benefit from an HDF5 reader in SCIFIO. :-)
> Hi Lucas,
>
>> The problem now is that ImageJ cannot read in that HDF5 data...
>
> So, MATLAB is the tool responsible for writing out this HDF5 data? If you
> really want it supported in ImageJ, someone would need to create a SCIFIO
> file format plugin. If you file an issue on the SCIFIO bug tracker, along
> with instructions on how to generate some sample HDF5 data using MATLAB,
> the core SCIFIO developers can at least keep it on the radar -- though no
> promises on timeline. Or if you (or a colleague) want to take a crack at
> implementing such a file format yourself, we would be delighted to help
> with any technical hurdles.
>
> Regards,
> Curtis
>
>
> On Thu, Jun 26, 2014 at 2:30 PM, Hadjilucas, Lucas <
>
[hidden email]> wrote:
>
>> 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>>
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>> ImageJ mailing list:
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>
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