flowcatchR (version 1.6.2)

preprocess.Frames: Preprocessing function for Frames objects

Description

Frames objects are processed according to the chosen set of parameters. Many of them refer directly to existing EBImage functions, please see the corresponding help for additional information

Usage

preprocess.Frames(frames, brush.size = 3, brush.shape = "disc",
  at.offset = 0.15, at.wwidth = 10, at.wheight = 10, kern.size = 3,
  kern.shape = "disc", ws.tolerance = 1, ws.radius = 1,
  displayprocessing = FALSE, ...)

Arguments

frames

A Frames object

brush.size

Size in pixels of the brush to be used for initial smoothing (low-pass filtering)

brush.shape

Shape of the brush to be used for initial smoothing (low-pass filtering)

at.offset

Offset to be used in the adaptive thresholding step - see also thresh. As an alternative thresholding method, see also otsu in the EBImage package.

at.wwidth

Width of the window for the adaptive thresholding step - see also thresh. As an alternative thresholding method, see also otsu in the EBImage package.

at.wheight

Height of the window for the adaptive thresholding step - see also thresh. As an alternative thresholding method, see also otsu in the EBImage package.

kern.size

Size in pixels of the kernel used for morphological operations - e.g., opening, which is an erosion followed by a dilation, and closing which is a dilation followed by an erosion - see also opening, closing

kern.shape

Shape of the kernel used for morphological operations

ws.tolerance

Tolerance allowed in performing the watershed-based segmentation (see also watershed)

ws.radius

Radius for the watershed-based segmentation (see also watershed)

displayprocessing

Logical, whether to display intermediate steps while performing preprocessing. Dismissed currently, it could increase runtime a lot

...

Arguments to be passed to methods

Value

• A Frames object, whose frame images are the preprocessed versions of the input images

Examples

data("MesenteriumSubset")
preprocess.Frames(channel.Frames(MesenteriumSubset,"red"))