HCTFOOD - Software

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).

Expertomica Metabolite Profiling

Program for LC/GC-MS measurement analysis. It works with text records of the measurement in Agilent ASCII, Thermo ASCII and JCAMP-DX ASCII formats. It performs filtration of random and systematic noise, peak detection and compound composition on the basis of probability theory. It enables visualization by graphs of detected peaks as well as noise parts.

Download Expertomica Metabolite Profiling

Expertomica Time-Lapse Microscopy Capture Tool

Program for capture of microscope images. It is designed for capturing of long image series, more detailed analysis of information content and processes occurring in the microscopy sample. In comparison to classical software tools, it has better possibilities in exposition setup, possibility to capture images with several camera setup at one time. One of typical applications is the possibility to capture several images with different exposition time and in this way to overcome the dynamic limit of camera. In the current version Olympus cameras are supported.

Expertomica Compute Entropy on GPU toolbox

Program for computation of information's content of individual pixels in one digitized image or between two images. It serves as one of the methods for image processing during automated image analysis. It is based on calculation of Shannon entropy for all combination's of lines and rows. This calculation is highly computationally intensive and this toolbox was developed to accelerate the original Matlab calculation using Vidia graphic cards. It reduces the computation time thousand times. In the case that the graphical card is not present in the computer, the computation is performed on the CPU in optimized C++ version of algorithm. The program is primarily developed for analysis of images captured by the phase contrast microscopy method. It can be utilized for any intensity (black and white or pseudo-RGB) images.

Expertomica Hela Cells 3.03 RC

Program for creation of computer description of cell culture development in time lapse microscopy. EHC is primarily developed for description of He-La cells with the experiment size of up to 1500 analyzed images and 30-50 cells per image. With certain restrictions it may be used for bigger experiments and other types of cells. EHC is written in Java which ensures almost non-restricted compatibility for all platforms and operation systems. The advantage is also small size of the program.


Expertomica DNG Reader

Program for conversion and unification of Raw fro mates from different images. This software first enables to work with original data from digital cameras. This is the first step for mapping of accessible chemical space information in biological cell images.

Expertomica Colony Reader

Software for readout of development of cell colonies

Expertomica Entropy Calculator

A principally new software for computation of information content of the image which enables to use different generalized entropies calculation. This proved to be able to highlight different cellular compartments


Expertomica Cell Marker

Software for manual marking and adoption of regions in the image. The need for this software was clear after all automated detection software's failed.


Netlogo 3D model of Lorenz attractor

Netlogo 3D model of Lorenz attractor

Netlogo 3D may be downloaded from http://ccl.northwestern.edu/netlogo/3DPreview5/

Expertomica Cell Labeller


Expertomica Colony Size


Expertomica ECell

The software is designed for manual time-lapse microscopy image series of cell monolayer labeling. The software brings fast and efficient way for cell cycle analysis of cell monolayer. Many statistics can outcomes from the labeling cell cycle duration, comparison of cell states, cell cycle vocabulary. User cell state vocabulary can be created for any individual type of objects.


Expertomica Metabolite Profiling Hi-Res

The software was developed for analysis of datasets with high resolution from Liquid chromatography mass spectrometry. It works with several ascii and xml datafiles. Native Matlab and specified cdf files are also supported. Application performs precison and resolution estimation, mass peaks centroidisation, unsupervised noise and mobile phase removal, iterative peak deconvolution and confidence factors evaluation. No information is lost during the processing. Program enables graphical user interface with basic plotings (Total Ion Current chromatograms and Mass spectra) of raw, processed and resulted data.


Expertomica PIE Extractor

Program for calculation of PIE (Point information entropy) from the time-lapse microscopy images of cells. For each image and each value of alpha parameter, single PIE value is calculated. The values of PIE are used for analysis of the cell behavior.


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. 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.