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

Thu Jul 31 09:01:12 EDT 2008

I'd have thought that extending the existing ITK tif reader to deal
with ome tif would be a very useful starting point, and potentially
quite simple. That would provide a relatively simple conversion path
into ITK : bioformats conversion to ome tif and then read. If I
remember correctly, ome tif is regular tif with an extra tag
containing a long string of xml meta data. I certainly anticipate
using such tools in the not too distant future.

On Thu, Jul 31, 2008 at 8:14 PM, Dan White <white at mpi-cbg.de> wrote:
>>
>> 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 )
>>>>
>>>>
>>>>
>>>>
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