M.Sc Thesis

M.Sc StudentHershko Eran
SubjectMulticolor Localization Microscopy and Point-Spread-Function
Engineering by Deep Learning
DepartmentDepartment of Electrical and Computer Engineering
Supervisors ASSOCIATE PROF. Tomer Michaeli
ASSOCIATE PROF. Yoav Shechtman
Full Thesis textFull thesis text - English Version


Deep learning has become an extremely effective tool for image classification and image restoration problems. Here, we apply deep learning to microscopy, and demonstrate how neural networks can exploit the chromatic dependence of the point-spread function to classify the colors of single emitters imaged on a grayscale camera. While existing single-molecule methods for spectral classification require additional optical elements in the emission path, e.g. spectral filters, prisms, or phase masks, our neural net correctly identifies static as well as mobile emitters with high efficiency using a standard, unmodified single-channel configuration. Furthermore, we demonstrate how deep learning can be used to design new phase-modulating elements that, when implemented into the imaging path, result in further improved color differentiation between species, and experimentally demonstrate simultaneous measurement of four species in a single image. Examination of the designed optimized phase pattern shows us that it enables the net to achieve excellent performance even when the SNR is extremely low and emitters’ density is high. Our implementation of the useful architecture for discriminating different PSFs according to color can also be used for analyzing any other effecters on the shape of the PSF (e.g. z-position, molecular orientation, movement dynamics, number of contributing emitters, etc.).