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The cross-dependency of noise level and photobleaching in microscopy was discussed in a previous work and an efficient compressed sensing (CS) method was proposed to simultaneously reduce the noise level and the photobleaching. Here we present an improved CS denoising framework for fluorescence microscopy images, exploiting Non-Local means filtering to merge multiple reconstructions. This framework enables high-quality reconstruction of low exposed microscopy images based on random Fourier sampling schemes and multiple CS reconstructions. Practical experiments on fluorescence images demonstrate that even performing 10% of the measurements, the signal-to-noise ratio can be significantly improved while keeping reduced exposure time, preserving edges and the image sharpness.