voxelize: Voxelize xyz coordinates

In valeriabonapersona/abc4d: Analysis of Brain Cells in 4 Dimensions

Description

Converts xyz coordinates in pixels to voxels of a specified µm size. The function summarizes the number of samples per group. It outputs a list where the first element ("data") is the data voxelized, and the second element ("summary") is the data summarized, i.e. the number of samples per voxel per group

Usage

voxelize(data, conv_factor = 5.16, voxel_size = 30)

Arguments

data	dataframe with xyz coordinates ("xPos", "yPox", "zPos") for example output of calculate_density(). It includes a variable ("sample_id") that is the quantity that will be summarizes over the group variable ("group").
conv_factor	number to be used for the conversion. The conversion factor depends on the imaging settings. For more information, see for example: https://mindresearchfacility.nl/wp-content/uploads/2019/12/Zoom-factor-and-corresponding-NA-and-resolution-by-pixel-size.pdf Defaults to 5.16
voxel_size	in µm. Defaults to 30. If you want to specify in pixels, put conv_factor = 1

Examples

x <- data.frame(
xPos = rnorm(100, 300, 100), yPos = rnorm(100, 300, 100), zPos = rnorm(100, 300, 100),
group = rep(c("control", "exp"), each = 50),
sample_id = rep(c(1:10), each = 10)
)
y <- voxelize(x, voxel_size = 100)

valeriabonapersona/abc4d documentation built on Dec. 23, 2021, 2:09 p.m.