Import HDF5/H5 files to omero

Hello Omero team,

Out of curiosity, why is it that one can’t upload HDF5 or .h5 files to omero?
Is it because the feature is not developed yet or because there is something intrinsically different in the way data in stored in a .h5 versus say .tif ?

I like the fact that the size on disk of .h5 files seem to be significantly smaller than .tif
For example I have 1095 files .h5 for 1.77GB but the same files in .tif are 16.9 GB. Why is that ?

Thank you

Hi @LPUoO,

When it comes to HDF5, the answer is often “it depends”. Since TIFFs were initially created as an image format, just about any TIFF will be importable to OMERO somehow. It may not always do so as you expect, but it is fundamentally an image.

HDF5 files can be anything. They are designed for storing, most broadly, “hierarchical collections of multidimensional arrays with metadata”. One could argue OMERO should try to interpret every array as in image, but there’s just not been a driver for that. Instead there are a number of dialects of HDF5 that we support.

Where did the HDF5 and the TIFF come from? How were they created?

That depends again. One possibility is that a better compression setting was used when creating the HDF5.

~Josh

2 Likes

On that score https://github.com/ome/bioformats/pull/2473#issuecomment-676089759 may be of interest: generation settings greatly affect resulting TIFF size.

3 Likes

Seconding the answers mentioned above. For information, below is the list of HDF-based image file formats that should be detected and supported by the current version of Bio-Formats 6.5.1 and hence OMERO:

2 Likes