OMEROPy and Bioformats

[icaoberg]

Are there libraries and/or helper packages that connect OMEROPy and Bioformats? Or there any python bindings for Bioformats?

Ivan

[jmoore]

At the moment there is no native and/or Python library support for Bio-Formats, but that is certainly something we'll be looking into in the near future. Other options include using scripts via OMERO, using a separate standalone process like [url=https://github.com/CellProfiler/subimager]subimager, or if at all possible, using Jython.

What exactly are you trying to achieve?

Cheers,
~Josh

[icaoberg]

a very simple task. i want to use Bioformats within python to read a local image file and get a numpy array.

the future goal is to add this functionality to our pyslid package so we can read ome-tiffs in the near future.

[wmoore]

Depending on what format you need, I have used EMAN2 to get numpy data for a number of formats. Have a look at http://blake.bcm.edu/emanwiki/EMAN2ImageFormats

Or you could use PIL for png, jpeg, (tiff?).

[chrism]

Hi,

I've experimented with JPype (http://jpype.sourceforge.net) and JCC http://lucene.apache.org/pylucene/jcc/index.html to access the bio-formats Java API. JCC builds a Python wrapper module for JARs and seemed to work better (better error messages and code completion).

Here is a simple JCC build file to wrap ome-xml.jar:

https://gist.github.com/3697132

Hope this helps,

\m/ Christian