Dr. Ing. Jan Schier
research associate

Biography
Publication list
Education and affiliation
Jan Schier received his M.Sc. degree in Technical cybernetics from the Faculty of Electrical Engineering, Czech Technical University in Prague in 1989 and his Ph.D. degree from the Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague in 1995. During his Ph.D. studies, he has joined the Institute of Information Theory and Automation, Academy of Sciences of the Czech Republic, Prague. Recently, he has been with the Department of Image Processing.
Visiting appointments and visiting positions
Between 1995-1997 he held several short visiting appointments with the Faculty of Electrical Engineering, Mathematics and Computer Science (EWI), TU Delft, the Netherlands. In 1998-2002 he held visiting position with the SISTA/ESAT group, KU Leuven, Belgium. In both cases, he has been contributing in the field of applied signal processing (signal processing and object detection for the FMCW collision-avoidance radar, fixed-point implementation of ADSL equalization algorithms).
Professional activities
In 2015 and 2014, he has been program co-chair of the BIOIMAGING conference, in 2012 of the BIOINFORMATICS conference, all held with the frame of the BIOSTEC conference, organized by INSTICC, Portugal. In 2018, he has chaired the Doctoral consortium of the BIOSTEC conference.
Reviewer for the Journal of Real-Time Image Processing (Springer) (2007-now)
Supervised bachelor project
Anna Mikeštíková, MFF UK (2022-2023) Analysis of mitotic spindle microscopy images captured with light-sheet
microscope
Dissemination activities
In the recent years, he has been supervising several secondary-school students in the frame of the Open science program of the Academy of Sciences. In 2023, in the frame of "Digital image processing using neural networks" internship, he supervises Luka Králík and Jan Martin Macháček. The internship has been focused on processing of scans of historical maps as well as on bioimaging data, using the convolutional neural networks.
You could also meet him at the UTIA stand at the Science Fair popularization event.
Outcomes of the supervision of the secondary-school students
- His students Jiří Wolker and Maria Šimůnková have won the 2020 Student conference in the "Formal Sciences" section with their work "Spindle segmentation in big image data using convolution network DenoiSeg".
- Jiří Wolker, under supervision of Jan Schier, has placed second in the INGENIUM category of the "Česká hlavička" competition in 2021, with his work "An interactive viewer of three-dimensional raster images". It's Czech competition rewarding talented secondary school students.
- This viewer is, as the HyperStackView utility, displayed for public use in the Python Package Index (PyPI) repository (December 2021)
- Jiiří Wolker has succsessfully defended his final project "Graphical application for interactive display of 3D raster images" at the "SPŠ stavební akademika Stanislava Bechyně" secondary school (57 pages, May 2022)
Awards
His conference paper "Automated counting of yeast colonies using the Fast Radial Transform algorithm", jointly authored with Bohumil Kovář, has been awarded the Best paper award at the BIOINFORMATICS 2011 conference, organized by INSTICC.
