Výpis publikací

PENGO, Thomas; Kristopher E KUBOW; Angel MANCEBO; David SVOBODA a Richard W COLE. Comparison of Independent Analyses of Identical Image Sets Reveals Significant Analyst-to-Analyst Variability. Journal of Biomolecular Techniques. Association of Biomolecular Resource Facilities, 2025, roč. 36, č. 2, s. 1-30. ISSN 1524-0215. Dostupné z: https://doi.org/10.7171/3fc1f5fe.60f1999c.

NEČASOVÁ, Tereza; Daniel MÚČKA a David SVOBODA. COMPYDA: An online tool for verifying the similarity of image datasets. 2024.

NEČASOVÁ, Tereza; Daniel MÚČKA a David SVOBODA. COMPYDA: An online tool for verifying the similarity of image datasets. Online. In 2024 IEEE International Symposium on Biomedical Imaging (ISBI). Athens, Greece: IEEE, 2024, s. 1-5. ISBN 979-8-3503-1334-5. Dostupné z: https://doi.org/10.1109/ISBI56570.2024.10635415.

WIESNER, David; Julian SUK; Sven DUMMER; Tereza NEČASOVÁ; Ulman VLADIMÍR; David SVOBODA a Jelmer WOLTERINK. Generative modeling of living cells with SO(3)-equivariant implicit neural representations. Medical Image Analysis. Netherlands: Elsevier, 2024, roč. 91, č. 1, s. 1-18. ISSN 1361-8415. Dostupné z: https://doi.org/10.1016/j.media.2023.102991.

BURGOS, Ninon a David SVOBODA. Biomedical Image Synthesis and Simulation - Methods and Applications. 1st ed. Elsevier, 2022, 674 s. ISBN 978-0-12-824349-7.

WIESNER, David; Julian SUK; Sven DUMMER; David SVOBODA a Jelmer WOLTERINK. Implicit Neural Representations for Generative Modeling of Living Cell Shapes. Online. In Linwei Wang, Qi Dou, P. Thomas Fletcher, Stefanie Speidel, Shuo Li. International Conference on Medical Image Computing and Computer Assisted Intervention. Switzerland: Springer Nature Switzerland, 2022, s. 58-67. ISBN 978-3-031-16439-2. Dostupné z: https://doi.org/10.1007/978-3-031-16440-8_6.

NEČASOVÁ, Tereza; Ninon BURGOS a David SVOBODA. Validation and evaluation metrics for medical and biomedical image synthesis. In Ninon Burgos, David Svoboda. Biomedical Image Synthesis and Simulation - Methods and Applications. 1st ed. Neuveden: Elsevier, 2022, s. 573-600. The MICCAI Society book Series. ISBN 978-0-12-824349-7. Dostupné z: https://doi.org/10.1016/B978-0-12-824349-7.00032-3.

SVOBODA, David; Ninon BURGOS; Jelmer M. WOLTERINK a Can ZHAO. Simulation and Synthesis in Medical Imaging. 1. vyd. Cham: Springer, 2021, 154 s. ISBN 978-3-030-87591-6. Dostupné z: https://doi.org/10.1007/978-3-030-87592-3.

ČAPEK, Martin; Michaela BLAŽÍKOVÁ; Ivan NOVOTNÝ; Helena CHMELOVÁ; David SVOBODA; Barbora RADOCHOVÁ; Jiří JANÁČEK a Ondrej HORVÁTH. The Wavelet-Based Denoising Of Images in Fiji, With Example Applications in Structured Illumination Microscopy. Image Analysis & Stereology. International Society for Stereology & Image Analysis, 2021, roč. 40, č. 1, s. 3-16. ISSN 1580-3139. Dostupné z: https://doi.org/10.5566/ias.2432.

KOZLOVSKÝ, Martin; David WIESNER a David SVOBODA. Transfer Learning in Optical Microscopy. Online. In Svoboda D., Burgos N., Wolterink J., Zhao C. Simulation and Synthesis in Medical Imaging. LNCS 12965. Neuveden: Springer, 2021, s. 77-86. ISBN 978-3-030-87591-6. Dostupné z: https://doi.org/10.1007/978-3-030-87592-3_8.

