EC CL - Extract Connected Clusters

(3/2/00)

PURPOSE

Segments a volume that contains two or more unconnected objects of the same intensity. The resulting volume can be used for masking or with other 'EC' operations.

'EC CL' works by reading a SPIDER 3D volume file and a threshold level. It locates connected clusters of voxels that are above the threshold. Each cluster is given a number. A new 3D image file is created that contains a cluster number for each object voxel or zero for background voxels. Connectivity is six fold here (left, right , up, down, top & bottom).   Example.

SEE ALSO

EC SELECT [Extract Connected Clusters - Selection]
EC CLOSE [Extract Connected Clusters - merge close clusters]
EC FILTER [Extract Connected Clusters - Filter]
EC STAT [Extract Connected Clusters - Statistics]

USAGE

.OPERATION: EC CL

.INPUT FILE: VOL001
[File containing SPIDER image/volume to be segmented.]

.SLICE NUMBERS: 1-64
[Range of image slices the user wants to search.]

.THRESHOLD LEVEL: 1.3
[Finds connected clusters that have a value greater than this threshold.]

.CLUSTER OUTPUT FILE: VVV001
[Output cluster image/volume file name.]

NOTES

  1. If the following output message is observed, Original:    0   clusters mapped to:    0   then no clusters were found for the given threshold value. Try a larger threshold value.

  2. Usually you will want to follow this operation with the 'EC STAT' operation.

  3. The connected object you want should have high densities, you may have to invert the contrast of your input volume so that the objects densities are high (white).

SUBROUTINES

CONINT, FILSLI, CCONECT, GOTBRANCH, EMPSLI, SHOSLI, SHOSLI2, MAKTAB, MAPIM

CALLER

UTIL6

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