stackObjects {EBImage} | R Documentation

## Generate a stack of images for detected objects, one object per image

### Description

From an indexed image the functions generates an image stack with one image per object placing each object in the middle of the image. Objects can be automatically rotated to align them along the horizontal axis.

### Usage

      ## S4 methods for signatures 'x=IndexedImage,ref=Image,index=character'
      ## and 'x=IndexedImage,ref=Image,index=list' and
      ## S4 method for signature 'IndexedImage, Image,
      ##   numeric':
      stackObjects(x, ref, index, ...)

      ## S4 method for signature 'IndexedImage, Image,
      ##   missing':
      stackObjects(x, ref, index, combine, rotate, bg.col, ext, centerby, rotateby, ...)

### Arguments

`x` | An object of `IndexedImage`. Images must be Grayscale and carry object indexing information, like those returned by `watershed` or `propagate`.
`ref` | A reference image containing images of the objects to be stacked using `x` both as index and the mask. Can be in any color mode.
`index` | Indexes of objects to stack. See details for supported types.
`combine` | Called on a stack if images, specifies if the resulting list of image stacks with individual objects should be combined into a single image stack. Defaults to `FALSE`.
`rotate` | Specifies if the objects should be aligned rotationally. Defaults to `TRUE`.
`bg.col` | Color for pixels outside the mask defined by `x`. Defaults to `TRUE`.
`ext` | Extension of the target bounding box. See details. If not given, `ext` is calculated from data.
`centerby,rotateby` | If `ref` is a TrueColor image, these character values specify which channel should be used to center and rotate objects. By default the image is converted by `channel(ref,"gray")`. Other possible values are `"red", "green"` or `"blue"`.
`...` | Reserved.

### Details

The bounding box is set to be a square, which centre coinsides with the geometric center of the object. The `ext` argument can be used to specified its size, where edge length will be given by `2*ext+1`. If `ext` is not specified, it is calculated from the data by taking the 95% quantile of the vector of `h.s2major` descriptor of `hullFeatures` taken over all, objects in the image. This descriptor specifies the extension of the object along its major axis starting from its center.

The size of the bounding box is fixed for all frames to enable combining the resulting frames into a single multiframe image.

`index` must be coersable to numeric to specify object indexes that are taken into the resulting stack. It can be specified as `numeric` directly only for images with 1 frame. For images with multiple frames it can be either a `list` or a `character`. If specified as a `list`, it can be a named list of numeric indexes where names are converted to `character` frame indexes in an arbitrary order, or it can be an unnamed list of the same length as the number of frames. If specifies as `character`, each element must contain two numbers separated by a dot where the first number is the index of the frame and the second one is the index of the object within the frame, e.g. `"2.035"` will specify frame 2 and object 35.

### Value

An image stack or a list of image stacks if `x` was itself a stack (contained more than one image).

### Author(s)

Oleg Sklyar, osklyar@ebi.ac.uk, 2006-2007

### See Also

`tile, combine, paintObjects`

### Examples

      ## load images
      f <- paste( system.file(package="EBImage"), "images/Gene1_G.tif", sep="/" )
      ii = readImage(f)
      ## normalize images
      ii = normalize(ii, separate=TRUE)
      ## segment
      mask = thresh(ii, 25, 25, 0.02)
      ## refine segmentation with morphology filters
      mk3 = morphKern(3)
      mk5 = morphKern(5)
      mask = dilate(erode(closing(mask, mk5), mk3), mk5)
      ## index objects with 'watershed'
      io = watershed( distmap(mask), 1.5, 1)
      if (interactive()) display(io)

      ## stack individual objects
      s = stackObjects(io, ii, combine=FALSE)
      ## display stack of objects of from the first image
      if (interactive()) display(s[[1]])
      ## combine stacks of objects into a single stack
      s = combine(s)
      ## tile the stack into one frame
      t = tile(s)
      if (interactive()) display(t)

[Package EBImage version 2.6.0 Index]