[Insight-users] LSM Reader in ITK / VTK - bio-formats

[Dan White]

>
> Hi Karthik,
>
> We already had some discussion about relicensing parts of BXD vtk and
> itk C++ kits
> to BSD / VTK license, and I am currently qualifying what happened  
> there
> with our programmers in Finland.
> As I understand there were no show stoppers that would prevent that
> happening.
>
> It would be very cool to add the readers we have written to VTK/ITK,
> and I have always had that intension in mind...
>
> However the more important points are:
>
> 1) Bio-formats (from LOCI  OME project) is a java toolkit
> for reading very many biological / microscopy formats.
> Instead of reinventing the wheel, VTK/ITK needs to
> use and collaborate in development of bio-formats,
> as this is by far the most sane and efficient way to
> bring the required data format reading functionality to VTK/ITK
> Gaetan Lehmann has already written a WrapITK module for bio-formats,
> and that is a fantastic start (see previous emil to lists from him).
> However, there is much more to do, in terms of helping maintain
> and add new reader to bio-formats, and squeezing the best
> possible performance out of it.
>
> 2) Meta Data - Meta Data - Meta Data.
> Most of the proprietary image data formats that bio-formats
> reads contain large amounts of meta data which is very
> important to be able to read and use for many image processing tasks.
> You need to know the physical size of the pixels if you want to  
> measure
> distances. For fluorescence microscopy images you need to know what
> excitation light was used (laser lines, excitation filters, what
> emission
> filters / bands were used, what exactly was the objective lens
> mag, numerical aperture, immersion medium etc .etc .etc.
> These are called different things by different manufacturers,
> and it is a big task to standardize all this stuff.
>
> What we need is continuous development of an open biological image
> standard data format
> that handles multi dimensional (x, y, z, colour channels, time, more)
> image data and preserves meta data in an
> open standardised XML schema.
> This is what a large part of the work that the
> Open  Microscopy Environment  (OME)
> is undertaking. See their OME-TIFF and OME-XML open file formats.
> http://www.openmicroscopy.org
>
> A meta data framework for VTK/ITK should be, or be derived from
> the great work they have already done there.
> Again VTK/ITK should benefit from their hard work,
> and not once again re invent the wheel.
>
> The BioImageXD project is also making a metadata structure,
> on an as needed basis, but in the long term, it would
> make the most sense for us to share that open standardised
> microscopy meta data structure with OME.
>
> For this to work out as I describe above,
> we all need to talk to each other,
> and plan iout how to implement these things,
> such that they works as well as possible
> for al these interested parties.
>
> Hopefully, these discussions will be initiated by the current exchange
> of emails.
> I am very happy to be involved from an organisational point of view
> (I'm not a programmer - yet)
> as I have direct interests in bio-formats, open microscopy meta data
> standards,
> and microscopy data format reading in ITK / VTK due to my
> involvement in both BioImageXD and Fiji (Fiji is just ImageJ -  
> improved)
>
> There are plenty of good reasons to get this cooperation working  
> right,
> and now is good time to get the ball rolling.
>
>
> cheers
>
> Dan
>
>
>
>
>
> On Jul 30, 2008, at 11:53 PM, Karthik Krishnan wrote:
>
>> Dan:
>>
>> Here at Kitware, we have a proprietary vtkLSMReader,
>> used in VolView (and unlike ITK's reader, handles multi-channel
>> LSM's). It also handles compressed LSM's (basically all the
>> compression formats that TIFF supports). However it does not
>> bother to parse meta-data.
>>
>> I'd be happy to add it to VTK CVS (of course under a BSD license).
>>
>> We would like more support for microscopy formats in VTK/ITK;
>> there have been requests for it on the ITK and VTK users list, and
>> addition of these readers would broaden the toolkits' adoption by
>> folks in microscopy.
