Fluorescent dyes are frequently used as markers in many biological samples. They are used in research labs to track different tissues, cells and individual molecules. Studying these interactions is a key part of understanding physiology and developing new cures to common diseases. Fluorescent markers are also used in many analytical chemistry tests in hospitals for assisting the diagnosis of a health condition and evaluating the progression of a treatment. Applications of molecular markers, including the use of fluorescent markers as anatomical and functional markers in the body, have grown rapidly in recent years. This course will include cover the fundamental properties of fluorescent dyes, optimizing and matching an optical imaging system to specific dye spectra, and tailoring the optical system modules for specific applications such as bench-top microscopes, three-dimensional high resolution cellular imaging, and in vivo fluorescence imaging in pre-clinical studies and in clinical applications. We will also review common applications of fluorescent dyes and fluorescence imaging in current research and clinical activities.

The brain is the most widely studied body organ, and yet our understanding of its operation and the connection between changes to the physiology and the progression of disease is quite limited. Modern imaging tools, including optical imaging techniques, have enabled the study of many neural diseases and conditions and have assisted in evaluating the effect of drugs in model animal pre-clinical studies and in medical diagnosis. This course will review the principles and major optical techniques used for optical brain imaging. We will review the main cellular types in the brain and the organization of the anatomical regions into functional units. We will compare the major optical techniques used in brain imaging and discuss the contrast mechanisms that are used in each technique.<p> </p> We will review the use of external markers (mainly fluorescent markers), compare them to optical imaging techniques that use intrinsic contrast mechanisms (scattering, absorption, coherence, auto-fluorescence), and give examples in functional imaging of blood flow, oxygen levels, and neuronal activity. New methods using genetic introduction of proteins to control brain activity (Optogenetics) and selectively label cells will be described. Finally, we will discuss, with the help of examples, the relevance of these optical techniques in pre-clinical studies and clinical diagnosis.

Advances in medicine and technology are opening a new era of portable healthcare. Together with health apps, wearable/portable health monitoring systems are targeting medical diagnosis or health and wellness. The development of Wearable Health Monitoring Systems (WHMS) has been motivated mainly by increasing healthcare costs and by an aging world population. Fluorescent dyes are frequently used to mark biological samples, and track tissues, cells and individual molecules. In the lab, fluorescence is used to understand physiology and develop new cures to common diseases. In the clinic, fluorescence is used to diagnose health conditions and to evaluate treatments. Translating fluorescence imaging to portable healthcare systems will help us take better care of ourselves. <p> </p> This course will review fundamental properties of fluorescent dyes, tissue absorption and scattering and show how these can be used to track vital signs and provide wellness indicators during a physical activity. Focusing on fluorescence imaging and sensing as a major technique for biomedical and healthcare applications, we will describe the design and optimization of an optical imaging system to specific dye spectra, and tailoring the optical system modules for specific applications such as bench-top microscopes, portable healthcare imaging, and in vivo fluorescence imaging in pre-clinical and clinical studies. We will review examples of portable fluorescence imaging systems in rapid disease diagnosis, and in health monitoring.

Optical systems allow for non-invasive sensitive detection of absorption, scattering, and fluorescent light emission in live tissues. Detection systems can be divided into two main categories: macro- and micro-scale optical systems. Recently, drug discovery and the Human Genome mapping have accelerated the development of dedicated miniature detection systems for fast and sensitive readout of micro-arrays and bio-chips. In addition, bio-chip fabrication was greatly improved using advanced microelectronics fabrication methods and automated parallel arrayers. In parallel to these developments, advanced scanning microscopy techniques like two-photon and confocal microscopy were improved to allow high-resolution three-dimensional image collection from live tissues. These detection systems complement each other in many cases and will be reviewed as part of this course. Optical design considerations and sensor system integration and optimization issues will be presented with emphasis on miniature sensor systems.