Vebjorn Ljosa

# ljosaprobseg

This package contains an implementation of Ljosa and Singh's
probabilistic segmentation algorithm, described in the following
paper:

Vebjorn Ljosa and Ambuj
K. Singh: "Probabilistic
Segmentation and Analysis of Horizontal Cells," in Proceedings
of the 2006 IEEE International Conference on Data Mining (ICDM),
December,
2006, doi:10.1109/ICDM.2006.129.

The program is written in C, and simulates a random walk on the
image. We also have an eigenvector-based solution, but that is not
included in this package at this time. We may incorporate it in the
future. A Matlab MEX interface is provided.

The software is released under the BSD license. See the file
LICENSE for details.

## Download

The latest version is 1.0, and can be downloaded
here: http://www.ljosa.com/~ljosa/software/ljosaprobseg/download/ljosaprobseg-1.0.tar.gz.

The individual source code files are available here, in case you would like to take a look at the
code before downloading.

## Installation and use

Just typing `make` should build the stand-alone program
`ljosaprobsegsim` as well as a Matlab MEX module called
`ljosaprobseg`. The stand-along program can, for instance, be
invoked as follows:

`./ljosaprobsegsim -o output.pgm -n 2 -8 -r 0.0001 7cap33x.pgm \`

5000 206,467 207,467 206,468

Do `./ljosaprobsegsim -h` to learn about the available
options. Type `help ljosaprobseg` in Matlab to learn how to
invoke the Matlab module, or see the example
in `demo_ljosaprobseg.m`. The image used in the demo was
provided by Geoffrey P. Lewis from the laboratory of Steven K. Fisher
at UCSB.

The programs are multithreaded in order to improve their running time
on machines with multiple processors or cores. For the stand-alone
program, use the "-n" option to specify the number of worker threads.
The Matlab module is hardcoded to use two worker threads. (This can
easily be changed in the source code, if desired.)

Contact Vebjorn Ljosa
with any questions.

Last updated:
2007-07-06