Provided by: mia-tools_2.4.7-8ubuntu1_amd64 
NAME
mia-3dsegment-local-cmeans - Run a c-means segmentation of a 3D image.
SYNOPSIS
mia-3dsegment-local-cmeans -i <in-file> [options]
DESCRIPTION
mia-3dsegment-local-cmeans This program runs the segmentation of a 3D image by applying a localized c-
means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a
global c-means clustering, and then separates the image into overlapping regions where more c-means
iterations are run only including the locally present classes, i.e. the classes that relatively contain
more pixels than a given threshold. This program implements algorithm described in:
Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of
paleontological material. PeerJ 6:e4374. ⟨https://doi.org/10.7717/peerj.4374⟩
OPTIONS
File-IO
-i --in-file=(required, input); io
image to be segmented
For supported file types see PLUGINS:3dimage/io
-o --out-file=(output); io
class label image based on merging local labels
For supported file types see PLUGINS:3dimage/io
-G --out-global-crisp=(output); io
class label image based on global segmentation
For supported file types see PLUGINS:3dimage/io
-C --class-prob=(output); io
class probability image file, filetype must support floating point multi-frame images
For supported file types see PLUGINS:3dimage/io
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and higher priorities. Supported
priorities starting at lowest level are:
trace ‐ Function call trace
debug ‐ Debug output
info ‐ Low level messages
message ‐ Normal messages
warning ‐ Warnings
fail ‐ Report test failures
error ‐ Report errors
fatal ‐ Report only fatal errors
--copyright
print copyright information
-h --help
print this help
-? --usage
print a short help
--version
print the version number and exit
Parameters
-g --grid-spacing=15; int in [3, inf)
Spacing of the grid used to modulate the intensity inhomogeneities
-c --cmeans=kmeans:nc=3
c-means initializer
For supported plugins see PLUGINS:1d/cmeans
-e --c-means-epsilon=0.0001; float in (0, inf)
c-means breaking condition for update tolerance
-t --relative-cluster-threshold=0.02; double in [0, 1)
threshhold to ignore classes when initializing the local cmeans from the global one.
-B --ignore-background
Don't take background probablities into account when desiding whether classes are to be
ignored
-L --label-threshold=0; float in [0, 1]
for values <= 0.5: create segmentation based on highest class probability, labels start at
0. For values >0.5: create labels only for voxels with a class probability higher than the
given value, labels start at 1 and voxels without an according class probability are set to
0; this output is suitable for the seeded watershed filter.
Processing
--threads=-1
Maxiumum number of threads to use for processing,This number should be lower or equal to
the number of logical processor cores in the machine. (-1: automatic estimation).
PLUGINS: 1d/cmeans
even C-Means initializer that sets the initial class centers as evenly distributed over [0,1],
supported parameters are:
nc =(required, ulong)
Number of classes to use for the fuzzy-cmeans classification.
kmeans C-Means initializer that sets the initial class centers by using a k-means classification,
supported parameters are:
nc =(required, ulong)
Number of classes to use for the fuzzy-cmeans classification.
predefined
C-Means initializer that sets pre-defined values for the initial class centers, supported
parameters are:
cc =(required, vdouble)
Initial class centers fuzzy-cmeans classification (normalized to range [0,1]).
PLUGINS: 3dimage/io
analyze Analyze 7.5 image
Recognized file extensions: .HDR, .hdr
Supported element types:
unsigned 8 bit, signed 16 bit, signed 32 bit, floating point 32 bit, floating point 64
bit
datapool Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom Dicom image series as 3D
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
hdf5 HDF5 3D image IO
Recognized file extensions: .H5, .h5
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit,
unsigned 32 bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64
bit
inria INRIA image
Recognized file extensions: .INR, .inr
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32
bit, floating point 32 bit, floating point 64 bit
mhd MetaIO 3D image IO using the VTK implementation (experimental).
Recognized file extensions: .MHA, .MHD, .mha, .mhd
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32
bit, floating point 32 bit, floating point 64 bit
nifti NIFTI-1 3D image IO. The orientation is transformed in the same way like it is done with
'dicomtonifti --no-reorder' from the vtk-dicom package.
Recognized file extensions: .NII, .nii
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32
bit, signed 64 bit, unsigned 64 bit, floating point 32 bit, floating point 64 bit
vff VFF Sun raster format
Recognized file extensions: .VFF, .vff
Supported element types:
unsigned 8 bit, signed 16 bit
vista Vista 3D
Recognized file extensions: .-, .V, .VISTA, .v, .vista
Supported element types:
binary data, signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit,
unsigned 32 bit, floating point 32 bit, floating point 64 bit
vti 3D image VTK-XML in- and output (experimental).
Recognized file extensions: .VTI, .vti
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32
bit, floating point 32 bit, floating point 64 bit
vtk 3D VTK image legacy in- and output (experimental).
Recognized file extensions: .VTK, .VTKIMAGE, .vtk, .vtkimage
Supported element types:
signed 8 bit, unsigned 8 bit, signed 16 bit, unsigned 16 bit, signed 32 bit, unsigned 32
bit, floating point 32 bit, floating point 64 bit
EXAMPLE
Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20
pixels), and a class ignore threshold of 0.01.
mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01
AUTHOR(s)
Gert Wollny
COPYRIGHT
This software is Copyright (c) 1999‐2015 Leipzig, Germany and Madrid, Spain. It comes with ABSOLUTELY
NO WARRANTY and you may redistribute it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3
(or later). For more information run the program with the option '--copyright'.