Chip Based Optical Nanoscopy: System Integration and Automation

An integrated photonic chip based nanoscopy system has previously been developed at UiT, which allows for several advantages over conventional total internal reflection fluorescence microscopy and nanoscopy (i.e. super-resolutionnanoscopy). While the proof-of-concept has been demonstrated, there were several important system optimization tasks that were needed for making the system practical and more usable. This thesis tackles three major system optimization tasks, namely efficient and automatic coupling of light into waveguide in the photonic chip, precise control and stablization of feed point into the waveguide, and synchronization of illumination and collection arms of the photonic chip based microscope. For a novel and more flexible light feed setup designed at the department, a new mechanism for measuring the coupling efficiency was designed, an initial coupling and parasitic interaxis cross-talk compensation mechanism was designed, and two optimiztion algorithms were explored for the final fine coupling. Testing of the implementation showed promising results with close to optimal coupling efficiency achieved in a reasonable amount of time. A piezoelectric stage with large travel range was tuned to provide the best possible performance for controlling illumination. This was used to adapt a nanoscopy algorithm named multiple signal classification algorithm (MUSICAL) for exploiting the variable illumination property of multimode waveguides on the photonic chip. Lastly, imaging and illumination control was inplemented in software allowing the capture of datasets suitable for use with MUSICAL. Thus, the goals of this thesis were achieved successfully and the practical use ofthe photonic-chip for microscopy and nanoscopy was greatly enhanced

One-shot phase-recovery using a cellphone RGB camera on a Jamin-Lebedeff microscope

Jamin-Lebedeff (JL) polarization interference microscopy is a classical method for determining the change in the optical path of transparent tissues. Whilst a differential interference contrast (DIC) microscopy interferes an image with itself shifted by half a point spread function, the shear between the object and reference image in a JL-microscope is about half the field of view. The optical path difference (OPD) between the sample and reference region (assumed to be empty) is encoded into a color by white-light interference. From a color-table, the Michel-Levy chart, the OPD can be deduced. In cytology JL-imaging can be used as a way to determine the OPD which closely corresponds to the dry mass per area of cells in a single image. Like in other interference microscopy methods (e.g. holography), we present a phase retrieval method relying on single-shot measurements only, thus allowing real-time quantitative phase measurements. This is achieved by adding several customized 3D-printed parts (e.g. rotational polarization-filter holders) and a modern cellphone with an RGB-camera to the Jamin-Lebedeff setup, thus bringing an old microscope back to life. The algorithm is calibrated using a reference image of a known phase object (e.g. optical fiber). A gradient-descent based inverse problem generates an inverse look-up-table (LUT) which is used to convert the measured RGB signal of a phase-sample into an OPD. To account for possible ambiguities in the phase-map or phase-unwrapping artifacts we introduce a total-variation based regularization. We present results from fixed and living biological samples as well as reference samples for comparison