file format plugin. If you file an issue on the SCIFIO bug tracker, along
promises on timeline. Or if you (or a colleague) want to take a crack at
> Hi Antoine,
>
> The actual reason for using hdf5 is because I have some very large arrays
> I need to pass from Matlab -> Fiji.
> I tried using Miji with the command CreateImage to instantiate a new image
> from within Matlab but because the array is so big I get Java Heap Out of
> Memory errors. This is despite having adjusted the Matlab Java heap space
> and having enough memory on my machine. It is also painfully slow to
> instantiate a large array with MIJ.createImage. For some reason it appears
> to be faster to just write the data on disk and load it with
> MIJ.run('Open...', 'path=[filepath]')
>
> I used to use FITS for writing the large volume as a single file but the
> FITS libraries on windows Matlab have an issue reading files over 4GB
> (despite being 64-bit). Therefore I worked around that by replacing FITS
> with the HDF5 format which Matlab appears to be more comfortable with
> reading/writing when it comes to file size of 4GB+.
>
> The problem now is that ImageJ cannot read in that HDF5 data...
>
> Kind regards,
> Lucas
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Antoine Bergamaschi
> Sent: 26 June 2014 15:03
> To:
[hidden email]
> Subject: Re: HDF5 support
>
> Hi,
>
> The HDF group has developed a software named Hdf5 view <
>
http://www.hdfgroup.org/products/java/index.html>. You can use this soft
> to read and extract your dataset and then use imageJ to analyse the data.
>
> ++
>
> Antoine Bergamaschi
>
>
> 2014-06-26 15:37 GMT+02:00 Mario Emmenlauer <
[hidden email]>:
>
> > 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_plug> > ins/hdf5.html
> > >
> > > I had a quick look in the bioformats plugin but could not find
> > > anything
> > compatible to plain hdf5 format.
> > >
> > > Kind regards,
> > > Lucas
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >
> >
> > --
> > A: Yes.
> > > Q: Are you sure?
> > >> A: Because it reverses the logical flow of conversation.
> > >>> Q: Why is top posting annoying in email?
> >
> > Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489
> > Balanstrasse 43 mailto: mario.emmenlauer * unibas.ch
> > D-81669 München
http://www.marioemmenlauer.de/> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>