Multi-level model of Synechococcus elongatus PCC 7942   Cell Segmentator   LIL Convertor 

 Image Info Extractor Professional   Organelle Extractor 

The study was financially supported by the Ministry of Education, Youth and Sports of the Czech Republic - projects „CENAKVA“ (No. CZ.1.05/2.1.00/01.0024), “CENAKVA II“ (No. LO1205 under the NPU I program)

Multi-level model of Synechococcus elongatus PCC 7942

Software is a part of a complex description of cyanobacterial cell Synechococcus elongatus PCC 7942, available on page Software represent a kinetic model of prime carbon metabolism for changing environment, namely CO2.

Software runs simulations of changing metabolic concentrations of Calvin cycle, glycolysis, carbohydrates synthesis and photorespiration. Model outputs are metabolic data in high and low CO2 conditions. Software enables understanding of metabolic network topology and isozymes influence on the metabolic regulation. Results of simulations can be used to design new experiments or to use it for genomic modeling; for such purpose it is possible to calculate the fluxes via reactions.

Binary Software License Multi-level model of Synechococcus elongatus PCC 7942

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Cell Segmentator

Software enables to segment an unlabelled live cell from a bright-field optical transmission microscopic z-stack. Segmentation is based on calculation of subtractive images, where zero pixels of the subtractive image serves for creation of binary segmentation mask.

Binary Software License Cell Segmentator

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LIL Convertor

Software performs reduction of multibit RAW files to 24-bit images and multibit grayscale images to 8-bit images, respectively, at the condition of least information loss. In process of transformation of RAW files to RGB images enables selection of algorithms non-interpolating and interpolating images to size of the original RAW file, removing calibration rows and columns, as well as thresholding minimal and maximal values of images suitable for conversion.

Binary Software License LIL Convertor

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Image Info Extractor Professional

Software servers as a tool for calculation of Point Information Gain, Point Information Gain Entropy, Point Information Gain Entropy Density, and Point Divergence Gain values from digital images and pictures (e.g., [1, 2]). It processes images of colour depth in the range of 2- and 48-bit in .png, . tiff, . jpg, and .bmp format. Output data is stored in *.mat files (Matlab®). Software enables also automatic removing error and calibration pixels from digital images obtained using digital camera.

Binary Software License Image Info Extractor Professional

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Organelle Extractor

The package of m-files serves as a tool for segmentation of time-stable objects (mainly object spread functions of non-movable diffracting and autofluorescent organelles of living cells) from bright-field transmission microscopic z-stack. For each segmented object at each z-stack level, it enables to find focal plane of the observed object and all isocontours, which correspond to intensities of Airy diffraction patterns down to the core of the object (mainly organelles themselves). Finally, each segment is reconstructed in 3D space.

Binary Software License Organelle Extractor

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