CV

Education

• B.S. in Biomedical Engineering and Bioinformatics, Brno University of Technology, 2017
• M.S. in Biomedical Engineering and Bioinformatics, Brno University of Technology, 2019
• Ongoing PhD in Advanced Nanotechnologies and Mictotechnologies, Central European Institute of Technology, expected to finish in 2023

Work experience

• Jul 2019 - now: Research assistant: Micro and nano computed tomography
  • CEITEC BUT
  • Duties included: Work on various tasks in the X-ray micro- and nano- computed tomography workflow from practical measurements and raw data processingto preparation of final outputs for both research publications and industrial partners. Work with specialized image processing software (Avizo, VG Studio) and development of new tools in Python.
• Jul 2018 − Jul 2019: Undergraduate student: Methods for image segmentation
  • CEITEC BUT
  • Duties included: Development of a robust method for soft tissue segmentationin microCT images with focus on machine learning methods for image processing. Mainly working with Python and relevantimage processing (OpenCV, Scikit image) and deep learning(Tensorflow, Keras) libraries.
• Oct 2016 − Feb 2018: Internship: Administrative Manufacturing Support
  • Thermo Fisher Scientific
  • Duties included: Reporting, creating and maintaining VBA scripts, maintaining manufacturing databases, new employee support, maintaining 5s, realization of continuous process improvement ideas.

Skills

• Python, Matlab and R programming
• Image data processing and analysis
• Avizo, VG Studio MAX and Dragonfly software for image data analysis

Publications

Segmentation of cartilage tissue in micro CT images of mouse embryos with modified U-net convolutional neural network

MATULA, J. SEGMENTATION OF CARTILAGE TISSUE IN MICRO CT IMAGES OF MOUSE EMBRYOS WITH MODIFIED U-NET CONVOLUTIONAL NEURAL NETWORK. In Proceedings of the 25th Conference STUDENT EEICT 2019. Brno: Brno University of Technology, 2019. p. 191-194. ISBN: 978-80-214-5735-5.

X-ray microtomography–based atlas of mouse cranial development

Jan Matula, Marketa Tesarova, Tomas Zikmund, Marketa Kaucka, Igor Adameyko, Jozef Kaiser, X-ray microtomography–based atlas of mouse cranial development, GigaScience, Volume 10, Issue 3, March 2021, giab012, https://doi.org/10.1093/gigascience/giab012

Summer schools and training

• Thermo Fisher Scientific Avizo training, Berlin (Germany), 2020
• XV School on Synchrotron Radiation “Gilberto Vlaic”: Fundamentals, Methodsand ApplicationsTwo week school, Muggia (Italy), 2019

Teaching

Introduction to Medical Informatics

Obtained grants

• CEITEC BUT specific research grant, Deep learning assisted segmentation of X-ray computed tomography images, 2020