Laboratory of experimental complex systems (LECOS)
Past half-year was the most successful in the history of the laboratory. The highlight of this
period were three invited lectures by Prof. Štys and Dr. Rychtáriková at IBM Research in
Zurich on topics: (1) Measures in Information Space: Point Information Gain Entropy
Density and Rényi entropy in Image analysis, Experiments with fish behavior, swarm
Intelligence, (2) Low discriminability limits in brightfield microscopy and liquid
chromatography: Data handling aspects and Imaging examples and (3) Chemical SelfOrganisation modelling, Cellular Automata and Low Noise Limits for natural processes.
From the individual results I chose:
1. We have completed work on analyzing the properties of Point Information Gain (PIG), Point
information Gain Entropy and Point Information Gain Entropy Density. We managed to
explain why at α = 2 is the dependence of the number of points on the value PIG linear.
The article was completed: Rychtarikova R.., Korbel J., Machacek P., Cisar P., Urban J. and
Stys D., Point information gain, point information gain entropy and point information gain
entropy density as measures of semantic and syntactic information of multidimensional
discrete phenomena, http://arxiv.org/pdf/1501.02891v4.pdf and submitted to IEEE Trans.
Inf. Theory
The dependence of the number of points on the value PIG at α=1 for Lévy, Gaussian and
Cauchy discretized distribution
The dependence of the number of points on the value PIG for Lévy discretized distribution
for different values of α (0.1, 0.5, 0.99, 2, 2,5 a 3)
2. We have advanced in the analysis of behaviour of the model Belousov-Zhabotinsky
reaction hodgepodge machine in the presence of noise and we gradually publish partial
results. Among others, we clarify some basic knowledge on the impacts of levels on the
system behaviour and found the boundary continuum of behaviour (semi-continuous
system). We found that the behaviour of de facto discreet and truly diffuse is a qualitative
difference and that there is a real possibility that the majority of published simulations of
systems of differential equations is affected by this fact. Articles: Stys D., Rychtarikova R.,
Nahlik T., Zhyrova A. and Papacek S., Model of the Belousov-Zhabotinsky reaction part 1:
Influence of the ignition constants, http://arxiv.org/pdf/1507.08783v1.pdf a Stys D.,
Rychtarikova R., Nahlik T., Zhyrova A. and Papacek S., Model of the Belousov-Zhabotinsky
reaction Part 2: Central role of the internal excitation growth rate,
http://arxiv.org/pdf/1507.08789v1.pdf were sent to the LCNS collection. We are
completing a key article of the hodgepodge model with noise and the article will be sent
during November.
In the event that the hodgepodge machine has allowed only 7 levels, the whole simulated
surface will not be covered (a). When we increase the number of levels to 8, which
corresponds to the number of points in the area, the surface is covered (b). Limit set is
similar to the experimentally observed behavior well at 280 levels (c) and at 2800 levels will
only increase the smoothness of spirals (d). With more than 24 levels the behavior and
structure of the limit set depends only on the mathematical description of the model.
During summer school, we tested a number of other models, including those that are
similar to the reaction-diffuse systems. Also here we found a strong dependence on the
number of levels. For reasons of time, we decided not to study semi-continuity in these
systems.
3. In the field of high resolution microscopy we completed and verified analysis of one cell
and perform a three-dimensional reconstruction of objects that do not change during the
measurement. An article describing the results is ready and will be sent by the end of
November. Also patent application was submitted: Štys, D., Rychtáriková, R., Náhlík, T.,
Urban, J., Císař, P., 2015. Method of acquisition of microscopic slides and their subsequent
processing and apparatus for performing this method, patent application no. PV 2015-434.
Three-dimensional reconstruction of the cell interior. From left to right red, green and blue
channel, upper line diffractive objects, bottom line autofluorescence and constructive
interference. Intensity observed at a given point is a color range. In the red and blue
channels, where no averaging is, we found more objects than in the green, where the
averaging occurs. This shows that the method is not affected by noise (then it would be
advantageous averaging), but are detected real signals.
4. We have also made a number of other experiments and simulations, we have prepared and
submitted several articles and developed and validated several algorithms.
Laboratory of Signal and Image Processing ( LoSIP )
BioWES:
The paper 'BioWes - From Design of Experiment, through Protocol to Repository, Control,
Standardization and Back-Tracking' was sent on request to BioMedical Engineering OnLine, open
access, peer-reviewed journal that is dedicated to publishing research in all areas of biomedical
engineering (impact factor is 1.43). Currently the paper is on reviewing process.
Dmytro Soloviov have lead the Summer School 2015 project, 'Extending functionality of software
for gathering and sharing scientific data'. The main goal of the project was to create the prototype
of BioWes Web API which can serve as single entry point to the database for clients (Desktop, Web
and custom clients) and modules. The initial version of API web service is implemented using
Python programming language with Flask framework and Pymssql library (Microsoft SQL database
driver). All the communications with API are done with HTTP requests. JSON is used as a
request/response protocol. Several 'GET' HTTP methods are implemented: information about
users, specific user, number of users, templates, specific template, number of templates, protocols,
specific protocol, number of protocols which can be used for gathering statistical information
about the system usage. Example clients for showing statistical information are implemented in
Python, PHP, and JavaScript languages. Every language which is able to send HTTP requests and
parse JSON can be used to create a tools using BioWes Web API.
Img 1. Uploaded Protocols by author (Python).
Img 2. Number of Protocols uploaded during the Summer School (Python).
Img 3. Protocol / Template uploading dynamics (PHP).
BioWES, the system for management of experimental data and metadata is in the last phase of
development. The system was successfully tested during the summer school and the improvement
based on student comments are going to be implemented. Mobile version of the system was
developed for mobile devices. I tis designed to perform field experiments. The system will further
developer in the frame of AQUAEXCEL2020 project and is going to be presented at Aquaculture
Europe 2015 conference.
