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Peter Jurica
I am a scientific programmer, I work with researchers and consult for various businesses. I spent most of my professional career at RIKEN Brain Science Institute in Wako-shi Japan. I came to RIKEN as an ordinary software engineer, using mostly C/C++ and Microsoft COM. In the first year at RIKEN I developed a COM component based simulation framework similar to MATLAB's Simulink. My focus shifted to Python upon realizing I could recreate the system in Python in a few weeks. Most of what I do now revolves around Python.
I program with and for scientists. My favorite topics are vision neuroscience, psycho-physics and related mathematical modeling, stochastic optimization, algorithms and acceleration of methods on computers.
My MSc degree is in signal processing and neural networks. I have two years of experience as a software engineer in industry, before joining RIKEN I worked for Siemens on a platform for maintenance of a large telecom switching system with teams in a number of countries. Since I moved to research I have programmed computers of all sizes with all major operating systems. I think in Python but use many programming languages. I am always looking for new ones.
I used to experiment with two humanid robots Nao H25, record and analyze EEG, track motion using Microsoft Kinect and connect all of it using Python.


You can find more about my projects at the Human-Robot Interaction page at RIKEN. The lab where I work is called Cichocki Laboratory for Advanced Brain Signal Processing.
While supporting other researchers I often have to use MATLAB. I love Python and I wanted to make it easier to reuse my code. My ideas solidified in a form of an interpreter of m-files for Python programming language.
VisionPyg is a minimalist approach to psycho-physics using Python. VisionPyg differs from other similar tools in the amount of code and minimal dependencies. VisionPyg's core library is a single file with around 400 lines of code. Presentation of stimuli can be controlled remotely and from other programming languages, examples are available for MATLAB and R.


You can download VisionPyg from here and documentation here.

The next iteration of this project is called mPsy. The upgrade will be finished in the first half of 2015 and the source code including more tutorials and examples will be hosted at GitHub/mPsy.

Other recent projects

Most of my output is in the form of software, other packages that I am currently working on are:

CogExTools - my contribution to detection of Alzheimer's Disease and cognitive impairment. CogExTools is being developed to enable possible transition of cognitive health examination from paper to computers, tablets and handwriting digitizers.
Multi-fractal Detrended Analysis in Python - IPython notebooks, my re-implementation and optimization of Introduction to multifractal detrended fluctuation analysis in Matlab in Python.

In early 2014 I have been awarded the RIKEN Research and Technology Incentive Award 2014 for “Platform development for human-robot interaction and brain-robot interface research and smart data analysis of animal behavior”. Software for both of these projects and the recent projects above are at the moment used internally within RIKEN, they may be published in the future.

My network

I worked with the researchers of Perceptual Dynamics Lab (while based at RIKEN in Japan) between 2001 and 2011. I worked on models of adaptation in visual cortex using stochastic optimization (with Sergei Gepshtein), eye-movements and EEG with (Andrey Nikolaev and Chie Nakatani), analysis of travelling waves in brain signals (with David Alexander). Many of the projects are ongoing. Since 2011 I work with mostly mathematicians and machine learning experts at the Lab for Advanced Brain Signal Processing. A number of advancements mostly in tools for analysis and collection of time-series have been done in collaboration with Zbigniew Struzik (at the time at RIKEN). Since our encounter in 2006 at RIKEN, I closely collaborate with Sergei Gepshtein at the Salk Institute for Biological Studies on many projects that relate to low and high level biological vision (mPsy, Stochastic Tuning and others).

Publications

Jurica P, Struzik ZR, Li J, Horiuchi M, Hiroyama S, Takahara Y, Nishitomi K , Ogawa K, Cichocki A, 2018

Combining behavior and EEG analysis for exploration of dynamic effects of ADHD treatment in animal models. Journal of Neuroscience Methods 298, 24-32.

Yokota T, Struzik ZR, Jurica P, Horiuchi M, Hiroyama S, Li J, Takahara Y, Ogawa K, Nishitomi K, Hasegawa M, Cichocki A, 2018 Semi-Automated Biomarker Discovery from Pharmacodynamic Effects on EEG in ADHD Rodent Models. Scientific Reports 8 (1), 5202.


Alexander, D.M., Nikolaev, A.R., Jurica, P., S., Zvyagintsev, M., Mathiak, van Leeuwen, C., 2016

Global Neuromagnetic Cortical Fields Have Non-Zero Velocity. PLoS ONE, March 8 2016, http://dx.doi.org/10.1371/journal.pone.0148413.


