Provided by: mia-tools_2.4.7-13_amd64 
NAME
mia-2dsegment-local-cmeans - Run a c-means segmentation of a 2D image.
SYNOPSIS
mia-2dsegment-local-cmeans -i <in-file> [options]
DESCRIPTION
mia-2dsegment-local-cmeans This program runs the segmentation of a 2D 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 a 2D prototype of the 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:2dimage/io
-o --out-file=(output); io
class label image based on merging local labels
For supported file types see PLUGINS:2dimage/io
-G --out-global-crisp=(output); io
class label image based on global segmentation
For supported file types see PLUGINS:2dimage/io
-C --class-prob=(output); io
class probability image file, filetype must support floating point
multi-frame images
For supported file types see PLUGINS:2dimage/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.
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: 2dimage/io
bmp BMP 2D-image input/output support. The plug-in supports reading and writing of
binary images and 8-bit gray scale images. read-only support is provided for
4-bit gray scale images. The color table is ignored and the pixel values are
taken as literal gray scale values.
Recognized file extensions: .BMP, .bmp
Supported element types:
binary data, unsigned 8 bit
datapool Virtual IO to and from the internal data pool
Recognized file extensions: .@
dicom 2D image io for DICOM
Recognized file extensions: .DCM, .dcm
Supported element types:
signed 16 bit, unsigned 16 bit
exr a 2dimage io plugin for OpenEXR images
Recognized file extensions: .EXR, .exr
Supported element types:
unsigned 32 bit, floating point 32 bit
jpg a 2dimage io plugin for jpeg gray scale images
Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg
Supported element types:
unsigned 8 bit
png a 2dimage io plugin for png images
Recognized file extensions: .PNG, .png
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit
raw RAW 2D-image output support
Recognized file extensions: .RAW, .raw
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
tif TIFF 2D-image input/output support
Recognized file extensions: .TIF, .TIFF, .tif, .tiff
Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit, unsigned 32 bit
vista a 2dimage io plugin for vista images
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
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-2dsegment-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'.