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

Thu Jul 31 09:52:11 EDT 2008

Le 31 juil. 08 à 15:35, Dan White a écrit :

> 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.
>

For sure, it would be very nice to have support for that format in ITK/ 
VTK.

> 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).

This code simply extract a 3D image from file using bioformat, and  
write it to the disk in tiff format. It only takes the memory of a  
single image, but it does take disk space — for ex., I'm frequently  
working with images of 140 MB per channel these days — and of course  
it takes time.
The next step is to copy everything in memory, with a pipe for  
example, and in C++.

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

sure. BTW, the unstable wrapitk has a way better support for ITK's  
metadata dictionaries :-)

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

What would be the required attributes? Can't it fit in itk's metadata  
dictionaries?
I didn't looked much at OME XML. Is it able to store all the metadata  
from all those file format we can find all around?

Gaëtan

>
>
> 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 )
>
>
>
>
>
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users

-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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