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

[Josh Moore]

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