Error opening HDF5 file via File › Import › HDF5... command


Is any news about opening SVI h5 files in FIJI? File>Import>HDF5 still gives me an error: rank 5 of type unit8 not supported (yet).




Hi Yury,

not that I know of.
@joshmoore from bio-formats might know more about this…

:slight_smile: Slighty cheeky … but a very fair reminder for me to come back to this, @Christian_Tischer. @Yury_Belyaev, I don’t have any updates for you, but I will try to find the cycles to do some testing. Thanks for the reminder both. ~J.

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Hi @joshmoore, yes sorry, in fact, upon second thought I am not exactly sure why I pinged you here… I think I felt that SVI h5 maybe could be an official image file-format that might be supported by Bio-Formats. But…is it?

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@Christian_Tischer: no worries, but, no, SVI h5 is not yet supported. That being said, I think this issue is a valid one of the more generalized HDF5 reading. ~J


The File › Import › HDF5… command comes from the HDF5_Vibez plugin. I figured that out by typing “HDF5…” into the search bar, selecting the correct plugin from the results list, and looking at the “Location” shown. Clicking the “Source” button opens the exact Java source file for that command.

So if anyone is currently able to investigate and respond to this question, it would be @radoslaw.ejsmont, that plugin’s current maintainer. Of course, as typical with community maintainership, it will depend on whether he has time right now.

@joshmoore, it would indeed solve our problems if one can open SVI h5 files in Bio-formats, just let me know if you need and example data sets.