Books and chapters
- Biomedical Engineering Systems and Technologies, Springer (Berlin Heidelberg, 2013) Download DOI: 10.1007/978-3-642-38256-7 [2013] :
- Simple Tool for Semi-automated Evaluation of Yeast Colony Images, Biomedical Engineering Systems and Technologies, 4th International Joint Conference, BIOSTEC 2011, Revised Selected Papers, p. 110-125, Eds: Fred Ana, Filipe Joaquim, Gamboa Hugo Download [2013] :
Journal articles
- Spatio-temporal requirements of Aurora kinase A in mouse oocyte meiotic spindle building, iScience 27 Download DOI: 10.1016/j.isci.2024.110451 [2024] :
- A computer-assisted system for handheld whole-breast ultrasonography, International Journal of Computer Assisted Radiology and Surgery 14 3 (2019), p. 509-516 Download Download DOI: 10.1007/s11548-018-01909-7 [2019] :
- Automated Analysis of Microscopic Images of Isolated Pancreatic Islets, Cell Transplantation 25 12 (2016), p. 2145-2156 Download DOI: 10.3727/096368916X692005 [2016] :
- A transgenic minipig model of Hungtington´s disease, Journal of Huntington´s Disease 2 1 (2013), p. 47-68 DOI: 10.3233/JHD-130001 [2013] :
- GSFAP Adaptive Filtering Using Log Arithmetic for Resource-Constrained Embedded Systems, ACM Transactions on Embedded Computing Systems 9 3 (2010), p. 1-31 Download DOI: 10.1145/1698772.1698787 [2010] :
- Scheduling of Iterative Algorithms with Matrix Operations for Efficient FPGA Design—Implementation of Finite Interval Constant Modulus Algorithm, Journal of Vlsi Signal Processing Systems for Signal Image and Video Technology 46 1 (2007), p. 35-53 Download [2007] :
- Analysis of a normalized QR filter using Bayesian description of propagated data, International Journal of Adaptive Control and Signal Processing 13 6 (1999), p. 487-505 [1999] :
- Estimation of transport delay using parallel recursive modified Gram-Schmidt algorithm, International Journal of Adaptive Control and Signal Processing 11 5 (1997), p. 431-442 Download [1997] :
- Inverse updated systolic RLS algorithm with regularized exponential forgetting, Kybernetika 32 3 (1996), p. 209-234 Download [1996] :
- A systolic algorithm for block-regularized RLS identification, Integration, the VLSI Journal 20, p. 85-100 Download [1995] :
Other publications
- BOREC tool for processing of hyperspectral data (2021) Download [2021] :
- Technická zpráva o snı́mánı́, aplikacı́ch a knihovnách pro zpracovánı́ multispektrálnı́ho obrazu, ÚTIA AV ČR (Praha, 2019) Download [2019] :
- Software pro sledování pohybu UZ sondy (2017) Download [2017] :
- Evaluating Spatial Coverage of Breast Examination with Free-hand Ultrasound Transducer, BISTEC 2017 10th International Joint Conference on Biomedical Engineering Systems and Technologies, p. 128-133, Eds: Silveira Margarida, Fred Ana, Gamboa Hugo, Vaz Mário Download DOI: 10.5220/0006249101280133 [2017] :
- Softwarový modul projektu SONO (2014) Download [2014] :
- GenExLib C/C++ knihovna, Referenční příručka, ÚTIA AV ČR (Praha, 2014) Download [2014] :
- GenExLib C/C++ knihovna (2014) Download [2014] :
- BIOIMAGING 2014, 1st International Conference on Bioimaging Download [2014] :
- GenEx Software library for object detection in genetical analysis evaluation: User manual, ÚTIA AV ČR (Praha, 2014) Download [2014] :
- ImageJ plugin for the Snell segmentation method (2014) [2014] :
- An inexpensive system for quantitative analysis of mosaic form of Turner/Klinefelter syndrome, 18th International Microscopy Congress Proceedings Download [2014] :
- GenEx: nízkonákladový systém pro hodnocení chromozomových aneuploidií v nízkofrekvenčních mozaikách, Genetická konference GSGM 2014, p. 83-83 Download [2014] :
- GenEx Software library for object detection in genetical analysis evaluation (2014) Download [2014] :
