Author: Vignette Author
Date: 2018-02-02

# STAPLE Example

#### Vignette Author

#### 2018-02-02

## STAPLE Example

Simultaneous truth and performance level estimation (STAPLE) is a method for estimating a image segmentation. Commonly an image is segmented from a set of raters or readers. Here, we have an image that has been segmented from 3 different readers. Each is a binary segmentation, which includes areas of lesions from one person’s image.

## Running STAPLE

Here we will use STAPLE to fuse the data:

    library(stapler)
    images = staple_example_data()
    res = staple(x = images, set_orient = TRUE)
    #> Reshaping images
    #> All images are niftiImage ojects
    #> Warning in `orientation<-`(`*tmp*`, value = ori): Image qform and sform
    #> codes are both zero, so it cannot be reoriented

    #> Warning in `orientation<-`(`*tmp*`, value = ori): Image qform and sform
    #> codes are both zero, so it cannot be reoriented

    #> Warning in `orientation<-`(`*tmp*`, value = ori): Image qform and sform
    #> codes are both zero, so it cannot be reoriented
    #> There are 2 levels present
    #> Removing elements where all raters agree
    #> Making multiple, matrices. Hot-one encode
    #> iter: 25, diff: 3.66012170454591e-14
    #> Convergence!
    #> Creating output probability images/arrays
    #> Creating output label image/array
    print(names(res))
    #> [1] "sensitivity"           "specificity"           "probability"
    #> [4] "label"                 "prior"                 "number_iterations"
    #> [7] "convergence_threshold" "convergence_value"     "converged"

We use the `set_orient = TRUE` argument so that if the images headers are different, then they will be set to the same orientation when run. The `staple` function will read in the images, reshape the data into a matrix, compute a prior for each element (voxel, in this case), run STAPLE. The output probability image, labeled image (if probability \(\geq 0.5\)), and prior image are given in the output `res`.

## Multi-class STAPLE

STAPLE works with multi-class data as well. The data do not need to be binary, but they need to be consistently labeled for each image/segmentation. Here we will

    x = matrix(rbinom(5000, size = 5, prob = 0.5), ncol = 1000)
    table(x)
    #> x
    #>    0    1    2    3    4    5
    #>  166  829 1574 1502  767  162
    res_mult = staple_multi_mat(x)
    #> There are 6 levels present
    #> Removing elements where all raters agree
    #> Making multiple, matrices. Hot-one encode
    #> iter: 25, diff: 2.93374683379977e-07
    #> iter: 50, diff: 1.18448029162721e-11
    #> iter: 75, diff: 7.7715611723761e-16
    #> Convergence!
    ncol(res_mult$probability)
    #> [1] 6
    colnames(res_mult$probability)
    #> [1] "0" "1" "2" "3" "4" "5"