SVOBODA, David a Tereza NEČASOVÁ. Image-based Simulations of Tubular Network Formation. Online. In 17th IEEE International Symposium on Biomedical Imaging. Neuveden: IEEE, 2020, s. 1608-1612. ISBN 978-1-5386-9330-8. Dostupné z: https://doi.org/10.1109/ISBI45749.2020.9098736.

WIESNER, David; David SVOBODA; Martin MAŠKA a Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics. Oxford University Press, 2019, roč. 35, č. 21, s. 4531-4533. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btz417.

WIESNER, David; Tereza NEČASOVÁ a David SVOBODA. On Generative Modeling of Cell Shape Using 3D GANs. Online. In Ricci Elisa, Rota Buló Samuel, Snoek Cees, Lanz Oswald, Messelodi Stefano, Sebe Nicu. Image Analysis and Processing – ICIAP 2019. LNCS 11752. Trento: Springer, 2019, s. 672-682. ISBN 978-3-030-30644-1. Dostupné z: https://doi.org/10.1007/978-3-030-30645-8_61.

EISELLEOVÁ, Lívia; Viktor LUKJANOV; Šimon FARKAŠ; David SVOBODA; Karel ŠTĚPKA a Irena KOUTNÁ. The role of RNA Polymerase II contiguity and long-range interactions in the regulation of gene expression in human pluripotent stem cells. Stem Cells International. Hindawi, 2019, roč. 2019, Article ID 1375807, s. 1-12. ISSN 1687-966X. Dostupné z: https://doi.org/10.1155/2019/1375807.

MAŠKA, Martin; Tereza NEČASOVÁ; David WIESNER; Dmitry SOROKIN; Igor PETERLÍK; Vladimír ULMAN a David SVOBODA. Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy. Online. In 26th IEEE International Conference on Image Processing. Taipei: IEEE, 2019, s. 819-823. ISBN 978-1-5386-6249-6. Dostupné z: https://doi.org/10.1109/ICIP.2019.8803721.

NEČASOVÁ, Tereza a David SVOBODA. Visual and Quantitative Comparison of Real and Simulated Biomedical Image Data. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134. Munich, Germany: Springer, 2019, s. 385-394. ISBN 978-3-030-11023-9. Dostupné z: https://doi.org/10.1007/978-3-030-11024-6_28.

SOLÁR, Peter; Zdeněk MACKERLE; Hana VALEKOVÁ; Markéta HERMANOVÁ; Michal HENDRYCH; Radim JANČÁLEK a David SVOBODA. ADC mapy ve vztahu k peritumorózní buněčné infiltraci u glioblastomu. In XLII. Brněnské onkologické dny 2018. 2018.

SOROKIN, Dmitry; Igor PETERLÍK; Vladimír ULMAN; David SVOBODA; Tereza NEČASOVÁ; Katsiarina MORGAENKO; Lívia EISELLEOVÁ; Lenka TESAŘOVÁ a Martin MAŠKA. FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells with Growing and Branching Filopodia. IEEE Transactions on Medical Imaging. IEEE, 2018, roč. 37, č. 12, s. 2630-2641. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2018.2845884.

PETERLÍK, Igor; David SVOBODA; Vladimír ULMAN; Dmitry SOROKIN a Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. Online. In Simulation and Synthesis in Medical Imaging. Cham: Springer, 2018, s. 71-79. ISBN 978-3-030-00535-1. Dostupné z: https://doi.org/10.1007/978-3-030-00536-8_8.

SVOBODA, David; Tereza NEČASOVÁ; Lenka TESAŘOVÁ a Pavel ŠIMARA. Tubular Network Formation Process Using 3D Cellular Potts Model. In Gooya A., Goksel O., Oguz I., Burgos N. Simulation and Synthesis in Medical Imaging. LNCS 11037. Neuveden: Springer, 2018, s. 90-99. ISBN 978-3-030-00535-1. Dostupné z: https://doi.org/10.1007/978-3-030-00536-8_10.

