DOKK / manpages / debian 12 / mia-tools / mia-2dsegment-local-cmeans.1.en
mia-2dsegment-local-cmeans(1) General Commands Manual mia-2dsegment-local-cmeans(1)

mia-2dsegment-local-cmeans - Run a c-means segmentation of a 2D image.

mia-2dsegment-local-cmeans -i <in-file> [options]

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.

image to be segmented
For supported file types see PLUGINS:2dimage/io
class label image based on merging local labels
For supported file types see PLUGINS:2dimage/io
class label image based on global segmentation
For supported file types see PLUGINS:2dimage/io
class probability image file, filetype must support floating point multi-frame images
For supported file types see PLUGINS:2dimage/io

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

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.

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).

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]).

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

Virtual IO to and from the internal data pool

Recognized file extensions: .@

2D image io for DICOM

Recognized file extensions: .DCM, .dcm

Supported element types:
signed 16 bit, unsigned 16 bit

a 2dimage io plugin for OpenEXR images

Recognized file extensions: .EXR, .exr

Supported element types:
unsigned 32 bit, floating point 32 bit

a 2dimage io plugin for jpeg gray scale images

Recognized file extensions: .JPEG, .JPG, .jpeg, .jpg

Supported element types:
unsigned 8 bit

a 2dimage io plugin for png images

Recognized file extensions: .PNG, .png

Supported element types:
binary data, unsigned 8 bit, unsigned 16 bit

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

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

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

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

Gert Wollny

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