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Hi Stephan-<br>
<br>
Thanks for this comment. <br>
<br>
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.<br>
<br>
The EMBL group has released support for HDF5 through R, especially for HCS data:<br>
<br>
http://www.bioconductor.org/packages/devel/bioc/html/rhdf5.html<br>
<br>
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:<br>
<br>
http://www.nature.com/nmeth/journal/v8/n6/full/nmeth.1600.html<br>
<br>
As you imply, there are others....<br>
<br>
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.<br>
<br>
We are also interested in mechanisms to transport files between different users and applications-- that's what OME-TIFF is all about:<br>
<br>
http://www.openmicroscopy.org/site/support/file-formats/ome-tiff<br>
<br>
OME-TIFF is based on great libraries for reading and writing TIFF and XML. These are well-established and available to all for use.<br>
<br>
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.<br>
<br>
Thanks again for the note.<br>
<br>
Cheers,<br>
<br>
Jason<br>
<br>
<br>
<br>
<br>
<br>
<br>
Jason Swedlow | Wellcome Trust Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee<br>
<br>
Stephan Gerhard <uni.designer.sg@gmail.com> wrote:<br>
<br>
<font size="2"><span style="font-size:10pt">
<div class="PlainText">Hi,<br>
<br>
More and more software is adopting HDF5 as an efficient storage<br>
mechanism for image data.<br>
<br>
I'd like to know what the current plans are in supporting HDF5 I/O for<br>
bioimage dataset, e.g. through<br>
Bio-Formats. For instance, I would like to have an easy way to save 4D<br>
or 5D images from ImageJ/Fiji<br>
to HDF5 for further processing.<br>
<br>
Thanks for the update,<br>
Stephan<br>
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