Expertomica Updopsi2dge Toolbox

The software was originally developed for unsupervised probabilistic detection of protein spots in two-dimensional gel electrophoresis images as a toolbox for Matlab


This work was supported and co-financed by the South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses (CZ.1.05/2.1.00/01.0024).

Description

The software was originally developed for unsupervised probabilistic detection of protein spots in two-dimensional gel electrophoresis images as a toolbox for Matlab. 2DE gel images are processed for background thresholding as automatic evaluation of each pixel probability to decide if it is a meaningful signal. The method is based on evaluation of noise signal behavior. Presence of useful signal can be detected as a violation in the noise behavior. Background in 2DE gel should be considered as a special case of noise. The fitted distribution depends only on the type of electrophoresis separation. Processing of one 2.5-MB-pixel greyscale image takes approximately 150 s in Matlab. The output of our algorithm pinpoints protein spots with high probability (> 94%), and produces clear contours without blurred areas.

Input Data

The toolbox processes the grayscale image loaded into Matlab workspace as image matrix using Matlab native function imread for common image files or mat matrix variable using Matlab native function load. Analysis supposes input grayscale images with darker background and lighter protein spots.

Output

The OUTPUT of analysis (run of function PROBFILTR.M in Matlab environment) will contains in Matlab structure as following:

Ur: is original image (e.g script_01.png in report);
Ir: is temporary index vector;
t: is temporary index vector;
t_old: is temporary index vector;
Urk: is image after row analysis (e.g script_02.png in report);;
cfP1: is probabilistic matrix of row filtration (e.g script_03.png in report);;
Us: is image after column analysis (e.g script_04.png in report);;
Is: is temporary index vector;
cfP2: is probabilistic matrix of whole analysis (e.g script_05.png in report).

Installation

You can download the last version of the software from http://www.janurban.webs.com/2degels/index.htm. Download UPDoPSi2DGE.zip and extract into selected directory. Then run your instaled Matlab (R14 or higher with Statistics_Toolbox required).

The package contains:
Directory EXAMPLE_DATASETS with two example grayscale images of 2DE gels as Matlab matrix Im.
Directory REPORTS with two reports of analysis done on example datasets.
File PROBFILTR.M as the main Matlab function for analysis of 2DE gels. It could be run in Matlab envinroment using command OUTPUT = probfiltr(Im);
File SCRIPT.M do the same as the file PROBFILTR.M, however there is fixed load of one example.
Files COMPTH2.P, KILLNOISE2.P, SLIS.P, and FILTR.M are just necessary support function for the main analysis.
File READ.ME is an ascii text files user guide about the Expertomica Updopsi2dge toolbox.

Requirements

Operation system: Windows XP, Vista (32 bit)

Software:
instaled Matlab (R14 or higher with Statistics_Toolbox). MATLAB is a registered trademark of The MathWorks (www.mathworks.com).

Hardware

The software require at least 512 MB of memory (exact amount depend on the size of input files).

Testing

Directory EXAMPLE_DATASETS contains two example grayscale images of 2DE gels as Matlab matrix Im. Example could be load into Matlab environment using command load('FILE_NAME');
Directory REPORTS contains two html reports of analysis done on example datasets. Reports were done running Matlab script SCRIPT.M, all steps are described in the reports.

Download

Expertomica Updopsi2dge Toolbox.exe - Software (11.4 MB)

Mirror #1 - http://expertomica.eu

Author

Urban, Štys