Posted by
Mario Emmenlauer-3 on
Jun 26, 2014; 1:37pm
URL: http://imagej.273.s1.nabble.com/HDF5-support-tp5008443p5008447.html
Hi,
I think the question is how your HDF5 file is internally formatted. HDF5
has not many constraints an internal structure, so it leaves full freedom
to you, to store your datasets in different internal paths or names or ...
It can not know, for example, how multiple channels would be stored, if
you have that, or how your x/y/z dimensions are stored, if you have that.
All this is free to decide when writing the file, and no reader can know
it in advance.
So there is not really a "plain" HDF5 reader because it would need to
know at least something about your internal structure of the file.
If you have that, it should be trivial to adjust one of the existing
readers to read your files.
All the best,
Mario
On 26.06.2014 13:15, Hadjilucas, Lucas wrote:
> Hi,
>
> I was wondering if there is a way to read in an hdf5 (.h5) dataset into ImageJ.
>
> I already tried using the plugin in the page below but it seems not to work for me for files above 4GB in size. I am using win7 64-bit along with 64-bit imagej&java so there should not be a 32-bit limitation in that respect.
>
>
http://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html>
> I had a quick look in the bioformats plugin but could not find anything compatible to plain hdf5 format.
>
> Kind regards,
> Lucas
>
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