Actual
I am leaving CMP (CTU in Prague) after almost 8 years;
I wish you only the best (not only in your research)!
We have organised ISBI 2019 workshop and presented results of ANHIR challenge.
The ANHIR image registration challenge went to final phase.
The webpage for ANHIR image registration challenge is up and running.
Our challenge proposal Automatic Non-rigid Histological Image Registration (ANHIR) has been accepted for ISBI 2019.
About me
My name is Jiří Borovec and actually I am a PhD candidate at CMP supervised by prof. Jan Kybic. My work is focused on Medical imaging and Computer vision, my research topic is
Other field that I am interested in are: Computer vision, Machine Learning, Mobile robotic
Research & Grants
Selected presentations and posters:
- (2019) Automatic Non-rigid Histological Image Registration challenge: Workshop.
- (2018) Benchmarking of image registration methods for differently stained histological slides.
- (2018) Fast registration by boundary sampling and linear programming.
- (2018) PhD defence on "Analysis of microscopy images"
- (2018) Image segmentation and BPDL in microscopy.
- (2017) Detection and localization of Drosophila egg chambers in microscopy images.
- (2016) BPDL for gene expression representation in drosophila imaginal discs.
- (2015) Fast registration of segmented images by normal sampling.
- (2014) jSLIC: superpixels in ImageJ.
- (2014) Automatic Simultaneous Segmentation and Fast Registration of Histological Images.
- (2013) Fully automatic segmentation of stained histological cuts.
Funding and Grants:
- Conference grant for Early Career Investigators working in ITCs; (2019) NEUBIAS, COST.
- Travel award ; (2017) MICCAI sociaty.
- NII intership "Automatic analyses microscopy images." (2017) National Institute of Informatics.
- SGS15/154/OHK3/2T/13 "Registration and segmentation histological section." (2015-2016) Czech Technical University in Prague.
- 14-21421S "Automatic analysis of spatial gene expression patterns." (2014-2016) Czech Science Foundation [PI J.Kybic].
- 14-10440S "Automatic analysis of microscopy images of Langerhans islets." (2014-2016) Czech Science Foundation [PI J.Svihlik].
- SGS12/190/OHK3/3T/13 "Registration, segmentation, detection and classification algorithms for biomedical image processing." (2012-2014) Czech Technical University in Prague [PI J.Kybic].
- P202/11/0111 "Automatic analysis of light and electron microscopy neuronal data." (2011-2014) Czech Science Foundation [PI J.Kybic].
Software & Source code
- pyImSegm - general superpixel segmentation & center detection & region growing
- pyBPDL - Binary Pattern Dictionary Learning algorithm
- BIRL - Benchmark on Image Registration methods with Landmarks
- ANHIR - Automatic Non-rigid Histological Image Registration challenge
- jSLIC & image segment. plugin for ImageJ
- CIMA Dataset - stain histology slices with landmark annotations
Intern-ships [academic]
03/2017 - 08/2017 National Institute of Informatics (NII), Tokyo, Japan
07/2012 - 11/2012 Centro de Investigación Médica Aplicada (CIMA), Pamplona, Spain
03/2011 - 08/2011 Institut de Recherche en Informatique de Toulouse (IRIT) on Project NAVIG , Toulouse, France
Teaching & Reviewing
Teaching exercises: Reviewing for:- conferences: ISBI; ICIP; EMBC; DC-BIOSTEC (program committee)
- journals: IEEE Transactions on Cybernetics; IEEE Journal of Biomedical and Health Informatics; PLOS ONE; IEEE Signal Processing Letters; Journal of Applied Research and Technology; Journal of Circuits, Systems and Computers
Education
2011 - 2018
PhD in computer science at CMP, CTU in Prague, Czechia
Doctoral hesis: Analysis of microscopy images
2009 - 2011
Diplom Master (French) et Ing. (Czech), IUP Systemes Intelligents, UPS Toulouse III, France; and FM, TU of Liberec, Czech Rep.
Master thesis: Fusion of heterogeneous data for better positioning of visually impaired pedestrians
since 2014 MOOC platforms (Massive Open Online Courses - Coursera, edX, Udacity)
- Machine Learning (Coursera, Stanford University)
- Control of Mobile Robots (Coursera, GeorgiaTech University)
- Artificial Intelligence Planning (Coursera, University of Edinburgh)
- Autonomous Navigation for Flying Robots (edX, Technische Universität München)
- Biomedical Imaging (edX, University of Queensland)
- Linear and Discrete Optimization (Coursera, EPFL)
- Introduction to Computer Science and Programming Using Python (@edX, MIT)
- Programming Mobile Applications for Android (Coursera, University of Maryland)
- An Introduction to Interactive Programming in Python (Coursera, Rice University)
- Introduction to Cloud Computing (edX, IEEE)