[ome-users] Flex File Format

[Curtis Rueden]

Hi Matt,

I hope you don't mind me CCing the OME list again, since your question is
increasingly common.

Is the duplicated data stored as an OME-TIFF file or similar, or something
> like an IFD section of a TIFF file.
>

The data is stored in a binary format within the OMERO data repository
folder (usually /OMERO/Files). This format is used because it is highly
efficient to extract individual image planes on demand. The format is
intended for OMERO server use only, not for data exchange.

Even if you did copy one of these binary files, it contains only the pixel
data without the relevant metadata, since the metadata is stored in the
OMERO database itself (e.g., PostgreSQL).

Conversely, the OME-TIFF format is specifically intended as a data
interchange format that maximizes compatibility with external software
packages.

My reason for asking is this... If we reach a point where the acquired image
> format is standard and most of the image analysis software uses this
> standard (e.g. OME-TIFF).  How do I get my data out of OMERO to the OME-TIFF
> compliant software?  a) write OME-TIFF file from pixel data and database
> records (metadata) or b) have server copy files or send reference to those
> files
>

It is a planned feature for OMERO to offer an OME-TIFF export feature. As
Chris Allan recently mentioned, the internal logic necessary for this
feature is already in place, and it is now just a matter of us "hooking it
up." As such, you should definitely see the ability to export to OME-TIFF
appear later this summer or fall, if not sooner.

Another option is to use software capable of direct communication with
OMERO. For example, the OMERO team has recently completed a preliminary
plugin for ImageJ to do this, which we are just polishing up now.

HTH,
Curtis

On Tue, May 12, 2009 at 3:35 PM, <Matthew.Smicker at sanofi-aventis.com> wrote:

>  Hi Curtis,
> Is the duplicated data stored as an OME-TIFF file or similar, or something
> like an IFD section of a TIFF file.
>
> My reason for asking is this... If we reach a point where the acquired
> image format is standard and most of the image analysis software uses this
> standard (e.g. OME-TIFF).  How do I get my data out of OMERO to the OME-TIFF
> compliant software?  a) write OME-TIFF file from pixel data and database
> records (metadata) or b) have server copy files or send reference to those
> files
>
> Matt
>
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