[ome-users] Python support for OME Tiff files

[Tjelvar Olsson (JIC)]

Hi Lee,

Thank you for the information about your project.

I was looking at your bioformats/omexml.py module and it does not appear
to have any dependencies on Java. Do you think that I could use it by it
by itself to work with OME XML extracted from an OME Tiff file using PIL
or libtiff?

Kind regards,

Tjelvar


On Mon, 2014-10-27 at 07:47 -0400, Lee Kamentsky wrote:
> Hi Tjelvar,
> 
> 
> 
> On Mon, Oct 27, 2014 at 5:13 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
> 
> 
> That's my group's project. It's very stable, not so hard to work with
> and gives you full access to Java as well as a set of straightforward
> functions to read and write images. It does require the JDK to build
> it and the JRE to run it and the JRE does add a bit to your memory
> footprint. Also, there is a little overhead transferring the in-memory
> image from the Java array to Numpy.
>         
>         
>         However, I have not managed to find a Python library that can
>         read and
>         manipulate OME Tiff files without the need for Java.
> 
> 
> We've used both libtiff (https://pypi.python.org/pypi/libtiff/0.4.0)
> and PIL/Pillow (http://www.pythonware.com/products/pil/). Both are a
> little tricky loading 16-bit TIFF images. You could use them to read
> and write the OME-TIFF tag, but you'd have to write the code to parse
> out what you wanted.
>         
>         Does anyone know if there is a "Java free" Python library for
>         working
>         with OME Tiff files?
>         
>         Thanks,
>         
>         Tjelvar
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>