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New Data and Visualization Tools for the Whole Brain Catalog

Researchers from the Center for Research in Biological Systems (CRBS) at the University of California, San Diego rolled out beta version 0.7.5 of the Whole Brain Catalog on January 25th. In this beta version, developers have improved features to enhance the Catalog’s usability as a free, open access environment in which neuroscientists can contribute, share and analyze data.

Over 200 brain regions from the Allen Brain Atlas are now available through the Whole Brain Catalog. Previously, only five brain regions from the Allen Atlas were available to the user, along with 30 mouse brain regions from the Waxholm-Space Brain Atlas. The broader integration of the widely used Allen Brain Atlas improves the Catalog’s multi-scale 3D imaging capabilities as well as its effectiveness as a reference tool for neuroscience data analysis by maximizing consistency across neuroanatomical reference resources.

As a result, the Catalog now provides full Allen region support to the user, as well as a more detailed and elegant 3D virtual mouse brain for researchers to explore and use as a framework for data analysis.

“The brain is the most complex structure in the universe with billions and billions of nerve cells -- as many neurons as there are stars in the Milky Way, and even more glial cells,” said CRBS Director Mark Ellisman, lead scientist on the Whole Brain Project and a professor in the department of neurosciences at UC San Diego. “We’re building a next-generation research environment to effectively collect, connect, share and communicate the billions and billions of gigabytes of data produced by researchers world-wide. Thanks to Ted Waitt’s vision and the Waitt Family Foundation’s commitment to social progress, scientific exploration, and gateways to knowledge, we’re entering a new frontier and making new connections with the global neuroscience community to openly share their work and cooperatively explore the burgeoning new discoveries about brain structure and function.”

The Whole Brain Catalog offers a powerful information integration tool to allow scientists to peer deep inside a virtual mouse brain to see their data in the context of datasets contributed from around the world -- all from their personal computer. Improved 3D controls facilitate the journey through this virtual environment by making the newly expanded mouse brain model more accessible and easier to manipulate. The Catalog’s interface now more clearly displays attribution information of data in the environment to better allow researchers to be credited for their data.

Researchers can access and navigate this “brain information system” via the Internet, much as students and consumers currently navigate today’s ubiquitous geographic information systems (GIS), including Google Earth and MapQuest. With a few clicks of the mouse, researchers can increase the explanatory power of their own scientific datasets by intermixing them with datasets contributed by others from around the world. Much as a motorist or homeowner might use Google Maps to get directions or find a house, scientists can zoom in for a “street view” perspective of their datasets uploaded to the Whole Brain Catalog, allowing them to understand the broader context of their research, and even explore alternative routes to new insights by reusing data imported from other researchers.

Developers are currently working on new features that will broaden the Whole Brain Catalog’s data visualization capabilities for future releases. Volume rendering support is under construction so that users will be able to upload and view their own 3D data sets. Round-trip simulation support is also in design so that the Catalog can one day execute dynamic simulations of neural events from within its interface.

The Search for Pannexin Expression: An Application of the Whole Brain Catalog

Researchers at NCMIR are pioneers in this new scientific methodology and are blazing the trail for other researchers to use the Catalog for data-intensive brain research. Post-doctoral fellow Angela Cone has begun to use the Whole Brain Catalog in her research on the newly discovered Panx family of gap junction-like proteins.

Cone explained that identifying molecular patterns within nervous tissue is a key method of understanding their large-scale neurological function. It is extremely difficult to compare separate whole brain sections to one another at a large scale and comparison of protein labeling to gene expression is complicated in the nervous system, because it requires knowledge of where the processes of neurons are located and their connectivity. She is using the Whole Brain Catalog to overcome the interoperability challenge.

The identification of Panx’s expression patterns and interactive partners within the brain requires wide-scale, high-resolution mouse brain tissue imaging. Cone uploads this data to the Cell Centered Database (CCDB), where it can be normalized to a standard spatial framework, the Allen Reference Atlas. By this process, the brain maps can be compared with one another as well as against other data in neuroinformatics image-based databases such as GENSAT and the Allen Brain Atlas. When Cone experiences an inconsistency between comparative data, the Whole Brain Catalog eases the problem by providing metadata and original images so that the discrepancy can be resolved or more fully understood.

“The Whole Brain Catalog functions as both tool and inspiration in the quest for the ability to map Panx expression and interactions through a high-resolution 3D model of the mouse brain,” said Cone. “The Catalog provides the multi-dimensional workspace in which high-resolution data can be incorporated into a more complete representation of Panx expression. And while the Whole Brain Catalog does not yet contain the complete multi-scale connectivity data that we need to significantly illuminate the function of the Panx protein family, it does provide an ideal environment into which this data will soon be integrated.”

This neuroinformatics approach to the Panx problem has broader impact for how to use shared frameworks to facilitate neuroscience research. The Catalog is at the cutting edge of this field working towards the integration of all the necessary tools into one resource.


The Whole Brain Catalog is the flagship of the Whole Brain Project, developed with generous support from the Waitt Family Foundation. CRBS neuroscientists and software engineers joined forces to establish the Whole Brain Catalog and rely on the Neuroscience Information Framework (NIF), a dynamic web search engine of neuroscience resources supported by the National Institutes of Health Blueprint for Neuroscience, and the Cell Centered Database (CCDB) as core infrastructural components.

The Catalog is undertaken in cooperation with the International Neuroinformatics Coordinating Facility (INCF), an international consortium established by the OECD Global Science Forum. The Catalog accesses the INCF’s Blue Gene supercomputer to rapidly simulate available brain models. The system also uses supercomputing resources available at UC San Diego.

Future phases of this new tool will rollout in the coming year, and the Whole Brain Project team in the Center for Research in Biological Systems at UC San Diego plans to further engage the scientific community in creating a strategic roadmap for the Catalog’s continued development.