[ome-devel] cellh5 reader for bio-formats

[Melissa Linkert]

Hi Christoph,

> 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.

Thank you for your interest in writing a reader!

> 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.

A few package names have changed on the develop branch, but otherwise
there has been no refactoring on the official branches.

> 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?

Yes, those are the correct instructions.

> 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?

The develop branch of https://github.com/openmicroscopy/bioformats
should compile and pass all tests.  What sort of development environment
are you using?  How are you compiling and running tests?

> 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

We currently use netCDF for other HDF-based formats.  I would suggest
looking at some of the existing readers for HDF formats:

https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/ImarisHDFReader.java
https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/in/MINCReader.java

as well as the class that calls netCDF:

https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats/src/loci/formats/services/NetCDFServiceImpl.java

Regards,
-Melissa


On Thu, Apr 25, 2013 at 02:50:50PM +0200, Christoph Sommer wrote:
> 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
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