Parallel-scanning microscopy is designed to take advantage of an array of micro-mirrors to simultaneously acquire hundreds of partial images, or tiles. These tiles must then be reassembled to reconstruct a global image, which finally will benefit from a wide field of view while retaining excellent resolution. The reconstruction step, however, requires a delicate numerical handling of the tiles, to correct for both their geometry and for their photometry.

One out of many issues is the difficulty to mechanically align the geometry of the micro-mirrors with the scanning geometry. Fortunately, this misalignment can be compensated by software. The goal of this project is to design and implement in Java on ImageJ an algorithm that finds and applies the optimal overall angular alignment that results in the best stitching of the tiles. At first, the student will consider that all tiles suffer from the same misalignment. If time permits, the alignent of the tiles will then be refined individually, perhaps considering their individual translational movement as well.