[Insight-users] LSM reader in ITK / VTK - bioformats

Dan White white at mpi-cbg.de
Tue Sep 2 11:36:33 EDT 2008

Dear Alexandre,

you can go ahead and use the vtk LSM reader from in the BioimageXD  
source code tree
under a BDS license.
We have cleared it with the lawyers in Finland and its no problem to  
do that.

However, may I remind you that while our LSM reader is pretty feature  
and we have spent much effort on making it work well,
for the future it make a lot of sense to use and help develop the java  
bio-formats library from LOCI.

There is a wrapping function for bio-format in WrapITK already.




Sorry to get back to this a little late, this the first time since  
June I've had proper time to go through my inbox...

There are no problems with licensing the LSM reader under BSD, I  
thought I had already told everyone that. So by all means, go ahead  
with that! Just tell me when/how it's done. (Or is there something  
else that needs sorting out in this matter? Kalle? Lassi?)

In general do keep in mind, though, that the green light here applies  
only in this case and not automatically to any other module or feature  
we have created. Each situation needs to be evaluated separately. But,  
as said, for the LSM reader we are "go for launch".


Dan White wrote:
> Hi Guys, where did we get with this lsm reader re licensing issue...
> I thought we reached a solution?
> Dan
> Begin forwarded message:
>> *From: *Alexandre GOUAILLARD <alexandre_gouaillard at hotmail.com <mailto:alexandre_gouaillard at hotmail.com 
>> >>
>> *Date: *July 30, 2008 11:35:22 AM GMT+02:00
>> *To: *Dan White <white at mpi-cbg.de <mailto:white at mpi-cbg.de>>,  
>> Mathieu Malaterre <mathieu.malaterre at gmail.com <mailto:mathieu.malaterre at gmail.com 
>> >>
>> *Cc: *Luis Ibanez <luis.ibanez at kitware.com <mailto:luis.ibanez at kitware.com 
>> >>
>> *Subject: **Re: [vtkusers] LSM Reader in ITK / VTK - bio-formats*
>> Hi dan,
>> Following our conversation  a few months ago,
>> I’m still waiting to see if you can pass your lsm reader under BSD.
>> Matthieu is not working for kitware anymore, and , as far as we  
>> discussed, did not want to go into modifying the itkLSM code.  
>> Matthieu tu m arretes si je dit une connerie.
>> If your code was available under BSD (last time we discussed that,  
>> you had to deal with a university in Finland as they are the  
>> copyright holder), then I would volunteer to do all the work to  
>> synchronize your lsm reader with the itkLSM reader, to write a nice  
>> IJ paper with you, and submit this code to IJ for further  
>> integration in the toolkits.
>> As long as your code is GPL, I cannot look at any line of it.
>> Regards,
>> Alex.
>> On 7/30/08 5:03 PM, "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

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dan at chalkie.org.uk
( white at mpi-cbg.de )

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