[Insight-developers] IMAGE REGISTRATION / RECONSTRUCTION in MICROSCOPY : Special Topic

[Luis Ibanez]

We are hosting a Special Topic on

 "Image Reconstruction and Registration in Microscopy"

in the Frontier in Neuroscience Journal:

               http://www.frontiersin.org

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Special Topic
Image Reconstruction and Registration in Microscopy

Hosted By:

Mike Hawrylycz, Allen Institute for Brain Science, USA
James Gee, University of Pennsylvania, USA
Hanchuan Peng, Howard Hughes Medical Institute, USA
Luis Ibanez, KITWARE Inc., USA

http://www.frontiersin.org/neuroinformatics/specialtopics/image_reconstruction_and_regis/326

Deadline for abstract submission: 30 Jun 2011

Deadline for full article submission: 31 Oct 2011


Neuroscience research relies largely in the acquisition and analysis of
microscopy images of various modalities. As large communities of
neuroscientists explore different aspects of brain structure and behavior, it
becomes desirable to be able to integrate image information across data
acquired from different sources. This integration enables researchers to better
interpret their data, gain insight into the correlation between multiple
biological markers, discover unexpected interactions and relationships, and
finally share their findings in a way that can be reused by others. Examples of
resources supporting this type of data integration are the Allen Brain Atlas
and the brain atlases developed by INCF.

In order to perform data integration within images of different sources and
modalities, these images must be registered to a common coordinate system
first. Such processing, commonly involves reconstructing a 3D dataset out of a
collection of 2D images, as well as registering one or more 3D datasets to
another used as a reference, and sometimes registering one or more 2D images to
a 3D dataset.

A variety of techniques for performing these image management tasks have been
developed by many different groups in the domain of image analysis, and
unfortunately they do not always make their way in a usable form to the
biomedical researchers who need them.

In this Special Topic we set as our goal to collect and describe the image
reconstruction and registration resources that are available and to present
them into a comprehensive set of software tools that could be used by
biomedical researchers. The impact of this special topic will be to consolidate
the knowledge, methodologies and know-how on image registration that is
currently dispersed in many different image analysis groups, and finally make
it easily available to researchers outside of the image processing field, to
the point where they can seamlessly integrate it in their normal data analysis
workflows and pipelines.

Contributions to this special topic are expected to be based on publicly
available source code and to demonstrate their use on publicly available
datasets with the overall goal of enabling reproducibility and facilitating the
reuse of the tools by biomedical researchers.

Contributors are encouraged, but not required, to use datasets distributed by
the INCF Digital Atlasing program (http://www.incf.org/core/programs/atlasing)
available at (http://software.incf.org/software/waxholm-space/download), and
the Allan Brain Institute datasets available at (http://www.brain-map.org/).
Authors and biomedical researchers are also encouraged to provide new datasets,
as long as they can be publicly distributed (for example under the Public Data
Licenses http://www.opendatacommons.org/licenses/ ). These new datasets will
then be hosted at the INCF data sharing services.