[ome-users] Merging ome-xml from a companion file into an ome-tiff.

[Munro, Ian]

Hi Josh

Our assumption has been that the processing packages in question either use an out-of-date Bio-formats
or proprietary code to read the ome-tiffs as the companion files seem to work well with current bio-formats.

I’ll experiment with tiffcomment.

Many thanks

Ian

> On 15 Nov 2018, at 11:01, Josh Moore <josh at glencoesoftware.com> wrote:
> 
> On Thu, Nov 15, 2018 at 10:23 AM Munro, Ian <i.munro at imperial.ac.uk> wrote:
>> 
>> Hi All
> 
> Hi Ian,
> 
>> A colleague has been generating data as ome-tiff’s with the xml in companion files.
>> Unfortunately some of the tools that they wish to use with this data are unable to handle this format.
> 
> It would be good to know why the companion format isn't working since
> we foresee using this more rather than less.
> 
> 
>> Does anyone know of a fast, scriptable method of converting - i.e. inserting the ome-xml into the data file to make a
>> single ome-tiff?
>> bfconvert works well  but seems to be slow, presumably as the data is copied as well as the xmll.
> 
> tiffcomment[1] would be the simplest route to re-writing the comment
> block in each TIFF. If this works, perhaps bfconvert could be taught
> to more quickly and reversibly convert from companion to
> non-companion.
> 
> 
>> Many thanks
>> Ian
> 
> ~Josh
> 
> 
> [1] https://docs.openmicroscopy.org/bio-formats/5.9.2/users/comlinetools/edit.html
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