preprocess.Frames: Preprocessing function for 'Frames' objects

In federicomarini/flowcatchR: Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells

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 EBImage::thresh(). As an alternative thresholding method, see also EBImage::otsu() in the EBImage package.
at.wwidth	Width of the window for the adaptive thresholding step - see also EBImage::thresh(). As an alternative thresholding method, see also EBImage::otsu() in the EBImage package.
at.wheight	Height of the window for the adaptive thresholding step - see also EBImage::thresh(). As an alternative thresholding method, see also EBImage::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 EBImage::opening(), EBImage::closing()
kern.shape	Shape of the kernel used for morphological operations
ws.tolerance	Tolerance allowed in performing the watershed-based segmentation (see also EBImage::watershed())
ws.radius	Radius for the watershed-based segmentation (see also EBImage::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, [e-mail], 2014

Examples

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

federicomarini/flowcatchR documentation built on Dec. 21, 2024, 8:45 p.m.