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in this project i try to learn about localization microscopy

you capture long (10000s of frames) sequences of microscope images with blinking fluorophores (you get them to blink by adding some chemicals to the medium). in each frame only a few molecules are visible and you can estimate their exact position with a precision that depends on how many photons you collected. the resolution of your image does not depend on the quality of your objective, the wavelength of the light or the resolution of the camera.

once you have the localizations in the frames, the next step would be to find molecules that blinked in several frames. for this it is useful to build a kdtree, that will allow you to find nearest neighbors.