University of Pittsburgh

Systems approaches to biologic questions are becoming more important as scientists strive to understand how their favorite molecule or cell fits into the broader picture of organismal development, tissue organization or pathogenesis. Exciting technologies have emerged that enable whole organs and even organisms to be imaged at very high resolutions such that individual cells can be easily located among billions.  This facilitates the tracing of neuronal circuits, reconstruction of neuronal activity across whole brains, characterization of immune microenvironments and following the spread of pathogens among others.

My interests include the development of platforms to facilitate rapid high-resolution volumetric imaging of whole tissues. The success of these platforms depends upon a wide variety of technologies which include tissue preparation methods, high-speed imaging systems and infrastructure to collect, store and process tera- even peta-scale imaging data. I am fascinated by the way that these technologies influence how biologists ask questions, and I am excited by making our tools accessible to the basic biologist.

Towards these goals, we have developed the high-speed ribbon scanning confocal microscope (RSCM) into a platform for high-resolution cleared tissue imaging. Together with tissue clearing approaches, we can digitally reconstruct centimeter thick tissue with submicron detail. Consequently, the data acquired from large tissues can reach many terabytes which requires developing visualization and processing environments that handle exceptionally large datasets.  To support the RSCM and other high throughput imaging platforms, my lab has led the Center for Biologic Imaging in the development of a high-performance computing infrastructure which includes petabytes of file storage, specialized cluster / grid computing platforms, and software which makes interacting with these resources simple for people with no experience using otherwise complex computational tools.