[ome-devel] Beginners help

[Ashoka Bantumilli]

Hi,

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.

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<mailto: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<mailto: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

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