noble (1) mia-2dsegment-local-cmeans.1.gz
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=(input, required); 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'.