This award supports the preparation and sharing of high-resolution, high-quality, whole mouse brain neuronal and vascular data obtained from the Knife-Edge Scanning Microscope (KESM). KESM is capable of slicing and imaging whole small animal organs (such as the mouse brain) at less than 1 um resolution within 100 hours, with a resulting data size exceeding 2 TB per specimen. The amount and complexity of the KESM data necessitates innovative approaches in data organization, storage/retrieval, and dissemination. The research team will develop an informatics framework for 3D volume data dissemination and visualization.
The KESM, developed and housed in the PI's laboratory, has been used to dissect and image two whole mouse brains so far, one stained in Golgi to reveal the neuronal morphology, and the other in India ink to show the microvascular network in fine detail. The two data sets are unique in their detail and extent compared to other currently available data sets (orders of magnitude higher resolution along one or more of the x-, y-, and z-axis, and/or higher extent in the imaged volume). Such data enable researchers to conduct a full quantitative analysis of various morphological statistics and their variability across different brain regions and nuclei, estimate morphological parameters for computational simulation, and eventually help link structure to function.
A hybrid approach will be employed that integrates a web-based light-weight data browser and a local data viewer/analyzer, under a multi-scale data scheme. The specific objectives of this project are as follows: (1) Standardized data sets for improved access and interoperability with other data sources, (2) Light-weight web-based volume browser with an open Application Programming Interface (API) for enhanced freedom of access and annotation, and (3) Unit volume viewer for the visualization and analysis of small unit volumes downloaded through the web-based interface.
The data and software tools, including documentation, will be released in the public domain, to build a user/developer community that will help continued use and evolution of the framework.
The researchers at Texas A&M University launched a web-based atlas of microscopy data from the mouse brain. The atlas, called the Knife-Edge Scanning Microscope (KESM) Brain Atlas, is open to the public and the research community, and can be accessed at http://kesm.org (or http://kesm.cs.tamu.edu/home). The atlas serves data from three mouse brains, showing microscopic detail of neuronal circuits and blood vessel networks in the mouse brain. Data for the KESM Brain Atlas were collected using a unique instrument called the Knife-Edge Scanning Microscope. KESM cuts very thin sections of the mouse brain (1 micrometer-thin, 1/80th that of thick human hair) using a diamond knife while at the same time imaging the tissue sections with a high-speed digital line-scan camera attached to the microscope. Each brain results in about 1.5 TB to 2 TB of raw data. The main part of this research project was to design and build a web-based atlas framework to enable the exploration of the huge data sets. The research team customized and extended the functionality of the popular Google Maps interface, so that the multi-scale data set can be viewed in 3D. A novel overlaying technique was developed for the 3D effect. The main web page http://kesm.org includes the history of the project, a tutorial, media files (movies), and many other information related to this project. ?
