Hi everyone,<div class="gmail_quote"><div><br></div></div>Recently there have been several inquiries regarding the status of a <a href="http://www.loci.wisc.edu/software/bio-formats" target="_blank">Bio-Formats</a> plugin for ITK, so here is an update:<br>
<ol><li>We have created a <a href="http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/Building_C%2B%2B_Bindings" target="_blank">C++ layer for using Bio-Formats</a> via JNI, using Jace. This functionality has been tested and works on Windows, Mac OS X and Linux 32-bit and 64-bit systems.</li>
<li>We have coded a preliminary <a href="http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats/Building_ITK_Plugin" target="_blank">Bio-Formats ITK plugin</a> to read image data. Performance is now quite reasonable, but there are still some caveats:</li>
<ul><li>It is generally not well tested, especially on Windows.</li><li>The dimensional structure is hard-coded to 5D (XYZTC ordering).<br></li><li>There may be issues with multichannel data.</li><li>It does not populate m_Spacing due to a crash bug on Mac OS X systems.</li>
<li>The class hierarchy (based on Slicer's MGH ImageIO plugin) may be more complex than necessary.</li><li>The build system may not adhere to cross-platform C++ development best practices</li></ul></ol>You can <a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-itk/" target="_blank">browse the source</a> on our Trac; see <a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/native/bf-itk/itkBioFormatsImageIO.cxx" target="_blank">itkBioFormatsImageIO.cxx</a> for the bulk of the implementation.<br>
<br>We are now working to improve these tools; for details, see the relevant tickets in our issue tracking system:<br><ul><li><a href="http://imagejdev.org/trac/imagej/ticket/24" target="_blank">Generalize Bio-Formats C++ bindings into JAR-to-native-library generator</a></li>
<li><a href="http://imagejdev.org/trac/imagej/ticket/25" target="_blank">Improve Bio-Formats ITK plugin class structure and build system</a></li>
<li><a href="http://imagejdev.org/trac/imagej/ticket/26" target="_blank">Improve Bio-Formats ITK plugin implementation</a></li><li><a href="http://imagejdev.org/trac/imagej/ticket/27" target="_blank">Simplify compilation and deployment of FARSIGHT+Bio-Formats</a></li>
</ul>The simplest way to read microscopy data into ITK or VTK is to convert to TIFF using Bio-Formats. However, if you want to read the data directly into ITK from the original format, feel free to give the Bio-Formats ITK plugin a try. We welcome any feedback!<div>
<br>-Curtis<br><br><div class="gmail_quote">On Fri, Jan 16, 2009 at 12:16 PM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
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.<br>
<br>Cheers,<br><font color="#888888">Curtis</font><div><div></div><div><br><br><div class="gmail_quote">On Thu, Jan 8, 2009 at 3:11 PM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Hi everyone,<br><br>This email is about integration of Bio-Formats with
the VTK and/or ITK toolkits. It is fairly long, so please ignore if
uninterested.<br><br>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.<br>
<br>For those who don't know me, my name is Curtis Rueden and I am the project manager for Bio-Formats (<a href="http://www.loci.wisc.edu/ome/formats.html" target="_blank">http://www.loci.wisc.edu/ome/formats.html</a>).
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.<br>
<br>---<br>BENEFITS<br><br>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:<br>
<br>* Support for 60+ life sciences file formats within VTK/ITK, of course.<br><br>*
Support for these formats in Badri Roysam's FARSIGHT project at RPI,
which currently uses ITK's ImageIOBase/ImageIOFactory mechanism to read
images.<br>
<br>* Support for these formats in BioImageXD (<a href="http://www.bioimagexd.net/" target="_blank">http://www.bioimagexd.net/</a>), which I understand also uses ITK to read images.<br><br>* A cross-platform testbed for the Jace framework (<a href="http://sourceforge.net/projects/jace/" target="_blank">http://sourceforge.net/projects/jace/</a>) 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 (<a href="http://www.zeroc.com/ice.html" target="_blank">http://www.zeroc.com/ice.html</a><div>),
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.<br>
<br>* It might be useful for MeVis Research's MeVisLab environment (<a href="http://www.mevislab.de/" target="_blank">http://www.mevislab.de/</a>),
which has some ITK-related functionality -- although they have already
implemented preliminary support for Bio-Formats using vanilla JNI.<br>
<br>* Potential support from within other VTK/ITK-based applications (e.g., Mayavi2: <a href="http://code.enthought.com/projects/mayavi/" target="_blank">http://code.enthought.com/projects/mayavi/</a>)<br><br>---<br>PRIOR DISCUSSION<br>
<br>Back in July, Dan White briefly discussed a possible Bio-Formats integration with VTK/ITK on the VTK mailing list:<br>
<br><a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096253.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096253.html</a><br><a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096255.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096255.html</a><br>
<a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096276.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096276.html</a><br><a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096278.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096278.html</a><br>
<a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096280.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096280.html</a><br><a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096286.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096286.html</a><br>
<a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096287.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096287.html</a><br><a href="http://www.vtk.org/pipermail/vtkusers/2008-July/096291.html" target="_blank">http://www.vtk.org/pipermail/vtkusers/2008-July/096291.html</a><br>
<br>---<br>LICENSING<br><br>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.<br>
<br>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.<br>
<br>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.<br>
<br>This approach is a somewhat gray area; see:<br><a href="http://www.gnu.org/licenses/gpl-faq.html#GPLPluginsInNF" target="_blank">http://www.gnu.org/licenses/gpl-faq.html#GPLPluginsInNF</a><br><br>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.<br>
<br>If anyone with a better understanding of open source licensing has
further thoughts or corrections on this issue, I would greatly
appreciate it.<br><br>---<br>METADATA<br><br>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.<br>
<br>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. <b>The primary goal of Bio-Formats is to standardize proprietary metadata into this common data model.</b>
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.<br>
<br>---<br>PERFORMANCE<br><br>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.<br>
<br>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.<br>
<br>---<br>QUESTIONS AND DISCUSSION<br><br>My goal with this email is
to kickstart some discussion about integrating Bio-Formats with
VTK/ITK. Specifically, my questions for the community are:<br><br>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?<br>
<br>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?<br>
<br>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.<br>
<br>4) Any thoughts on the GPL/BSD licensing issue?<br><br>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!<br>
<br>Regards,<br><font color="#888888"><font color="#888888">Curtis Rueden</font></font></div>
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