Vladimír Ulman born 1st April 1980 in Pilsen in Czechoslovakia married, 2 children researcher, project leader ORCID: 0000-0002-4270-7982

Department

IT4Innovations National Supercomputing Center
VSB - Technical University of Ostrava,
Studentská 6231/1, 708 00 Ostrava-Poruba,
Czech Republic
https://www.it4i.cz/

Centre for Biomedical Image Analysis
Faculty of Informatics, Masaryk University
Botanická 68a, 602 00 Brno,
Czech Republic
http://cbia.fi.muni.cz/

Central European Institute of Technology
CEITEC, Masaryk University
Kamenice 753/5, 625 00, Brno
Czech Republic
https://www.ceitec.eu

Contact

• Email: vladimir dot ulman et vsb dot cz
• Email: ulman et fi dot muni dot cz
• Snail mail: the addresses of the departments
• Room: 4th floor in the IT4I building Studentska street
• Room: A307 in the block A at Botanická street

Education and Academic Qualifications

• 2011: PhD, computer science, FI MU, Brno. PhD thesis: "Fast Anisotropic Filtering and Performance Evaluation Tool for Optical Flow in Biomedical Image Analysis"
• 2006: RNDr, computer science, FI MU, Brno. RNDr thesis: "Mosaicking of High - Resolution Biomedical Images"
• 2004: MSc, computer science, FI MU, Brno. Master thesis: "Image Composition"

Employment History

• 2022-present: Researcher CEITEC
• 2021-present: Researcher and group leader at IT4Innovations
• 2020-2020: Researcher IT4Innovations
• 2020-present: Researcher and teacher CBIA
• 2016-2020: Researcher/post-doc MPI-CBG
• 2009-2016: Researcher CBIA
• 2006-2014: ICT Administrator

Teaching Activities

• 2020-present: Teaching practicals on Java and Python programming languages
• 2020-present: Teaching practicals on programming in OpenGL
• 2013-2015: Teaching practicals on elementary algorithms and data structures
• 2010-2015: Teaching practicals on image processing programming in C and C++
• 2005-2015: Advising bachelor and master students' theses
• 2005: Teaching practicals on (general) programming in C and C++

Scientific and Research Activities

• 08/2022: 2 weeks, Instructor at EMBL Practical Course “Light Sheet Microscopy”
• 01/2020: 1 week EMBL Course “Deep Learning for Image Analysis”
• 09/2014: 2 weeks EMBO Practical course “Microscopy, modeling and biophysical methods”
• since 2012: CellTrackingChallenge.net
• I'm interested in biomedical image processing, analysis, and simulation. In particular, in the following topics:
• big (image) data processing
• high performance computing
• 3D+t data visualization
• simulations: generation of artificial live cell populations for testing quality of algorithms
• time-lapse sequences
• tracking
• mosaicking and processing extensive images acquired in a part-by-part manner

Links

• Cell Tracking Challenge
• HPC Workflow Manager for Fiji
• Annotate microscopy images using the Segment Anything Model (SAM)
• Mastodon – a large-scale tracking and track-editing framework for large, multi-view images
• HPC DataStore
• GitHub/xulman
• GitHub/fiji-hpc

Publications

To see my list of publications, please, click here.