[Insight-developers] Bio-Formats integration with VTK/ITK

[Curtis Rueden]

Thanks to everyone for the helpful advice and comments. It sounds like the
ITK ImageIO plugin mechanism is the way to go, and will avoid any licensing
issues. My plan remains to create a general C++ wrapper layer for
Bio-Formats, which will be usable by any C++ application, then once that is
working to implement the ITK I/O plugin using it. So applications will have
a choice whether to access Bio-Formats directly, or via ITK. I will post to
the list again when I have a prototype functional enough to be of interest.

Cheers,
Curtis

On Thu, Jan 8, 2009 at 3:11 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi everyone,
>
> This email is about integration of Bio-Formats with the VTK and/or ITK
> toolkits. It is fairly long, so please ignore if uninterested.
>
> My apologies for cross posting to multiple mailing lists, but I thought
> this topic might be of interest to a variety of people, and I would rather
> err on the side of inclusion. I am new to some lists, so I also apologize if
> I have missed any relevant prior discussion. Also, the message was rejected
> the first time due to "too many recipients" so I am resending -- please
> forgive the duplicate if you already received this.
>
> For those who don't know me, my name is Curtis Rueden and I am the project
> manager for Bio-Formats (http://www.loci.wisc.edu/ome/formats.html).
> Bio-Formats is a standalone Java library for reading and writing life
> sciences image file formats. It is capable of parsing both pixels and
> metadata for a large number of formats (64 at this writing), as well as
> writing to several (11) formats.
>
> ---
> BENEFITS
>
> In recent months it has become apparent that a robust Bio-Formats C++
> interface would significantly benefit the community. In particular,
> integrating Bio-Formats with VTK/ITK would provide several advantages:
>
> * Support for 60+ life sciences file formats within VTK/ITK, of course.
>
> * Support for these formats in Badri Roysam's FARSIGHT project at RPI,
> which currently uses ITK's ImageIOBase/ImageIOFactory mechanism to read
> images.
>
> * Support for these formats in BioImageXD (http://www.bioimagexd.net/),
> which I understand also uses ITK to read images.
>
> * A cross-platform testbed for the Jace framework (
> http://sourceforge.net/projects/jace/) for deploying Java APIs from within
> native code. Background: Jace produces C++ proxies corresponding to a Java
> API, allowing C++ code to call Java methods transparently via JNI
> Invocation. This technique requires a Java Runtime Environment on the
> machine, but is more performant than shared VM messaging solutions such as
> Ice (http://www.zeroc.com/ice.html), CORBA or XML-RPC. If Bio-Formats had
> a set of cross-platform Jace-driven C++ bindings, it would simplify calling
> Bio-Formats from VTK/ITK. Once the bindings exist, our regular testing and
> maintenance would strengthen the Jace project itself.
>
> * It might be useful for MeVis Research's MeVisLab environment (
> http://www.mevislab.de/), which has some ITK-related functionality --
> although they have already implemented preliminary support for Bio-Formats
> using vanilla JNI.
>
> * Potential support from within other VTK/ITK-based applications (e.g.,
> Mayavi2: http://code.enthought.com/projects/mayavi/)
>
> ---
> PRIOR DISCUSSION
>
> Back in July, Dan White briefly discussed a possible Bio-Formats
> integration with VTK/ITK on the VTK mailing list:
>
> http://www.vtk.org/pipermail/vtkusers/2008-July/096253.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096255.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096276.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096278.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096280.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096286.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096287.html
> http://www.vtk.org/pipermail/vtkusers/2008-July/096291.html
>
> ---
> LICENSING
>
> First, I want to address the licensing concern raised by Karthik Krishnan
> regarding use of Bio-Formats within ITK/VTK: Bio-Formats is GPL, while ITK
> and VTK are BSD. Unfortunately, this means that a combined ITK/VTK +
> Bio-Formats work becomes GPL -- in other words, Bio-Formats cannot be
> distributed with ITK/VTK under the BSD license.
>
> To be clear, LOCI and Glencoe Software strongly support open source
> software, including BSD-licensed software. Ideally, our wish is for
