Institute of complex systems

Institute of complex systems was established as one of the four institutes of the faculty in 2012.The main aim of the institute is the research in the field complex systems and creation of the closed loop cycle from the experiment design over experimentrealization, data processing and analysis till the data management.


The laboratory is focused on the processing and analysis of the discretized signals and images, especially from the biological (biochemical, biophysical) measurements. An integral part is the description of the actual measuring process in terms of measurement theory, representations of the fundamental attributes of measurement, and data formats. Laboratory provides service activities dedicated tasks, implementation of custom solutions and collaboration with other laboratories of the Institute of Complex Systems.


Key activities:

  • image segmentation
  • operations of mathematical morphology
  • noise filtering
  • conversion of data formats
  • color space transformations
  • calibration of digital cameras
  • design and implementation of the systems for objects detection and tracking

Mass Spectrometry:

Long term project encapsulate the whole information flow from the measurement itself to the information and knowledge data mining. It consists of the processing and analysis of mass spectrometry measurement datasets, development, testing, and implementation of methods from artificial intelligence.
The project offers:
  • Solution for the mathematical description of the dataset model, consistent with the theory of measurement.
  • Unambiguous definitions of the fundamental terms of resolution, resolving power, distinguishability and discriminability, accuracy, precision.
  • Novel approach to the chemical noise filtration based on probabilistic theory and digital data acquisition.
  • Mass peak deconvolution and chromatographic peak decomposition.
  • Time alignment, similarity metrics and reliability factors.
  • This project is done via collaboration with Nofima, the Norwegian Institute of Food, Fisheries and Aquaculture Research, and Institute of Microbiology ASCR.

BioWes:The project is aimed at creating a system for the management of experimental data and metadata. It is a complete solution from design protocol experiment, through the implementation of an experiment to sharing and retrieval of data.

The basic functionality of the system:

  • Local data storage - data + metadata.
  • Support for arbitrary data format.
  • Electronic protocol experiment and its re-usability.
  • Direct connection of experimental data and experiment description.
  • Support of standardized terminology (Bioportal).
  • Automatic retrieval of the measurement device settings.
  • Easy and user friendly sharing.
  • Searching function in experiments metadata.
  • Specialized plugin modules for specific data processing.

A test version of the system is available on the project website

This project is done via collaboration with DataPartner, University of Vienna, and Aquaexcel consortium.


This project is focused on monitoring of water quality based on fish and crayfish, and development of the system for fish shoal motion tracking and analysis:

  • Crayfish cardiac activity monitoring.
  • Fish and crayfish motion tracking.
  • 24h/day recording.

This project is done via collaboration with Nofima, the Norwegian Institute of Food, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Laboratory of Ethology of Fish and Crayfish at FFPW of the University of South Bohemia, and Aquaexcel consortium.

 Image Processing

Wide complementary subtopics are under solution in the image processing and analysis tasks:

  • Fish and seahorses skin color changes evaluation.
  • Segmentation of fluorescence microscopy images.
  • Time lapse phase contrast micro-photography and growth curve estimation.
  • Subtractive imaging in confocal fluorescence microscopy.
  • Image registration.

These project are done via collaboration with University of Vienna, Institute of Microbiology ASCR, University of Las Palmas, and laboratories of Institute of Complex Systems.

Digital Calibration

This long term minor project is focused on testing and calibration of the digital image capturing devices:

  • Color representation.
  • Resolution, discriminability, distinguishability.
  • Bit depth, sampling, quantization.
  • Image file formats.

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