In the past decades, spectral-domain optical coherence tomography (SD-OCT) has transformed into a widely popular imaging technology which is used in many research and clinical applications. Despite such fast growth in the field, the technology has not been readily accessible to many research laboratories either due to the cost or inflexibility of the commercially available systems or due to the lack of essential knowledge in the field of optics to develop custom-made scanners that suit specific applications. This paper aims to provide a detailed discussion on the design and development process of a typical SD-OCT scanner. The effects of multiple design parameters, for the main optical and optomechanical components, on the overall performance of the imaging system are analyzed and discussions are provided to serve as a guideline for the development of a custom SD-OCT system. While this article can be generalized for different applications, we will demonstrate the design of a SD-OCT system and representative results for in vivo brain imaging. We explain procedures to measure the axial and transversal resolutions and field of view of the system and to understand the discrepancies between the experimental and theoretical values. The specific aim of this piece is to facilitate the process of constructing custom-made SD-OCT scanners for research groups with minimum understanding of concepts in optical design and medical imaging.

In this article, we report the development of a minimally invasive fiber optic based fluorescence probe which can reach deep brain objects and measure the intensity and spatial distribution of fluorescence signals in the tissue. In this design, the brain is scanned by a single penetrating side-firing optical fiber which delivers excitation light pulses to the tissue at different depths and orientations and simultaneously collects samples of fluorescence emission signals. Signal-to-noise ratio of the measurements is improved by adapting the pulse compression technique and the theory of optimal filters. Effects of each design parameter on the overall performance of the scanner, including the spatial resolution and speed of scanning, are analyzed and experimentally measured. In vivo experiments show that the new device, despite the simplicity of the design, provides valuable information particularly useful in optogenetic stimulation experiments where the exact position of the fiber tip and the radiation orientation can change the outcome of a test.