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

Dan White white at mpi-cbg.de
Thu Jul 31 12:18:12 EDT 2008 

Hi Richard,

I don't think it is sensible to "port" bio-formats into ITK style C++
and make it part of ITK, that's not the idea.

Rather it should be used as an external toolkit,
and code to support that in ITK/VTK would do the job.

(I still think IO speed might be the killer here)

For instance the new WrapITK support for the bio-formats java code
and a microscopy meta data ITK dictionary that mirrors the XML meta  
data schema
of the OME file standards, so you would have the same metadata  
structure in both?
Developments in the OME XML meta data schema could be reflected in
the ITK microscopy data dictionary?

then everyone speaks the same meta data language (after the initial  
import by boi-formats)
which can only be a good thing, so long as the relevant people/projects
chip in with improvements for bio-formats and OMS XML schema?

Dan

On Jul 31, 2008, at 5:17 PM, Richard Beare wrote:

> It would definitely be nicer to have fully native support - i.e. a
> complete port of bioformats to itk. But you have to start somewhere
> and perhaps a port of the format considered standard is the place to
> start.
>
> I don't remember exactly what is in the xml in ome tif. I'd imagine
> there is a lot of stuff to do with excitation frequencies and cameras
> and so on that don't have current equivalents in ITK, but can probably
> be mapped sensibly into the data dictionary. The OME XML scheme, which
> is presumably what is in OME tiff, is hopefully a good summary of what
> microscopy experts think should be captured. I'd assume there'd be no
> major hassles writing it to the data dictionary, but deciding whether
> there is already overlap with currently supported data dictionary
> fields might be a challenge.
>
> On Thu, Jul 31, 2008 at 11:35 PM, Dan White <white at mpi-cbg.de> wrote:
>> 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 )
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Insight-users mailing list
>>>> Insight-users at itk.org
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>
>>
>> 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 )
>>
>>
>>
>>
>>
>>

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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