ImageSet-class: Class to represent an imaging dataset.

In gusef/Iris: A package to extract spatial features based on multiplex IF images

Description

Class to represent an imaging dataset.

Slots

samples

A list of samples each containing multiple coordinates.

counts

A list of counts of different cell types for each coordinate in each sample.

nearest_neighbors

A list of mean and std of nearest neighbor distances for each samples.

interactions

A list of interaction information for each sample.

proximity

A list of mean and std of nearest neighbor distances for each sample.

microns_per_pixel

Scalar value that indicates the length of a pixel in micrometers.

markers

A vector of strings indicating all different cell types considered.

invasive_margin_in_px

The width of the invasive margin in pixels

readMasks

Flag indicating whether the "_Tumor.tif" and "_Invasive_Margin.tif" should be read (default: True)

ignore_scoring

Flag indicating whether the scoring file should be ignored (default: FALSE)

gusef/Iris documentation built on May 14, 2019, 2:42 p.m.