Does HDF5_Vibez support external links in HDF5 files?

Tags: #<Tag:0x00007fb87e1d19e0>


This seems to be a good thread to ask this question, but pardon me if there is a better forum; I’m relatively new to ImageJ and the community.

I have many hdf5 files, each storing only one 3D DataArray, but in each case of large size. I would like to read them all into Fiji at once as a 4D hyperstack (txyz). I thought creating a container hdf5 file and using external links (using h5py, see here) to each of the individual files would be the best way to do it, then open the container file using HDF5_Vibez plugin, and select all the external links to load as a hyperstack. However, as far as I can tell, HDF5_Vibez does not seem to recognize external links. Does anyone know for sure if that is the case? If it generally does recognize external links (and can load them), then something must be wrong with the way I’m encoding the external links, but I’d like to rule out that it’s simply not a feature first.

Looking for a headless HDF reader

I also tested it and also could not open external links, but I am getting this log:

/DataSet/ResolutionLevel 0:GROUP
/DataSet/ResolutionLevel 0/TimePoint 0:GROUP
/DataSet/ResolutionLevel 0/TimePoint 0/Channel 0:EXTERNAL_LINK
/DataSet/ResolutionLevel 0/TimePoint 0/Channel 1:EXTERNAL_LINK
/DataSetInfo/Channel 0:GROUP
/DataSetInfo/Channel 1:GROUP

Seems like it is not possible…

But I have another suggestion for you.

  1. Add the EMBL-CBA update site
  2. Plugins > BigDataTools > Data Streaming Tools

This allows you to load data from multiple hdf5 z-stacks as a time-series. The hdf5 stacks just have to be in the same folder and have the stack stored with the same hdf5 data set name, which you can enter in the UI (this is a drop down list, but you can actually also write into it).

Let me know if it works. You could also send me few of your stacks to test for you.