> benefit from an HDF5 reader in SCIFIO. :-)
> Hi Curtis and others (Mark?),
>
> if there is going to be any development in the HDF5 direction, we'd
> absolutely love to see the Image Standard [1] of HDF5 being supported! This
> would actually solve quite some of our time-consuming format-juggling
> exercises...
>
> I'm pretty sure we're not the only ones out there that would really
> benefit from an HDF5 reader in SCIFIO. :-)
>
> Regards,
> Niko
>
> [1]
http://www.hdfgroup.org/HDF5/doc/ADGuide/ImageSpec.html>
>
> On 16.07.2014 21:45, Curtis Rueden wrote:
>
>> 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>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
>
> --
> Niko Ehrenfeuchter
> Imaging Core Facility
> Kragenbau, Room G1055
> Biozentrum, University of Basel
> Klingelbergstrasse 50/70
> CH-4056 Basel (Switzerland)
>
> Office: +41 (61) 26 72673
> Email:
[hidden email]
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>