Jurica, P., 2015
Multifractal analysis for all. Frontiers in Physiology, 6(27), doi: 10.3389/fphys.2015.00027


Jurica, P., Gepshtein, S., Tyukin, I., van Leeuwen, C., 2013

Sensory Optimization by Stochastic Tuning. Psychological Review, 120(4), 798-816.


Jurica, P. Valenzi S., Struzik, Z. Cichocki, A., 2015

Methods for Transition Toward Computer Assisted Cognitive Examination. Methods of Information in Medicine, 54, 256-261.

(CogExTools software)

Valenzi, S., Islam, T., Jurica, P., Cichocki, A., 2014

Individual Classification of Emotions Using EEG. Journal of Biomedical Science and Engineering, 7, 604-620.


Nikolaev, A.R., Jurica, P., Nakatani, C., Plomp, G., van Leeuwen, C., 2013

Visual encoding and fixation target selection in free viewing: presaccadic brain potentials. Front. Syst. Neurosci., 27 June 2013.


Alexander, D.M., Jurica, P., Trengove, C., Nikolaev, A.R., Gepshtein, S., Zvyagintsev, M., Mathiak, K., Schulze-Bonhage, A., Rueschere, J., Ball, T., van Leeuwen, C., 2013

Traveling waves and trial averaging: The nature of single-trial and averaged brain responses in large-scale cortical signals. NeuroImage 73, 95–-112.


Nikolaev A.R., Nakatani C., Plomp G., Jurica P., van Leeuwen C., 2012

Combined analysis of EEG and eye movements in perception research: application to change blindness. Front. Hum. Neurosci. Conference Abstract: Belgian Brain Council. doi: 10.3389/conf.fnhum.2012.210.00089.


Nikolaev A.R., Nakatani C., Plomp G., Jurica P., van Leeuwen C., 2011

Eye fixation-related potentials in free viewing identify encoding failures in change detection. NeuroImage, 56 (3), 1598--1607.


Jurica, P., van Leeuwen, C., 2009

OMPC: an open-source MATLAB(R)-to-Python compiler. Frontiers in Neuroinformatics, 3 (5), 1--9.


Kwok, H. F., Jurica, P., Raffone, A., van Leeuwen, C., 2007

Robust emergence of small-world structure in networks of spiking neurons. Cognitive Neurodynamics, 1, 39--51.



In proceedings

Shimizu K., Aminaka D., Kodama T., Nakaizumi C., Jurica P., Cichocki A., Makino S., Rutkowski TM.
Brain-robot Interfaces Using Spatial Tactile and Visual BCI Paradigms - Brains Connecting to the Internet of Things Approach
The International Conference on Brain Informatics & Health - Type II Paper: Proceedings 2015; 01/2015

Rutkowski TM., Shimizu K., Aminaka D., Kodama T., Jurica P., Cichocki A.
Brain--robot Interfaces Using Spatial Tactile and Visual BCI Paradigms - Symbiotic Brain--robot Applications
Proceedings of The 2015 International Workshop on Symbiotic Interaction (SYMBIOTIC 2015); 01/2015

Rutkowski TM., Shimizu K., Kodama T., Jurica P., Cichocki A., Shinoda H.
Controlling a Robot with Tactile Brain-computer Interfaces
Abstracts of the 38th Annual Meeting of the Japan Neuroscience Society - Neuroscience 2014; 01/2015

Shimizu K., Kodama T., Jurica P., Cichocki A., Rutkowski TM.
Tactile BCI Paradigms for Robots' Control
6th Conference on Systems Neuroscience and Rehabilitation 2015 (SNR 2015); 01/2015

Nikolaev A., Nakatani C., Jurica P., Plomp G., van Leeuwen C.
Eye movement segmentation of EEG activity related to memory encoding
20th Annual Meeting of the Organization for Human Brain Mapping (OHBM) 2014; 07/2014

Jurica P., Gepshtein S., Tyukin I., Prokhorov D. , van Leeuwen C.
Unsupervised adaptive optimization of motion-sensitive systems guided by measurement uncertainty
Intelligent Sensors, Sensor Networks and Information, 2007. ISSNIP 2007. 3rd International Conference on; 01/2008

Jurica P., Yang S.
Predictions on Trajectory and Velocity of Visually Guided Saccades Based on Gravitational Field Model of Occulomotor Movements
International Conference on Computational Cybernetics 2003.

Jurica P., Brinkers M., van Leeuwen C.
Component-based Framework for Design and Simulation of Neural Networks
KES 2002