Biomonitoring:
The article describing the novel approach and the IREF system for 3D fish tracking in indoor tanks
was revised after receiving the reviewers comments and later accepted by Aquacultural
Engineering journal.
Pautsina A., P. Císař, D. Štys, B. F. Terjesen, and Å. M. O. Espmark. 2015. Infrared reflection system
for indoor 3D tracking of fish. Aquacult. Eng. 69:7-17 [doi:10.1016/j.aquaeng.2015.09.002]. (IF
2014 = 1.181)
The experiments studying the effect of epinephrine on the crayfish cardiac activity were held in
cooperation with the colleagues from the Laboratory of Ethology of Fish and Crayfish and Robert
Huber, Ph.D. from Bowling Green State University, USA. The combined recording of crayfish
cardiac activity was done using the NICCAM and ECG systems. The analysis of the experimental
data is currently in progress.
The analysis of crayfish cardiac activity data using FFT based signal processing method was done
during the Summer School project at the Institute of Complex Systems, Nove Hrady. The
developed method included the signal noise filtering using Butterworth bandpass filter on the
preprocessing stage and analysis of the signal frequency spectrum obtained using FFT. The results
of data processing showed distinguishable spectra of the cardiac activities before and during the
treatments with the selected natural and artificial stimuli. Also they showed the potential
possibility of classification among the stimuli based on the response cardiac activity spectra. The
successful outcomes of the project allow considering the Fourier analysis of crayfish cardiograms a
promising method for crayfish-based water quality monitoring, particularly, for application in a
biological early warning systems.
Crayfish burrows analysis – for the project „analysis of crayfish burrowing“ supervised by Antonín
Kouba, the 3D scanning of the gypsums casts and the calculation of volume was realized. The
scanning was realized in the cooperation with Department of cybernetics in Plzen.
Analysis of fish behavior influenced by drugs – for the project analyzing fish behavior influenced
by drugs supervised by Daniel Červený, automatic detection of single fish in aquarium in progress.
The outcome of the task is the information about fish position in defined regions and total length
of the trajectory.
Project proposal „Fish E-farming“ was prepared and submitted to Horizon2020-FET OPEN call. The
project is focused on the analysis of fish behavior and appearance in fish tanks and cages. The fish
identification and early fish disease detection was proposed in the project in the cooperation with
partners from Norway (NOFIMA), Austria (PLUS) and Spain (ULPGC).
The US patent was granted. The patent describes new yeast tribe and screening method. The
patent was granted after 10 years of preparation.
Image processing and Digital calibration:
PhotoChamber + Control Software (PCCSW)
During third period LoSIP team continued on developing photo chamber prototype. Photochamber
is used for taking images of objects by exactly defined light conditions. Light is very important
parameter for color evaluation of taken images. Intensity of light can be set in specified range. In
addition, weight of the object can be measured and saved together with image. PCCSW is still in
development, but ready for use with our Photochamber prototype.
Photochamber prototype
Photochamber control software
Title: Application of Machine Vision Systems in Aquaculture with Emphasis on Fish: State-of-theArt and Key Issues

Traditional methods are usually time-consuming, expensive, labour and invasive. Using
rapid, inexpensive and non-invasive methods is therefore important and desirable. Optical
sensors and Machine Vision System (MVS) provide the possibility of developing faster,
cheaper and non-invasive methods for in-situ and after harvesting monitoring of quality in
aquaculture.
Title: Automated Multiple Fish Tracking in Three-Dimension Using a Structured Light Sensor

Studies about trajectory are usually based on tracking in two-Dimensional (2D)
environments; however, most organisms are included in three–Dimensional (3D)
environments, which influence ecological interactions extensively. Furthermore, in most 2D
image analysis, occlusion of fish is a frequent problem for analysis of fish tracking and
ultimately their behaviour. Recently, sensors based on 3D single point imaging technology,
which can provide geometric information of 3D environment with high frame rate in realtime inexpensively have been developed. These sensors practically provide the opportunity
to develop an affordable tracking system to study multiple fish movement in real-time.
Contact-less determination of tank flow and the simulation – during the summer school project,
the work on the system for modeling and determination of the flow in the fish tank started. The
aim is to develop contactless system for determination of the speed and direction of flow and its
simulation depending on different tank geometry. The work is part of the AQUAEXCEL2020 project.
The project will be realized in cooperation with SINTEF (Norway).
Mass Spec:
Mass Spectra Estimator Software (Spectrimator)
This software is at a beginning of creation process. It should help researchers to find known
substance (known structure) in mass spectrometry measurement. Few software, which do similar
work, already exist, but no one uses probabilistic approach. This should make Masstimator unique.
Obr. Masstimator main window design
Aquaponics:
During the summer school 2015, Antonín Bárta and Pavel Souček led Aquaponics project called:
Design, testing and automation of aquaponics systems. Firstly was created 3D model in Google
SktechUp for better understanding of water flow and volumes of aquariums and grow towers. After
3D model was finnished, we continue with construction part. Vertical aquaponics systems
conected with mini pc (Arduion and Raspberry) for continous measurement of pH, EC, DO and
temperature levels was created. Online view is now available at: http://160.217.215.134:8080/ap/
In the days of (8. – 13. 9. 2015) I attended Aquaponics Training school in Iceland University, under
the COST Action FA1305 EU Aquaponics hub. Design and construction of aquaponics farm was one
of the main topic. Members of COST action were presenting ideas and projects. Four projects were
selected as relevant topics from cca twenty presentations. Antonin Barta´s project – Aquaponics
Reality Show was one of them. Institute of Complex Systems and FFPW activities were
disseminated.