Project 3: Neuronal Structure and Function

1. Collection of data: Methods to improve data collection using confocal microscopy of single retinal neurons;
2. Classification of morphology: Tools to identify and classify a variety of morphological features of neurons that can be automatically extracted from retinal cell image data; the use of these features in content-based retrieval operations to retrieve database records based on morphological features as opposed to keywords;
3. Visualization of images and three dimensional datasets: Tools for querying and browsing images of neurons; an image browser will be implemented to allow a library of neuronal images to be viewed together and interactively rearranged in order to facilitate visual comparisons. In association with Project 1, the MacVol volume rendering package will be developed to handle more complex data sets and provide for porting of the system to other platforms.
4. Database construction: In association with Projects 1, 2 and 4, a multi-tiered  image and textual database of the primate lateral geniculate nucleus will be developed. Project 3 will assemble data regarding retinal inputs to the geniculate and its activities will be integrated with the other two core projects through the medium of database construction in Project 1. The various tools and concepts developed in this project are directly applicable to the analysis and classification of neurons in all other areas of the brain, including the neocortex, thalamus, hypothalamus and brainstem.

Contributions of Project 3 to the program as a whole

The contributions of this project to the program as a whole are: it provides high resolution images of retinal neurons and tools for manipulating them; it provides these images to the primate lateral geniculate database being produced by Project 1, along with details of the physiological properties and connectional relationships of the ganglion cells that form the principal subcortical afferent input to the lateral geniculate; it provides lexical data about these properties and connections for the database.

 Specific contributions of Project 3

 The contributions specific to this project are: it provides a database of the vertebrate retina that can stand alone if necessary; this database is accompanied by database-specific tools that can be used by other investigators for mining the visual components of the retinal database or for manipulating their own images, especially those derived from confocal microscopy.
 

Project 3 status

The research proposed in this grant extends, in innovative ways, several on-going research efforts begun under Phase I of our HBP grant. Our progress in this initial study has been considerable. The first section describes our work in database schema design. Such a schema is essential for comprehensive data management.  Our work on the design of a World Wide Web-oriented interface for the database is then introduced. Finally, our work in the development of object-oriented/vector-based stereotaxic atlases and tools for display, manipulation and linkage to a database of nuclear and cytological features is reviewed. Further details of our work, as well as demonstrations and materials available for downloading, can be found at our home page.

1. Database Schema Design Much of our ongoing work for the previous HBP grant addressed two key database design issues-What goes in the database and How do users interact with the database.  To address the first question we have developed a database schema that catalogs the collection of data objects, such as neurons and anatomy, and object relationships constituting the database.
2. Web-based Database Interface While a comprehensive schema, which adequately reflects the nature of the application domain, is an essential design of any database, tools that facilitate user interaction are equally vital. Appropriately, we have developed a prototype of a graphical Web-based interface to our database. This interface will enable the user to retrieve and display both textual and graphical information on the morphology of single neurons. A demonstration of the Web-based interface is available. The interface employs Java, HTML and a database backend engine written in C++, and is designed to illustrate the schema in use.
3. Stereotaxic Atlas in Object Oriented Format This project was initially started as a pilot project several years ago. The goal was to explore optimal ways of using computers for storing and using stereotaxic atlases of brains. In view of our involvement with the original pigeon stereotaxic atlas, familiarity with the material and freedom from copyright concerns, we used this atlas for testing. Although this animal is not widely used in neurobiology, the strategies we have developed are directly applicable to other species. We now have Ted Jones' digitized cat atlas (see Project 2) and will begin applying our techniques to that.

Personnel

Principal Investigator: Harvey J. Karten, UC San Diego
Co-PI: Leo M. Chalupa, UC Davis