Publication Records

Selected publication/outcome records

Prediction of localization and interactions of apoptotic proteins (2009)
Filtering with Anisotropic 3D~Gabor Filter Bank Efficiently Computed with 1D~Convolutions without Interpolation (2010)
Prediction of localization and interactions of apoptotic proteins (2009)
Improving Accuracy of Optical Flow of Heeger's Original Method on Biomedical Images (2010)
Boundary Treatment for Young-van Vliet Recursive Zero-Mean Gabor Filtering (2011)
Fast Anisotropic Filtering and Performance Evaluation Tool for Optical Flow in Biomedical Image Analysis (2011)
Tool for Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy (2011)
Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy (2012)
Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body co-localization in DNA lesions (2013)
CytoPacq v2.0 (2013)
Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations (2013)
Cell tracking accuracy measurement based on comparison of acyclic oriented graphs (2015)
A Benchmark for Comparison of Cell Tracking Algorithms (2014)
NON-RIGID CONTOUR-BASED TEMPORAL REGISTRATION OF 2D CELL NUCLEI IMAGES USING THE NAVIER EQUATION (2014)
PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage (2014)
Coilin is rapidly recruited to UVA-induced DNA lesions and gamma-radiation affects localized movement of Cajal bodies (2014)
On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy (2014)
Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation (2014)
HP1B-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs (2014)
On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy (2015)
Localized movement and morphology of UBF1-positive nucleolar regions are changed by gamma-irradiation in G2 phase of the cell cycle (2015)
RNA-dependent disassembly of nuclear bodies (2016)
TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells (2015)
Texture Analysis of 3D Fluorescence Microscopy Images Using RSurf 3D Features (2016)
Localized Movement and Levels of 53BP1 Protein Are Changed by gamma-irradiation in PML Deficient Cells (2016)
Vascular Network Formation in Silico Using the Extended Cellular Potts Model (2016)
Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections (2016)
Automatic Detection of Laser-Induced Structures in Live Cell Fluorescent Microscopy Images Using Snakes with Geometric Constraints (2016)
MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy (2017)
Automatic Detection and Segmentation of Exosomes in Transmission Electron Microscopy (2016)
Virtual cell imaging: A review on simulation methods employed in image cytometry (2016)
Non-rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model (2018)
Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis (2017)
FTutor: An Interactive Guide to the Fundamentals of Frequency Analysis (2017)
Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia (2017)
POTENTIAL OF hiPSCs DERIVED FROM DIFFERENT CELL TYPES TO DIFFERENTIATE INTO FUNCTIONAL ENDOTHELIAL CELLS (2017)
Hematopoietic developmental potential of human pluripotent stem cell lines is accompanied by the morphology of embryoid bodies and the expression of endodermal and hematopoietic markers (2017)
Self-Renewing Early Lung Epithelial Progenitor Cells Differentiated From Human Embryonic Stem Cells (2017)
Multimodal Simulations in Live Cell Imaging (2017)
Image-based surrogate biomarkers for molecular subtypes of colorectal cancer (2017)
Single image reconstruction of human faces using database of depth images (2017)
Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests (2017)
An objective comparison of cell-tracking algorithms (2017)
Reprogramming of Adult Peripheral Blood Cells into Human Induced Pluripotent Stem Cells as a Safe and Accessible Source of Endothelial Cells. (2018)
Correlation-based 2D Registration Method for Single Particle Cryo-EM Images (2017)
Standardized hiPSCs culture – vitronectin coating for cGMP compliant protocol (2017)
Segmentation of Actin-Stained 3D Fluorescent Cells with Filopodial Protrusions using Convolutional Neural Networks (2018)
Reprogramming of peripheral blood cells into hiPSCs as a source of endothelial cells (2018)
Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression (2018)
Computer-assisted engineering of hyperstable fibroblast growth factor 2 (2018)
Automatic detection of laser-induced structures in live cell fluorescent microscopy images using snakes with geometric constraints (2017)
FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia (2018)
Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia (2018)
Tubular Network Formation Process Using 3D Cellular Potts Model (2018)
Visual and Quantitative Comparison of Real and Simulated Biomedical Image Data (2019)
3-D Quantification of Filopodia in Motile Cancer Cells (2019)
How to Exploit Weaknesses in Biomedical Challenge Design and Organization (2018)
Why rankings of biomedical image analysis competitions should be interpreted with care (2018)
The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures (2018)
