiscan.com> wrote:
> Hi,

Hi Ashoka,


> Thank you for the information. Please let me know what are all the standard
> and useful TAGs for OME-TIFF files. For example,
>
> Height, Width, Horizontal resolution, vertical resolution, camera model, bit
> depth, compression etc.
>
> Like that for OME-TIFF what are the best/standard TAGs we need to maintain.

Just so we're on the same page: all of the OME-specific information is
stored in a single TIFF tag, namely the ImageDescription, as a single
block of XML. You can read more under
https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html

Are you then asking about the relevant OME-XML elements?

Cheers,
~Josh


> Thank you,
> Ashoka.
>

> From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On
> Behalf Of William Moore
> Sent: Tuesday, 30 June 2015 12:10 AM
>
> To: OME External Developer List
> Subject: Re: [ome-devel] Beginners help
>
> Hi Ashoka,
>
> "Resolution" would probably be stored under Image/Pixels.physicalSizeX and
> Pixels.physicalSizeY.
>
> I'm not sure exactly what you mean by "brightness".
>
>  Have a look at the Data Model Overview:
> http://www.openmicroscopy.org/site/support/ome-model/developers/model-overview.html,
> particularly
>
> the Image diagram at the top.
>
> The full OME schema can be browsed at
> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.html
>
> You might find it easier to browse some examples as OME-XML.
>
> We have several examples of typical confocal data here:
> https://github.com/openmicroscopy/samples
>
> If you can define what you mean by brightness, or there's any other tags you
> can't find, we can try to point you in
> the right direction.
>
>  Cheers,
>    Will.
>
> On 29 Jun 2015, at 06:12, Ashoka Bantumilli <AshokaB at optiscan.com> wrote:
>
>
>
> Hi,
>
> Thank you for the e-mail and information.
>
> Can you please let me know all the important tags that are useful for OME
> TIFF files.  I.e.:  resolution, brightness, etc.
>
> Thank you,
> Ashoka
>
> -----Original Message-----
> From: ome-devel [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On
> Behalf Of Roger Leigh
> Sent: Monday, 15 June 2015 5:38 PM
> To: OME External Developer List
> Subject: Re: [ome-devel] Beginners help
>
> On 15/06/2015 04:02, Ashoka Bantumilli wrote:
>
>
> I am a C# programmer and would like to start developing with OME-TIFF
> images. I read the material in the OME website but couldn't be able to
> start it.
>
>
> Note that C# as a language is not currently supported.  We support Java,
> MATLAB, and more recently C++.
>
>
> Here are few questions:
>
> 1)Where can I find OME-TIFF libraries (.dll) and how to integrate with
> VS2010/15, .Net 4.5
>
>
> These don't currently exist, I'm afraid.
>
> We do have a C++ library, but it doesn't yet work on Windows (I'm working on
> this right now, and it should be in the next point release unless any major
> difficulties are encountered).  This is a C++ rather than a C# API though;
> unless there's some automatic means to wrap a C++ API for C#, we won't
> support C# once the C++ API works on Windows.  This looks like a separate
> and potentially quite large task.
>
>
> 2)How can I make use of library API to read meta data about OME-TIFF images?
>
>
> As a starting point:
>
> C++:
> http://www.openmicroscopy.org/site/support/bio-formats5.1/developers/cpp/tutorial.html#metadata
> and
> http://downloads.openmicroscopy.org/bio-formats-cpp/5.1.2/api/classome_1_1bioformats_1_1FormatReader.html
> Java:
> http://downloads.openmicroscopy.org/bio-formats/5.1.2/api/loci/formats/FormatReader.html
>
>
> Kind regards,
> Roger
>