mrcomas

Description

We developed a Morphological reconstruction and Contrast mapping segmentation method, called MrComas, for the segmentation of the endocytic vesicle population that copes with the heterogeneity in their shape and intensity.

The method uses morphological opening and closing by reconstruction in the vicinity of local minima and maxima respectively thus creating the strong contrast between their basins of attraction. As a consequence, the intensity is flattened within the objects and their edges are enhanced.

The method accurately recovered quantitative characteristics of synthetic images that preserve characteristic features of the endocytic vesicle population.

Installation on GNU/Linux from source

Download the latest archive:
http://sourceforge.net/projects/prostack/files/7.0/prostack-7.0.8.tgz/download
Unpack the files.
In each directory

door prostak quastack glaz prostack iapee cmove prutik psocv examples

run

autoreconf -fi
./configure --prefix=$HOME
make
make install

Several developmental packages might be required. Names of the packages are tacken from Fedora 23, they may be different in other distributions.

java-1.8.0-openjdk-devel
tetex-tex4ht
goocanvas-devel
liberation-mono-fonts
gtk2-devel
gtk3-devel
glib2-devel
libtiff-devel
gnutls-devel
libsoup-devel
sqlite-devel
apr-devel
apr-util-devel
httpd-devel
gsl-devel
gts-devel
fftw-devel
opencv-devel
libtool
intltool
perl-XML-Parser
pkgconfig
texlive-collection-latex
texlive-collection-latexextra
texlive-collection-latexrecommended
texlive-collection-htmlxml
texlive-collection-langenglish
texlive-collection-langeuropean
texlive-collection-pictures
texlive-ifsym
texlive-latex-fonts
texlive-ltxtools
ImageMagick
gnuplot
curl
R

RPM installation on Fedora Linux

Packages are provided for several popular distributions at https://build.opensuse.org/project/repositories/home:mackoel:compbio

Install packages in R

install.packages('fpc', 'optparse', 'RColorBrewer')

Installation on Ubuntu Linux

The following steps describe the successfull installation on Ubuntu 16.04. They might be applicable for other versions also. The procedure is based on using the

alien

tool.

Install the dependencies

sudo apt-get install alien gsl-bin libgts-0.7-5
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.19 /usr/lib64/libgsl.so.0

Download, convert and install packages

sudo alien prostack-7.0.8-144.1.x86_64.rpm
sudo dpkg -i prostack_7.0.8-145.1_amd64.deb
sudo alien prostack-desktop-7.0.8-144.1.x86_64.rpm
sudo dpkg -i prostack-desktop_7.0.8-145.1_amd64.deb
sudo alien prostack-examples-7.0.8-144.1.x86_64.rpm
sudo dpkg -i prostack-examples_7.0.8-145.1_amd64.deb
sudo alien prostack-debuginfo-7.0.8-144.1.x86_64.rpm
sudo dpkg -i prostack-debuginfo_7.0.8-145.1_amd64.deb

Install R

sudo apt-get install r-base r-cran-optparse r-cran-rcolorbrewer r-cran-tcltk2

Install packages in R

install.packages('fpc')

Before using MrComas from terminal issue a command:

export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH

Installation on MS Windows

MrComas works on 32- and 64-bit versions of Windows 7, 8.1 and 10.
Install R
https://cran.r-project.org/bin/windows/base/R-3.3.0-win.exe
Install packages in R

install.packages('fpc', 'optparse', 'RColorBrewer')

Install ProStack
https://sourceforge.net/projects/prostack/files/7.0/ProStack-7.0.9-0.win.i386.setup.exe/download
On the second screen for selecting directory select the directory containing Rscript.exe

Running

After successfull installation run the command in the terminal:

prostack-execute -n -p mrcomas