LOMAR (version 0.5.0)

points2img: points2img

Description

Convert a data frame of point coordinates into an image. Expected photon count at each voxel is computed as in: F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, “Simultaneous multiple-emitter fitting for single molecule super-resolution imaging,” Biomed. Opt. Express 2(5), 1377–1393 (2011).

Usage

points2img(points, voxel.size, method, channels = NULL, ncpu = 1)

Value

an array of dimensions x,y,z and channels if applicable

Arguments

points

a point set as a data frame of coordinates with columns x,y,z.

voxel.size

a numeric vector of length 3 indicating the size of the voxel along x,y and z in the same unit as the coordinates (e.g. nm)

method

how to calculate voxel values. Available methods are:

• 'histogram': value is the number of points (i.e. emitters) in the voxel

• 'photon': value is the expected number of photons from the points in the voxel. Input data frame must have columns locprec, locprecz and phot[on].

channels

vector of channels to consider, must be values present in the input data frame channel column

ncpu

number of threads to use to speed up computation (default: 1)

Examples

point.set <- data.frame(x = c(-9.8,-5.2,12.5,2.5,4.5,1.3,-0.2,0.4,9.3,-1.4,0.5,-1.1,-7.7),
                        y = c(-4.2,1.5,-0.5,12,-3,-7.2,10.9,6.7,-1.3,10,6.7,-6.2,2.9),
                        z = c(3.4,-3.8,-1.4,1.8,3.5,2.5,2.6,-4.8,-3.8,3.9,4.1,-3.6,-4))
img <- points2img(point.set, voxel.size = c(2,2,2), method = 'histogram')