[ome-users] Python support for OME Tiff files

[William Moore]

Hi Tjelvar,

 This was discussed on our forums a while back. See examples etc at:
https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=7612

As Curtis suggests, PIL/Pillow works OK for reading the XML if that helps?

 Cheers,

  Will.



On 27 Oct 2014, at 11:01, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Tjelvar,
> 
> > Does anyone know if there is a "Java free" Python library for working
> > with OME Tiff files?
> 
> OME-TIFF is just XML inside a TIFF file [1]. So you could use Pillow [2] and ElementTree [3].
> 
> Longer term, an OME-XML library for Python would probably be handy. Fortunately, the current approach is to autogenerate the OME-XML library classes from the XML schema via a Python script [4]. The autogenerator currently supports Java and C++; I'm guessing that adding Python too would be feasible. 
> 
> Regards,
> Curtis
> 
> [1] https://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html
> [2] https://github.com/python-pillow/Pillow
> [3] https://docs.python.org/2/library/xml.etree.elementtree.html
> [4] https://github.com/openmicroscopy/bioformats/tree/v5.0.5/components/xsd-fu
> 
> On Mon, Oct 27, 2014 at 4:13 AM, Tjelvar Olsson (JIC) <Tjelvar.Olsson at jic.ac.uk> wrote:
> Dear all,
> 
> Is anyone aware of a Python library for working with OME Tiff files?
> 
> I noticed that there is a Python BioFormats project, which provides a
> wrapper around the BioFormats Java libraries.
> https://github.com/CellProfiler/python-bioformats
> 
> However, I have not managed to find a Python library that can read and
> manipulate OME Tiff files without the need for Java.
> 
> Does anyone know if there is a "Java free" Python library for working
> with OME Tiff files?
> 
> Thanks,
> 
> Tjelvar
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