ImageData: Constructor for ImageData objects

In nbenn/singleCellFeatures: Analyze single cell features stored in an openBIS instance

Description

Due to performance requirements (when a whole plate is imported, 3456 ImageData objects are created), there are two ways this function is executed: Either the data is supplied (at leas one of vec, mat, lst is not NULL), in which case barcode is expected to be a string, index the linear plate index and n.img in c(6, 9), the number of images per well. Nothing is checked to save time. If no data is supplied, it is fetched. In this case, barcode is expected to be a WellLocation object, index the image index inside the well and n.img to be NULL, as this has already been determined.

Usage

ImageData(barcode, index, n.img = NULL, counts.quantiles = NULL,
  counts.cells = NA, vec = NULL, mat = NULL, lst = NULL)

Arguments

barcode	Either the barcode of the plate or a WellLocation object corresponding to the image's well
index	Either the linearized index of the image within the whole plate or the image index within the well
n.img	Number of images per well (either 6 or 9)
counts.quantiles	The 0.05 and 0.95 quantiles of cell counts for the whole plate.
counts.cells	The number of cells in this image.
vec	All data than contains only a single value per feature
mat	All data which consists of a vector of values per feature
lst	All data than can only be expressed as a nested list per feature

Value

An ImageData object: a list with slots for plate barcode, well location within the plate (index and row/col), image location within the well (index, row/col), number of images per well and image data

Examples

data <- ImageData(WellLocation("J107-2C", "D", 15), 5)

nbenn/singleCellFeatures documentation built on May 23, 2019, 12:24 p.m.