- BIOIMAGING 2014 Proceedings of the International Conference on Bioimaging, SCITEPRESS – Science and Technology Publications (Lisabon, 2014) [2014] :
- BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, SciTePress (Vilamoura, Algarve, 2012) [2012] :
- Signal Selection Tool, ÚTIA AV ČR, v.v.i (Praha, 2012) Download [2012] :
- BIOINFORMATICS 2012, International Conference on Bioinformatics Models, Methods and Algorithms [2012] :
- BIOINFORMATICS 2012, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, SciTePress – Science and Technology Publications (Algarve, 2012) [2012] :
- Automated Detection of Interphase and Metaphase Nuclei in the FISH Images, BIOINFORMATICS 2012, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, p. 347-350, Eds: Schier Jan, Correia Carlos, Fred Ana, Gamboa Hugo DOI: 10.5220/0003797703470350 [2012] :
- Image Processing for Automated Analysis of the Fluorescence In-Situ Hybridization (FISH) Microscopic Images, Convergence and Hybrid Information Technology, p. 622-633 Download [2011] :
- A semi-automatic software tool for batch processing of yeast colony images, Proceedings of the Eighth IASTED International Conference on Signal Processing, Pattern Recognition, and Applications, p. 206-212 Download [2011] :
- Automated counting of yeast colonies using the Fast Radial Transform algorithm, BIOSTEC 2011 4th International Joint Conference on Biomedical Engineering Systems and Technologies, p. 22-27, Eds: Pellegrini Marco, Fred Ana, Filipe Joaquim, Gamboa Hugo Download DOI: 10.5220/0003129000220027 [2011] :
- Yeast Colony Counter (2010) [2010] :
- Using Matlab in quantitative analysis of yeast growth, Technical Computing Prague 2009, p. 1-9 Download [2009] :
- Counting of yeast colonies in Petri dish images (2009) [2009] :
- Preprocessing of images of Petri dishes (2009) [2009] :
- Vyhodnocování růstu kolonií kvasinek Saccharomyces cerevisia s použitím akcelerátoru Uni1P/DX64 (2008) [2008] :
- Rapid Prototyping Platform For Reconfigurable Image Processing, Technical computing Prague 2008. 16th annual conference proceedings, p. 62-62 Download [2008] :
- Configuration System for a DSP/FPGA-Based Embedded Accelerator, Digital Technologies 2007 Proceedings, p. 1-4 [2007] :
- Kompresní algoritmy a jejich implementace, ÚTIA AV ČR (Praha, 2007) [2007] :
- Kompresní algoritmy a jejich implementace (2007) [2007] :
- Configuration System for a DSP/FPGA-Based Embedded Accelerator, Digital Technologies 2007 Book of Abstracts, p. 32-33 [2007] :
- Simulink Model Converter for Embedded Video Accelerator, Technical Computing Prague 2007, p. 79-79 [2007] :
- Identifikace limitací dosavadních technologií v kontextu projektu VLAM, ÚTIA AV ČR (Praha, 2007) [2007] :
- A DSP/FPGA-based accelerator for video, Digital Technologies 2006, p. 1-5 [2006] :
- Efficient FPGA Implementation of Equalizer for Finite Interval Constant Modulus Algorithm, IEEE Symposium on Industrial Embedded Systems - IES 2006, Proceedings of, p. 1-10 [2006] :
- A DSP/FPGA-based accelerator for video processing, Digital Technologies 2006 Book of Abstracts, p. 13-13 [2006] :
- Simulink as Tool for Prototyping Reconfigurable Image Processing Applications, Technical computing Prague 2006. 14th annual conference proceedings, p. 52-57 [2006] :
- FPGA Implementation of Adaptive Filters based on GSFAP using Log Arithmetic, Proceedings of The 2006 IEEE Workshop on Signal Processing Systems Design and Implementation, p. 342-347, Eds: Badawy W., Boumaiza S. [2006] :
- Efficient Floating-Point Implementation of High-Order (N)LMS Adaptive Filters in FPGA, Reconfigurable Computing: Architecures and Applications. Proceedings of the Second International Workshop ARC, p. 311-316, Eds: Bertels K., Cardoso J. M. P., Vassiliadis S. [2006] :
