preprocess.Frames {flowcatchR} | R Documentation

## 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

### Author(s)

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

### Examples

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

[Package flowcatchR version 1.22.0 Index]