preprocess.Frames: Preprocessing function for 'Frames' objects

Description Usage Arguments Value Author(s) Examples

View source: R/preprocessing.R

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

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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

Author(s)

Federico Marini, marinif@uni-mainz.de, 2014

Examples

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flowcatchR documentation built on Nov. 8, 2020, 5:04 p.m.