- Optimization of finite interval CMA implementation for FPGA, Proceedings of the IEEE Workshop on Signal Processing Systems. SiPS 2005, p. 1-6 [2005] :
- Optimization of Finite Interval CMA Implementation for FPGA, ÚTIA AV ČR (Praha, 2005) [2005] :
- FPGA implementation of Finite Interval CMA, Proceedings of the first annual IEEE BENELUX/DSP Valley Signal Processing Symposium. SPS-DARTS 2005, p. 97-100, IEEE (Antverpy, 2005) [2005] :
- Reconfigurable image processing architecture, ICGST International Conference on Graphics, Vision and Image Processing. GVIP-05, p. 1-6 [2005] :
- Reconfigurable image processing architecture with simulink prototyping support, Technical Computing Prague 2005. 13th Annual Conference Proceeding, p. 1-4, Eds: Moler C., Procházka A., Walden B. [2005] :
- Using logarithmic arithmetic to implement the Recursive Least Squares (QR) algorithm in FPGA, Field-Programmable Logic and Applications. 14th International Conference FPL 2004. Proceedings, p. 1149-1151 [2004] :
- Architecture design for FPGA implementation of finite interval CMA, Proceedings of the 12th European Signal Processing Conference, p. 1-4, Eds: Hlawatsch F., Matz G., Rupp M. [2004] :
- FPGA implementation of recursive QR update using LNS arithmetic, Proceedings of the 4th IEEE Benelux Signal Processing Symposium, p. 1-4 [2004] :
- QR-RLS - Celoxica RC1000 Demo. (Program), ÚTIA AV ČR (Praha, 2003) [2003] :
- Logarithmic arithmetic for real data types and support for Matlab/Simulink based rapid-FPGA-prototyping, Proceedings of the International Parallel and Distributed Processing Symposium. IPDPS 2003, p. 1-6, IEEE Computer Society Press (Los Alamitos, 2003) [2003] :
- FPGA Prototyping Using Extensions to MATLAB/Simulink, UK ACM SIGDA 3rd Workshop on Electronic Design Automation, p. 1-3, University of Southampton (Southampton, 2003) [2003] :
- Using logarithmic arithmetic for FPGA implementation of the Givens rotations, Proceedings of the Sixth Baiona Workshop on Signal Processing in Communications, p. 199-204, Eds: Mosquera C., Perez-Gonzales F., Universidade de Vigo (Vigo, 2003) [2003] :
- MATLAB/Simulink based methodology for rapid-FPGA-prototyping, Field-Programmable Logic and Applications. Proceedings of the 13th International Conference, p. 984-987, Eds: Cheung P. Y. K., Constantinides G. A., de Sousa J. T., Springer (Berlin, 2003) [2003] :
- Logarithmic Arithmetic for Real Data Types and Support for MATLAB/SIMULINK Based Rapid-FPGA-Prototyping, ÚTIA AV ČR (Praha, 2002) [2002] :
- Using the System-C library for bit-true simulations in MATLAB, MATLAB 2002. Sborník příspěvků 10. ročníku konference, p. 497-504, VŠCHT (Praha, 2002) [2002] :
- Implementing Advanced Equalization Algorithms using Simulink with Embedded Alpha AXP Coprocessor, ÚTIA AV ČR (Praha, 2001) [2001] :
- Implementing advanced equalization algorithms using Simulink with embedded Alpha AXP coprocessor, Fifth IMA International Conference on Mathematics in Signal Processing, p. 11-14, University of Warwick (Warwick, 2000) [2000] :
- The COLORADO multistatic FMCW radar system, European Microwave. Proceedings, p. 449-454, Europeam Microwave Association (London, 1998) [1998] :
- PTT and OTT Enhancement: Part 2. Final Report, Technical University (Delft, 1998) [1998] :
- Robust adaptive controller with fine grain parallelism, Preprints of the IFAC Workshop on Adaptive Systems in Control and Signal Processing, p. 436-441, IFAC (Glasgow, 1998) Download [1998] :
- Fast fixed-point algorithm for estimation of the system time lag, Preprints of the 3rd European IEEE Workshop on Computer-Intensive Methods in Control and Data Processing, p. 151-154, Eds: Rojíček J., Valečková M., Kárný M., Warwick K., ÚTIA AV ČR (Praha, 1998) [1998] :
