[ome-devel] HDF5 support

[Jason Swedlow]

Hi Stephan-

Thanks for this comment.

Indeed, Bio-Formats has supported HDF5 formats for a few years. Imaris' .ims format uses HDF5, and Bio-Formats reads this format. This work was performed based on a good set of examples files, which we supported.

The EMBL group has released support for HDF5 through R, especially for HCS data:

http://www.bioconductor.org/packages/devel/bioc/html/rhdf5.html

Moreover, Sorger's group has published a specification (called "SDCubes") for a pair of HDF5 and XML files that provide a data vessel and specification:

http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1600.html

As you imply, there are others....

In OME, we're most interested in enabling access to these (and other, of course!) new formats. We always work with example data-- sets of files that comprehensively represent the data stored in these file formats. So, if you have examples of well-used format stored in HDF5, send us the data and we'll add it to the list of files we are working on.

We are also interested in mechanisms to transport files between different users and applications-- that's what OME-TIFF is all about:

http://www.openmicroscopy.org/site/support/file-formats/ome-tiff

OME-TIFF is based on great libraries for reading and writing TIFF and XML. These are well-established and available to all for use.

HDF5 might certainly be a way to transport metadata, analytics, etc. But there are a large number of different types of data that could be stored in an HDF5 file, including images, metadata, analytics, annotations, etc. If a common, well-defined and performant specification emerges for this, we will support it. We'd emphasise that this will require not just a good spec, but also good, supported, maintained, cross-platform software libraries for reading and writing these data types, and good, well-worked example files.

Thanks again for the note.

Cheers,

Jason






Jason Swedlow | Wellcome Trust Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

Stephan Gerhard <uni.designer.sg at gmail.com> wrote:

Hi,

More and more software is adopting HDF5 as an efficient storage
mechanism for image data.

I'd like to know what the current plans are in supporting HDF5 I/O for
bioimage dataset, e.g. through
Bio-Formats. For instance, I would like to have an easy way to save 4D
or 5D images from ImageJ/Fiji
to HDF5 for further processing.

Thanks for the update,
Stephan
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