[vtkusers] LSM Reader in ITK / VTK - bio-formats

Thu Jul 31 09:35:50 EDT 2008

Hi Richard,

Yes, you are right there I think.
In any case the OME-TIFF and OME-XML file format definitions are
totally open, so implementation of reading the image data part would  
be easy.

Using bio-formats to convert some proprietary file format
to OME-TIFF would work, then yes that could be read by ITK/VTK tiff  
readers...
but that would involve doubling the memory usage, or even rewriting  
the file.

Bear in mind that I commonly see multi gigabyte datasets from  
microscopes these days,
and our softwares built on VTK/ITK need to handle that fluidly.

Perhaps using bio-formats to read image data directly into
VTK Image / ITK Image objects is a better idea,
(see the new wrapITK code for wrapping bio-formats).

Another tricky part is what to do with the meta data....

I support the earlier suggestion of a VTK / ITK
microscopy meta data framework,
that parallels the structure of the OME XML meta data definitions.

cheers

Dan

On Jul 31, 2008, at 3:01 PM, Richard Beare wrote:

> 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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>>

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 )