- Numerical Analysis of a Normalized QR Filter Using Probability Description of Propagated Data, ÚTIA AV ČR (Praha, 1998) [1998] :
- HSLA 3D Monitor Package, ÚTIA AV ČR (Praha, 1998) [1998] :
- HSLA DSP Package, ÚTIA AV ČR (Praha, 1998) [1998] :
- Results of the Global Probability Analysis Approach, ÚTIA AV ČR (Praha, 1998) [1998] :
- Rapid prototyping of adaptive control algorithms on parallel multiprocessors, Signal Processing Symposium, p. 115-118, IEEE (Leuven, 1998) Download [1998] :
- Real-time signal processing for an obstacle warning radar, Signal Processing Symposium, p. 167-170, IEEE (Leuven, 1998) [1998] :
- PTT and OTT Enhancement - Final Report, University of Technology (Delft, 1996) [1996] :
- Object tracking and tracing for multi-static FM-CW radar - incremental approach, Computer-Intensive Methods in Control and Signal Processing. Preprints of the 2nd European IEEE Workshop CMP'96, p. 151-154, Eds: Berec L., Rojíček J., Kárný M., Warwick K., ÚTIA AV ČR (Praha, 1996) [1996] :
- Colorado System: Peak Tracking and Tracing Algorithm and its Parallel Implementation, Technische Universiteit (Delft, 1995) [1995] :
- A systolic algorithm for block-regularized RLS identification, Algorithms and Parallel VLSI Architectures III, p. 49-60, Eds: Moonen M., Catthor F., Elsevier (Amsterdam, 1994) [1994] :
- Parallel Algorithms for Robust Adaptive Identification and Square-Root LQG Control Synthesis. Dr.Dissertation, FJFI ČVUT (Praha, 1994) Download [1994] :
- A systolic algorithm for the block-regularized RLS identification. Abstract, Algorithms and Parallel VLSI Architectures. Abstracts, p. -, Katholieke Universiteit (Leuven, 1994) [1994] :
- Systolic algorithms for adaptive control, implementation in the Matlab environment, Distributed Control. Proceedings, p. 103-113, ČVUT FEL (Praha, 1994) [1994] :
- The block regularized linear quadratic optimal controller, IEE International Conference on Control '94, p. 1254-1259, IEE (London, 1994) Download [1994] :
- The systolic regularized linear quadratic controller, Computer-Intensive Methods in Control and Signal Processing, p. 133-140, Eds: Kulhavá L., Kárný M., Warwick K., ÚTIA AV ČR (Praha, 1994) [1994] :
- The Systolic Regularized Linear Quadratic Controller, ÚTIA AV ČR (Praha, 1994) [1994] :
- Systolic Algorithms for Adaptive Control, Implementation in the Matlab Environment, ÚTIA AV ČR (Praha, 1994) [1994] :
- A Systolic Algorithm for the Block-Regularised RLS Identification, ÚTIA AV ČR (Praha, 1994) [1994] :
- The Block Regularised Linear Quadratic Optimal Controller, ÚTIA AV ČR (Praha, 1994) [1994] :
- Fast quality evaluation in preliminary tuning of adaptive controller, Progress in Transputer Computing Technology, p. 33-44, Eds: Kulhavá L., Schier J., Kárný M., ÚTIA AV ČR (Praha, 1993) [1993] :
- Progress in Transputer Computing Technology, ÚTIA AV ČR (Praha, 1993) [1993] :
- A Systolic Block-Regularized Algorithm for the Recursive Least Squares Identification with the Inverse Update, ÚTIA AV ČR (Praha, 1993) [1993] :
- Estimation of Transport Delay Using Parallel Recursive Modified Gramm-Schmidt Algorithm, ÚTIA ČSAV (Praha, 1992) [1992] :
- Tools for Implementation of Parallel Algorithms for Adaptive Control and Signal Processing, 4th IFAC International Symposium on Adaptive Systems in Control and Signal Processing. ACASP '92, p. 727-730, Eds: Landau I. D., Dugard L., M'Saad M., Laboratoire d'Automatique (Grenoble, 1992) [1992] :
- A Parallel Algorithm for Estimation of the System Structure, Binary Control '92, p. -, Czech Technical University (Prague, 1992) [1992] :
- CAD systémů řízení s transputery, TRANSPUTER CS'92. Zborník prednášok, p. -, Ústav počítačových systémov (Bratislava, 1992) [1992] :