• Applications in cell biology, gene expression analysis, neuroscience, etc.
• Methods: 3D segmentation, tracing, registration, visualization, data mining, modeling
• Major challenges and future directions

Case Studies

• High resolution C. elegans digital map and single cell analyses
• Zebrafish image segmentation and informatics
• Fruit fly bioimage informatics (segmentation/tracing, registration, annotation, and modeling)
• Others & industrial applications (e.g. electron microscopy image alignment, segmentation and 3D reconstruction, cell segmentation and tracking, etc.)

• None invasive brain functional imaging - fMRI
• Intrinsic optical imaging and voltage-sensitive dye imaging - fast functional screening of the brain
• Two photon calcium imaging - to see what we record physiologically at single cell resolution
• Two photon structural imaging - to monitor the neural network and the dynamics of subcellular structure
• Super-resolution imaging - the approach to image big biological molecues
• Data analysis - common difficulties and current tools

• Imaging the Brain with Optical Tools. Springer, Roe et al, 2009.
• Grinvald A et al (1999). In-Vivo Optical Imaging of Cortical Architecture and Dynamics. The revised version was published in Modern Techniques in Neuroscience research. U Windhorst and H. Johansson (eds), Springer Verlag
• Rust et al (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods, DOI:10.1038/NMETH929
• Helmchen & Denk (2005) Deep tissue two-photon microscope. Nature Methods, 2, 932-940.

• What is Digital Pathology?
• Why is digital pathology so different from radiologic images?
• What are the unique questions one can pose with digital pathology?
• Need for unique image computing tools in digital pathology

• What is computer aided prognosis?
• Feature extraction and characterization fro digital pathology
• Classification of high dimensional feature spaces
• Use case of Computer aided prognosis in prostate cancer
• Use case in breast cancer