segment {bioimagetools} | R Documentation |

Segmentation of 3D images using EM algorithms

```
segment(
img,
nclust,
beta,
z.scale = 0,
method = "cem",
varfixed = TRUE,
maxit = 30,
mask = array(TRUE, dim(img)),
priormu = rep(NA, nclust),
priormusd = rep(NULL, nclust),
min.eps = 10^{
-7
},
inforce.nclust = FALSE,
start = NULL,
silent = FALSE
)
```

`img` |
is a 3d array representing an image. |

`nclust` |
is the number of clusters/classes to be segmented. |

`beta` |
is a matrix of size nclust x nclust, representing the prior weight of classes neighboring each other. |

`z.scale` |
ratio of voxel dimension in x/y direction and z direction. Will be multiplied on beta for neighboring voxel in z direction. |

`method` |
only "cem" classification EM algorithm implemented. |

`varfixed` |
is a logical variable. If TRUE, the variance is equal in each class. |

`maxit` |
is the maximum number of iterations. |

`mask` |
is a logical array, representing the voxels to be used in the segmentation. |

`priormu` |
is a vector with mean of the normal prior of the expected values of all classes. Default is NA, which represents no prior assumption. |

`priormusd` |
is a vector with standard deviations of the normal prior of the expected values of all classes. |

`min.eps` |
stop criterion. Minimal change in sum of squared estimate of mean in order to stop. |

`inforce.nclust` |
if TRUE enforces number of clusters to be nclust. Otherwise classes might be removed during algorithm. |

`start` |
not used |

`silent` |
if TRUE, function remains silent during running time |

A list with "class": 3d array of class per voxel; "mu" estimated means; "sigma": estimated standard deviations.

```
## Not run:
original<-array(1,c(300,300,50))
for (i in 1:5)original[(i*60)-(0:20),,]<-original[(i*60)-(0:20),,]+1
for (i in 1:10)original[,(i*30)-(0:15),]<-original[,(i*30)-(0:15),]+1
original[,,26:50]<-4-aperm(original[,,26:50],c(2,1,3))
img<-array(rnorm(300*300*50,original,.2),c(300,300,50))
img<-img-min(img)
img<-img/max(img)
try1<-segment(img,3,beta=0.5,z.scale=.3)
print(sum(try1$class!=original)/prod(dim(original)))
beta<-matrix(rep(-.5,9),nrow=3)
beta<-beta+1.5*diag(3)
try2<-segment(img,3,beta,z.scale=.3)
print(sum(try2$class!=original)/prod(dim(original)))
par(mfrow=c(2,2))
img(original)
img(img)
img(try1$class)
img(try2$class)
## End(Not run)
```

[Package *bioimagetools* version 1.1.8 Index]