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mia-3dsegment-local-cmeans(1) General Commands Manual mia-3dsegment-local-cmeans(1)

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.

OPTIONS

File-IO

image to be segmented
For supported file types see PLUGINS:3dimage/io
class label image based on merging local labels
For supported file types see PLUGINS:3dimage/io
class label image based on global segmentation
For supported file types see PLUGINS:3dimage/io
class probability image file, filetype must support floating point multi-frame images
For supported file types see PLUGINS:3dimage/io

Help & Info

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
print copyright information

print this help

-? --usage
print a short help

print the version number and exit

Parameters

Spacing of the grid used to modulate the intensity inhomogeneities

c-means initializer
For supported plugins see PLUGINS:1d/cmeans
c-means breaking condition for update tolerance

threshhold to ignore classes when initializing the local cmeans from the global one.

Don't take background probablities into account when desiding whether classes are to be ignored

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

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

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.

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.

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 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

Virtual IO to and from the internal data pool

Recognized file extensions: .@

Dicom image series as 3D

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

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 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

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-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 Sun raster format

Recognized file extensions: .VFF, .vff

Supported element types:
unsigned 8 bit, signed 16 bit

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

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

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'.

v2.4.7 USER COMMANDS