Software & Hardware
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COEDES: Configurable Emitter Density Simulator for Super-Resolution Fluorescence Imaging
Mohannad Sayed Ahmad, Ez-Alden Abo Hussein, Oren Solomon and Yonina C. Eldar
Introduction

Traditionally, spatial resolution in imaging is limited by one half of the optical wavelength. This limit is known as Abbe's diffraction limit. However, although information on sub-wavelength features is absent in the measurements, modern microscopic methods such as PALM and STORM enable super-resolution. Though such methods achieve spatial resolution of 20-40nm, require low fluorophore density in each acquisition cycle and tens of thousands of exposure for a single super-resolution image. Super-resolution optical fluctuation imaging (SOFI) enables the processing of images with much higher emitter density to achieve fast integration time (though with limited spatial resolution compared with STORM/PALM).

Main Idea

We present a MATLAB based simulation tool which simulates the acquisition process of a sequence of images (movie) of fluctuating emitters with varying densities in an epi-fluorescence optical microscope. The simulator is comprehensive, encompassing the physical aspects of the data acquisition process, including sample geometry, diffraction of light, camera quantization effects and noise. The simulator can be operated using a user friendly GUI or directly from the MATLAB command line, and is configurable via a simple text file. An example of the simulator output is given in Figure 1, in which a high density Movie was created along arbitrary 2D shapes.


Figure 1: Two examples of simulated objects, each row corresponds to a different object. (a, d) show the ground truth images, (b, e) a single movie frame of the objects in the high resolution grid, after convolution with the PSF and inclusion of out-of-focus layers and (c, f) show a single movie frame from the final low resolution movie after camera binning and addition of noise. In both cases high labeling density was used, such that in each frame many emitters are in the "on" state and their diffraction limited spots overlap each other.


References
  • M. S. Ahmad, E. A. A. Hussein, O. Solomon and Y. C. Eldar, "COEDES: Configurable Emitter Density Simulator for Super-Resolution Fluorescence Imaging", submitted to Bioinformatics, November 2016.

Software Download

The simulator is freely available for download and manipulation for academic use only, under the GNU license.

Installation:
1. Unzip.
2. Follow the instructions
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