>>
>> I noticed that as a part of vtkBXD:
>>  https://bioimagexd.svn.sourceforge.net/svnroot/bioimagexd/bioimagexd/trunk/vtkBXD/Processing/
>> you have:
>>
>> 1. vtkLSMReader - LSM file formats
>> 2. vtkLIFReader - Leica's .lif formats
>>
>> Both the readers would be great additions to VTK.
>>
>> If you would like to have the readers incorporated into VTK, in
>> keeping with VTK's quality testing process, we would need test
>> images from you (both single and multi-channel, compressed and
>> uncompressed), for regression testing.
>>
>> Dave Cole and I can help with the cleaning up of the code, merging
>> the readers and adding it to VTK.
>>
>> How are you handling the meta-data right now. Do you have a
>> specialized datastructure to house the same ? ITK has its own
>> meta-data dictionary. VTK has, for a while been using
>> vtkMedicalImageProperties. I think it might be time to create a
>> framework for microscopy meta-data in VTK as well.
>>
>> Mathieu Malaterre can be reached at mathieu.malaterre at kitware.com .
>> He left Kitware and is back in Lyon.
>>
>> Thanks
>> Regards
>> -- 
>> Karthik Krishnan
>> R&D Engineer,
>> Kitware Inc.
>> Ph: 518 371 3971 x119
>> Fax: 518 371 3971
>>
>> On Wed, Jul 30, 2008 at 5:03 AM, Dan White <white at mpi-cbg.de> wrote:
>>> Dear All,
>>> this message bounced from
>>> the kitware email address for Mathieu
>>> so I'll just forward it here(s)
>>> cheers
>>> Dan
>>>
>>>
>>> From: Dan White <white at mpi-cbg.de>
>>> Date: July 29, 2008 7:49:00 PM GMT+02:00
>>> To: Mathieu Malaterre <mathieu.malaterre at kitware.com>
>>> Subject: LSM reader - bio-formats
>>>
>>>
>>> Hi Mathieu,
>>>
>>> I just saw a post on the ITK list,
>>> mentioning the LSM reader you have added to ITK.
>>>
>>> We also spent a lot of time writing one for VTK,
>>> as part of BioImageXD project.
>>>
>>> We use both VTK and ITK in that project,
>>> but have kept our vtkLSMReader as part of out vtkBXD external C++
>>> kit.
>>> You can see it there in our svn repository.
>>>
>>> The LSM format is a real pig, as you probably know,
>>> and extracting all the important meta data is really important for
>>> post
>>> processing those images.
>>>
>>> It would probably make sense to merge our code,
>>> and have a single C++ LSM reader for ITK / VTK?
>>>
>>> We finally managed to get our reader to read the compressed LSM
>>> files...
>>> does the itkLSM code handle that?
>>>
>>> What do you think about a merge?
>>>
>>> Our code is currently GPL, but i think we can move stuff to be
>>> under the VTK
>>> style license without any real hassle.
>>>
>>> On the other hand.... for biological image format support,
>>> we should really all be working with the
>>> LOCI bio-formats project,
>>> and getting VTK/ITK to work with that java project..
>>>
>>> we already both reinvented the wheel once with the 2 LSM readers....
>>>
>>>
>>> cheers
>>>
>>> Dan
>>>
>>>
>>> Dr. Daniel James White BSc. (Hons.) PhD
>>> Senior Microscopist / Image Processing and Analysis
>>> Light Microscopy Facility
>>> Max Planck Institute of Molecular Cell Biology and Genetics
>>> Pfotenhauerstrasse 108
>>> 01307 DRESDEN
>>> Germany
>>>
>>>
>>> New Mobile Number!!!
>>>
>>> +49 (0)15114966933 (German Mobile)
>>> +49  (0)351 210 2627 (Work phone at MPI-CBG)
>>> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>>>
>>> http://www.bioimagexd.net
>>> http://www.chalkie.org.uk
>>> dan at chalkie.org.uk
>>> ( white at mpi-cbg.de )
>>>
>>>
>>>
>>>