Copy number

Follow this guide to deconvolute single-molecule images into actual copy numbers of fluorescent molecules.

This works by generating a simulated image (or images) of the fluorescent object by integrating a 3D point spread function (PSF) over a 3D model of the object. Then solving a set of linear equations to calculate the actual number of fluorophores generating that object.

Point Spread function

Generate a measured or simulated PSF. This code will generate a good PSF. Make sure each Z-plane is normalised to unitary intensity and you simulate enough z-planes for your 3D object.

Simulate shape

/Image Simulation/3Dshapes contains many functions for simulating shapes like spheres, shells and cylinders and combining them to create more complicated shapes like rod shaped bacterial cells.

Single compartment copy number

See /Copy Number/CopyNumberRodCell3.m CopyNumberRodCell3 for an example function to obtain the copy number of rod shaped cells like E.coli or B.subtilus

Multi compartment copy number

See /Copy Number/CopyNumberSphereCell.m CopyNumberRodSphereCell for an example function to obtain the copy number of cells with multiple compartments. In this case, a spherical yeast cell with a spherical nuclei.