> Bio-Formats to be freely available for use with other open source projects
> regardless of license. My concern is that a linking exception allowing
> Bio-Formats to be distributed with VTK/ITK (e.g., using the LGPL instead of
> the GPL) would also allow a combined work to be expropriated for use within
> proprietary software, sidestepping the GPL.
>
> One solution might be for ITK/VTK to provide a plugin infrastructure for
> use by a Bio-Formats plugin module, which the end user would install
> separately into ITK/VTK. We currently use this approach to provide a
> Bio-Formats plugin for ImageJ even though ImageJ itself is public domain
> software.
>
> This approach is a somewhat gray area; see:
> http://www.gnu.org/licenses/gpl-faq.html#GPLPluginsInNF
>
> The difference in this situation is that ITK/VTK is not a non-free program,
> so the combined work would not violate the GPL, but it might be "infected"
> by it.
>
> If anyone with a better understanding of open source licensing has further
> thoughts or corrections on this issue, I would greatly appreciate it.
>
> ---
> METADATA
>
> Also discussed in the prior thread are issues of metadata conversion, which
> I am willing to discuss but frankly would prefer to postpone until an
> initial integration is completed. Any C++ bindings for Bio-Formats would
> include full access to its MetadataStore API, which would allow C++
> applications to manipulate OME-XML metadata.
>
> In response to the questions about OME-XML: the goal of the OME-XML schema
> is to fully encapsulate the acquisition metadata from all supported
> microscopy formats, with regular (at least 2/year) releases to continuously
> improve and update the schema. *The primary goal of Bio-Formats is to
> standardize proprietary metadata into this common data model.* So I
> strongly agree with Dan that we want to preserve that standard whenever
> possible. It would likely be possible to express the OME-XML schema as part
> of the ITK metadata dictionary, though to be sure I would need to understand
> more about how ITK models metadata.
>
> ---
> PERFORMANCE
>
> I have done a lot of research on time and space performance of Java versus
> C++, as well as performance when integrating Java code with C++ through
> various means. Much of those results fall outside the scope of this email,
> but suffice to say that Java's I/O performance is comparable to C++, and
> Bio-Formats is mostly I/O-bound. Any observed speed difference in the
> Bio-Formats library compared to other implementations (e.g., Dan points out
> that BioImageXD's LSM support is faster than reading an LSM file into ImageJ
> using Bio-Formats) is most likely due to algorithm inefficiency in the
> Bio-Formats code rather than a relative deficiency in the language itself.
>
> Regardless, I think our best bet is to interface the Bio-Formats Java API
> with C++ in the most performant way available. Any solution more involved
> than that, such as language translating Bio-Formats into C++, has its own
> serious pitfalls, would require months of effort at best, and would be
> prohibitive for us to maintain. And less sophisticated solutions, such as
> conversion of life sciences formats into the open OME-TIFF standard, then
> reading the result into ITK, are not performant enough for many
> applications.
>
> ---
> QUESTIONS AND DISCUSSION
>
> My goal with this email is to kickstart some discussion about integrating
> Bio-Formats with VTK/ITK. Specifically, my questions for the community are:
>
> 1) Do others agree that this form of integration is a good idea? Or is
> there a better way to accomplish the bulleted goals above?
>
> 2) I don't know much about ITK or VTK yet. Where is the right integration
> point? Within ITK, accessible using ImageIOBase/ImageIOFactory? Or
> elsewhere? Does VTK/ITK have an appropriate plugin infrastructure?
>
> 3) Does anyone have experience using Jace cross-platform? Or does anyone
> know an open source solution other than Jace for accessing Java API from
> C++? Unfortunately, WrapITK & CableSwig go the other way -- wrapping C++
> code for access from Java -- which is not what we want here.
>
> 4) Any thoughts on the GPL/BSD licensing issue?
>
> This project is currently my top priority, but I am not a C++ expert and I
> would greatly appreciate help from anyone in these various communities.
> Thanks in advance for any comments and replies!
>
> Regards,
> Curtis Rueden
>
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