As someone who has struggled with getting some proprietary microscope images into python I would love to see this get into scikits.image.  The more coverage of formats I say the better given the flexibility of the plugin system.

I would be willing to write some code or help test to help make the integration happen.

Jake B.

2010/5/13 Stéfan van der Walt <>
Hi Ray

On 13 May 2010 18:00, Thouis (Ray) Jones <> wrote:
> 2010/5/13 Stéfan van der Walt <>:
>> [...]
>> I converted your wrappers to plugins for scikits.image.  At the
>> moment, it still segfaults---could you help me to iron out the
>> problems?
> (I mentioned this to Zach, but it may be of general interest to the
> imaging scikit developers as well, as another source of useful format
> information, if nothing else...)
> On a related note, we've been collaborating with the Bio-Formats
> project (, and we have a
> wrapper for their library in CellProfiler (but it's not too difficult
> to use separately).  This is probably *not* something for the majority
> of people, since it requires using a Java JNI wrapper (written in
> Cython).  And using it to save images on the Mac is risky in GUI
> applications.
> Examining the bio-formats code can be useful when writing new format
> parsers, as well.

We've added a plugin framework for I/O so that we can easily add this
sort of optional functionality.  The more formats we can support the
better!  Would you like to integrate said code?

The procedure is fairly straightforward:

1) Add a .ini file for the plugin.  Format something like:

description = Load x, y and z formats using the foo library.
provides = imread, imsave

2) Add a file, and provide the functions imread and imsave.