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It simulates a three-dimensional ground-truth that resembles aspects of a biological object like a spheroid. For each simulated view the signal is attenuated, convolved with an effective PSF, and anisotropically sampled using a Poisson process. 

This Matlab code simulates the noise of the confocal laser scanning microscope depending on the depth in the image stack (serial sections). Using the stack of binary images, it applies different levels of noise in the signal and background parts of the images to simulate confocal images. This is useful for generating "virtual ground truth" images with known values of sample rotation and distortion. 

Mean shift is a filter which acts as edge preserving filter similarly to non local mean or anisotropic diffusion. 

Mean shift can be used for denoising, segmentation or clustering. Two parameters are to be tuned, a spatial size of a patch and a gray level or color distance on which the algorithm is applied.

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks