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Digital Atlasing and Standardization in the Rodent Brain

Jyl Boline1*, Albert Burger2, Tsutomu Hashikawa3, Allan G. Johnson4, Maryann Martone5, Lydia Ng6, Jonathan Nissanov7, Luis Puelles8, Seth Ruffins9, Fons Verbeek10, Ilya Zaslavsky11 and Mike Hawrylycz6
  • 1 Informed Minds, United States
  • 2 MRC, Human Genetics Unit, United Kingdom
  • 3 RIKEN ,The University of Tokyo, Brain Science Institute (BSI), Japan
  • 4 Duke Center for In Vivo Microscopy, United States
  • 5 University of California, NCMIR, United States
  • 6 Allen Institute for Brain Science, United States
  • 7 Drexel University College of Medicine, United States
  • 8 University of Murcia, Spain
  • 9 University of California, Laboratory of Neuro Imaging, United States
  • 10 Leiden University, Institute of Adv Computer Sciences, Netherlands
  • 11 University of California, San Diego Supercomputer Center, United States

The purpose of the INCF Digital Atlasing Program and Task Force is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain widely accessible and usable to the international research community. This task force is investigating the state of rodent digital atlasing, formulating standards, guidelines, and making policy recommendations. Initial focus is on the adult C57BL/6J mouse, due to the wealth of data available for that model organism, and will be expanded to other strains, developmental stages, and species over time. The first objective has been a detailed analysis including the vision and description of an infrastructure, systems and methods capable of serving the digital atlasing goals of the community, as well as issues and challenges for achieving these goals. As part of the analysis, a detailed set of research community based use cases were compiled from different fields such as genetics, neuropharmacology, microarray experimentation, development, data mapping, registration, and analysis. This will be published in a series of INCF reports, and builds on recommendations in the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline, 2007, Nature Preceedings, doi:10.1038/npre.2007.1046.1).

The vision of this program is that appropriate infrastructure must be developed that allows digital atlases to act as data sharing hubs, and permits any researcher to share data from a variety of rodent based experimental modalities from any location, and to allow comparative analyses of these data. This group is specifying such an infrastructure, including the standards, services, and APIs that must be created in order to facilitate these goals (see Zaslavsky et al). Prototype development will be used to help specify infrastructure whenever possible.

To accomplish this ambitious goal, it is necessary to integrate a mass of complicated information from a variety of fields. The requirements for this system are that atlases act as the map to which data of multiple types and sources are linked for processing, upload, analysis, retrieval, and sharing, which requires both spatial and semantic normalization. This INCF program is creating a new high resolution MRI and Nissl dataset to act as a canonical reference space for the mapping and registration of anatomic based data (see Nissanov and Johnson). While the idea of a canonical reference space is not new, there is little standardization between existing rodent atlasing systems, thus this space will provide a spatial standard that allows translation between different digital atlasing efforts and the integration of existing key neuroinformatics resources. Other groups, especially those with large associated data sources are encouraged to map their atlases into this coordinate based standard space using one of multiple methods via this dataset.

Ideally, this canonical space in conjunction with a prototype driven infrastructure architecture will provide the scaffold needed to fulfill the vision of a multimodal digital atlasing data system shared by the international research community. This system will truly require a community effort, thus all interested parties are encouraged to provide input.

Conference: Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.

Presentation Type: Oral Presentation

Topic: Digital atlasing

Citation: Boline J, Burger A, Hashikawa T, Johnson A, Martone M, Ng L, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I and Hawrylycz M (2019). Digital Atlasing and Standardization in the Rodent Brain. Front. Neuroinform. Conference Abstract: Neuroinformatics 2009. doi: 10.3389/conf.neuro.11.2009.08.069

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Received: 21 May 2009; Published Online: 09 May 2019.

* Correspondence: Jyl Boline, Informed Minds, Hollywood, United States, jylboline@informedminds.info