Opening HDF5 files in ImageJ with SWMR enabled

I’m working with some data files written by the EPICS HDF5 plugin. When I switch on the file writer’s “single write multi read” (SWMR) mode, the files appear corrupted to the HDF5 reader in ImageJ. Switching this mode off allows the files to be read normally. I can read both versions of the files with both python and C++ readers, so it seems like the issue is isolated to the reader in ImageJ.

Has anybody else had experiences working with SWMR-on HDF5 files? As I understand it, this is a relatively new addition to the HDF5 specification, so maybe a feature request is in order? (Who maintains the HDF5 reader these days?)

SWMR was introduced in version 1.10 of the hdf5 library so make sure you don’t have an older version installed on your system.

Thanks, that’s good news! I’m using a version that came with Fiji, I think it’s the “Vibez” plug-in… where can I find a more up-to-date version?

Like several other plugins, it relies on the jhdf5 library which provides Java bindings to the hdf5 library. The latest jhdf5 version (19.04) is the first to work with hdf5 1.10 and was only released earlier this year. You should check if you have it installed/available on your system. I assume you already have hdf5 1.10 because SWMR seems to work from C++ code.

Installing that version of the hdf5 file loader solved the issue - thank you!! :slight_smile: