[ome-users] Python support for OME Tiff files

[Lee Kamentsky]

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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