Research Activities

Employment of computers in the optimization and automation of image acquisition process, especially in microscopy

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Image restoration, reconstruction and registration tasks in biomedical imaging including subsequent fusion of image data from different modalities or different acquisition modes

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Automatic or semi-automatic segmentation and quantification of cells or cellular components acquired using various imaging techniques, especially optical and electron microscopes

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Segmentation, tracking and characterization of live cells including their interaction with neighborhood

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Registration of time-lapse image sequences of live cells or their components

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Design and computation of features suitable for bioimaging and subsequent classification using machine learning techniques

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Development of simulators for the synthesis of digital cell phantoms, virtual microscopy and virtual image detection

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Benchmarking and comparison of biomedical image analysis methods based on annotated real as well as synthetic datasets

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Human pluripotent and adult stem cell research

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Czech-BioImaging (part of Euro-BioImaging)

National Infrastructure for Biological and Medical Imaging

Years: since 1/2016
Funding: Czech Ministry of Education, Youth and Sports, Large Infrastructure Projects No. LM2015062 (2016-2019), LM2018129 (2020-2022), LM2023050 (2023-2025), CZ.02.1.01/0.0/0.0/16_013/0001775 (2017-2020), and CZ.02.1.01/0.0/0.0/18_046/0016045 (2020-2023)

Center of Excellence

Chromosome dynamics and structure during the cell cycle and during differentiation under normal and pathological conditions

Years: 1/2005 - 12/2018
Funding: Czech Science Foundation, Centre of Excellence No. LC535 (2005-2011) and No. 302/12/G157 (2012-2018)


Network of European BioImage Analysts

Years: 5/2016 - 4/2020
Funding: EU COST Action CA15124 (2016-2020) and Czech COST Support No. LTC17016 (2017-2020)

Cell Tracking Challenge

Web resource for benchmarking cell segmentation and tracking methods

Years: since 9/2012
Funding: various projects

Multimodal Segmentation and Tracking

Segmentation and tracking of live cells in multimodal images

Years: 1/2017 - 12/2019
Funding: Czech Science Foundation, Project GA17-05048S

Cell Motility Characterization

Development of reliable methods for automated quantitative characterization of cell motility in fluorescence microscopy

Years: 1/2016 - 12/2018
Funding: Czech Science Foundation, Project GJ16-03909Y