[ome-devel] cellh5 reader for bio-formats

[Christoph Sommer]

Dear all,

I want to write a Bio-Formats reader for the new HDF5 based format 
CellH5 (http://cellcognition.org/software/cellh5browser) with the goal 
of being able to load CellH5 files in a standard Fiji installation. The 
CellH5 stores the raw data, segmentations, classification and tracking 
of objects along with experimental meta data.

As a start, I would like to just read in the raw data cubes (currently 
5D x-y-z-t-c). I saw that Bio-Formats is currently refactored into 
SCIFIO. I am wondering if the instructions in 
http://www.openmicroscopy.org/site/support/bio-formats/developers/reader-guide.html 
are still the way to go?

As a starting point I forked the devel branch of the bio-formats 
repository at github. After a quick inspection I see import errors for 
e.g. "import loci.formats.meta.MetadataStore;" in "ImarisReader.java". 
Also, I get 4 SCIFIO test errors in "Location". Do I have to worry about 
them?

What HDF5 library for Java would you recommend for native hdf5 access? 
To write these files (currently from Python) I we HDF5 1.8.7

Thanks a lot for providing the world with this incredibly useful and 
comprehensive library!
Cheers,
Christoph