Provided by: mia-tools_2.2.7-3_amd64 
NAME
mia-2dimagestack-cmeans - Calculate the c-means classification for a series of images.
SYNOPSIS
mia-2dimagestack-cmeans -i <in-file> -o <out-probmap> [options]
DESCRIPTION
mia-2dimagestack-cmeans This program first evaluates a sparse histogram of an input image series, then
runs a c-means classification over the histogram and then writes the probability mapping for thr original
intensity values
OPTIONS
File-IO
-i --in-file=(input, required); io
input image(s) to be filtered For supported file types see PLUGINS:2dimage/io
-o --out-probmap=(output, required); string
Save probability map to this file
Help & Info
-V --verbose=warning
verbosity of output, print messages of given level and higher priorities. Supported
priorities starting at lowest level are:
info ‐ Low level messages
trace ‐ Function call trace
fail ‐ Report test failures
warning ‐ Warnings
error ‐ Report errors
debug ‐ Debug output
message ‐ Normal messages
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
-T --histogram-thresh=5; float in [0, 50]
Percent of the extrem parts of the histogram to be collapsed into the respective last
histogram bin.
-C --classes=kmeans:nc=3
C-means class initializerC-means class initializer For supported plugins see
PLUGINS:1d/cmeans
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).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
Recognized file extensions: .BMP, .bmp
Supported element types:
binary data, unsigned 8 bit, unsigned 16 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 program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if
available), run cmeans with three classes on the non-zero pixels.
mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3
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'.
USER COMMANDS v2.2.7 mia-2dimagestack-cmeans(1)