The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures. (2018)
Age and gender-based human face reconstruction from single frontal image (2020)
DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed (2019)
Automatic Fusion of Segmentation and Tracking Labels (2019)
The role of RNA Polymerase II contiguity and long-range interactions in the regulation of gene expression in human pluripotent stem cells. (2019)
ADC mapy ve vztahu k peritumorózní buněčné infiltraci u glioblastomu (2018)
Fast and accurate compensation of signal offset for T2 mapping (2019)
Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy (2019)
CytoPacq: A web-interface for simulating multi-dimensional cell imaging (2019)
TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images (2019)
On Generative Modeling of Cell Shape Using 3D GANs (2019)
Multimodal Point Distribution Model for Anthropological Landmark Detection (2019)
Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images (2019)
Combined therapy of perifosine and ABT-737 results in higher cytotoxic effect but also induces expression of EMT markers in colon cancer cell lines (2019)
Tumor-specific microenvironment contributes to the perifosine resistance in 3D colorectal cancer (CRC) models (2019)
Quantitative Assessment of Anti-Cancer Drug Efficacy From Coregistered Mass Spectrometry and Fluorescence Microscopy Images of Multicellular Tumor Spheroids (2019)
The Effect of Uncoated SPIONs on hiPSC-Differentiated Endothelial Cells (2019)
Drug Penetration Analysis in 3D Cell Cultures Using Fiducial-Based Semiautomatic Coregistration of MALDI MSI and Immunofluorescence Images (2019)
When Deep Learning Meets Cell Image Synthesis (2020)
Fiducial-based semi-automatic coregistration and analysis of multimodal MALDI MS and immunofluorescent data (2019)
Image-based Simulations of Tubular Network Formation (2020)
Condensed U-Net (CU-Net): An Improved U-Net Architecture for Cell Segmentation Powered by 4x4 Max-Pooling Layers (2020)
Nonstructural carbohydrate-balance response to long-term elevated CO2 exposure in European beech and Norway spruce mixed cultures: biochemical and ultrastructural responses (2017)
BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows (2020)
BIAS: Transparent reporting of biomedical image analysis challenges (2020)
Difuzní léze jater (2020)
A Behavioral Assay to Study Effects of Retinoid Pharmacology on Nervous System Development in a Marine Annelid (2019)
Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation (2020)
Akutní končetinová ischemie při konkomitantní systémové a plicní embolizaci (2020)
Lactic Acidosis Interferes With Toxicity of Perifosine to Colorectal Cancer Spheroids: Multimodal Imaging Analysis (2020)
Morfologie Corpus Callosum a klinický stav u pacientů s depresivní poruchou (2020)
Topology Preserving Segmentation Fusion for Cells with Complex Shapes (2021)
Transfer Learning in Optical Microscopy (2021)
Simulation and Synthesis in Medical Imaging (2021)
Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production (2019)
Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining (2022)
Multimodal Imaging of 3D Cell Aggregates (2021)
Implicit Neural Representations for Generative Modeling of Living Cell Shapes (2022)
Review of cell image synthesis for image processing (2022)
Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy (2023)
On-the-fly Adaptation of Patrolling Strategies in Changing Environments (2022)
Federated learning enables big data for rare cancer boundary detection (2022)
Differentiation of high grade glioma and brain metastasis using intravoxel incoherent motion MRI (2022)
Privacy risks of whole-slide image sharing in digital pathology (2023)
The Cell Tracking Challenge: 10 years of objective benchmarking (2023)
xOpat: eXplainable Open Pathology Analysis Tool (2023)
Generative modeling of living cells with SO(3)-equivariant implicit neural representations (2024)
Shedding light on the black box of a neural network used to detect prostate cancer in whole slide images by occlusion-based explainability (2023)
MAPHIS-Measuring arthropod phenotypes using hierarchical image segmentations (2024)
Gravitational Cell Detection and Tracking in Fluorescence Microscopy Data (2024)
ImgLib2 and BigDataViewer Hackathon Brno (2023)
Spatiotemporal cell surface generator (2023)
MAPHIS - Measuring arthropod phenotypes using hierarchical image segmentations (2023)
Cell Tracking based on Integer Linear Programming and Probability Scores (2024)
Why is the winner the best? (2023)
Possibilities of Using Multi-b-value Diffusion Magnetic Resonance Imaging for Classification of Brain Lesions (2024)
Antarstick: Extracting Snow Height From Time-Lapse Photography (2024)
Brain MRI Screening Tool with Federated Learning (2024)
Interpreting convolutional neural network classifiers applied to laser-induced breakdown optical emission spectra (2024)
Metrics reloaded: recommendations for image analysis validation (2024)
Understanding metric-related pitfalls in image analysis validation (2024)

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