ULMAN, Vladimír; Martin MAŠKA; Klas E G MAGNUSSON; Olaf RONNEBERGER; Carsten HAUBOLD; Nathalie HARDER; Pavel MATULA; Petr MATULA; David SVOBODA; Miroslav RADOJEVIC; Ihor SMAL; Karl ROHR; Joakim JALDÉN; Helen M BLAU; Oleh DZYUBACHYK; Boudewijn LELIEVELDT; Pengdong XIAO; Yuexiang LI; Siu-Yeung CHO; Alexandre C DUFOUR; Jean-Christophe OLIVO-MARIN; Constantino C REYES-ALDASORO; Jose A SOLIS-LEMUS; Robert BENSCH; Thomas BROX; Johannes STEGMAIER; Ralf MIKUT; Steffen WOLF; Fred A HAMPRECHT; Tiago ESTEVES; Pedro QUELHAS; Ömer DEMIREL; Lars MALMSTRÖM; Florian JUG; Pavel TOMANCAK; Erik MEIJERING; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, roč. 14, č. 12, s. 1141-1152. ISSN 1548-7091. Dostupné z: https://doi.org/10.1038/nmeth.4473.

SEČKÁŘ, Petr a David SVOBODA. FTutor: An Interactive Guide to the Fundamentals of Frequency Analysis. Computer Applications in Engineering Education. Wiley, 2017, roč. 25, č. 3, s. 508-520. ISSN 1061-3773. Dostupné z: https://doi.org/10.1002/cae.21817.

SVOBODA, David a Vladimír ULMAN. MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. IEEE Transactions on Medical Imaging. IEEE Engineering in Medicine and Biology Society, 2017, roč. 36, č. 1, s. 310-321. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2016.2606545.

SOROKIN, Dmitry; Igor PETERLÍK; Vladimír ULMAN; David SVOBODA a Martin MAŠKA. Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Motile Cells with Growing Filopodia. Online. In 14th IEEE International Symposium on Biomedical Imaging. Melbourne: IEEE, 2017, s. 822-826. ISBN 978-1-5090-1172-8. Dostupné z: https://doi.org/10.1109/ISBI.2017.7950644.

SVOBODA, David a Michal KOZUBEK. Multimodal Simulations in Live Cell Imaging. In Tsaftaris S., Gooya A., Frangi A., Prince J. Simulation and Synthesis in Medical Imaging. LNCS 10557. Neuveden: Springer, 2017, s. 89-98. ISBN 978-3-319-68126-9. Dostupné z: https://doi.org/10.1007/978-3-319-68127-6_10.

SVOBODA, David; Vladimír ULMAN; Peter KOVÁČ; Barbara ŠALINGOVÁ; Lenka TESAŘOVÁ; Irena KRONTORÁD KOUTNÁ a Petr MATULA. Vascular Network Formation in Silico Using the Extended Cellular Potts Model. In 2016 IEEE International Conference on Image Processing. Piscataway, NJ, USA: IEEE Signal Processing Society, 2016, s. 3180-3183. ISBN 978-1-4673-9961-6. Dostupné z: https://doi.org/10.1109/ICIP.2016.7532946.

ULMAN, Vladimír; David SVOBODA; Matti NYKTER; Michal KOZUBEK a Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, roč. 89A, č. 12, s. 1057-1072. ISSN 1552-4922. Dostupné z: https://doi.org/10.1002/cyto.a.23031.

SVOBODA, David. Next Step Toward the Automation of Screening for Cervical Cancer. Cytometry Part A. John Wiley & Sons, 2015, roč. 87a, č. 3, s. 195-196. ISSN 1552-4922. Dostupné z: https://doi.org/10.1002/cyto.a.22564.

SVOBODA, David; Vladimír ULMAN a Igor PETERLÍK. On Proper Simulation of Chromatin Structure in Static Images As Well As in Time-Lapse Sequences in Fluorescence Microscopy. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging. Stoughton (WI, USA): Engineering in Medicine and Biology Society, 2015, s. 712-716. ISBN 978-1-4799-2374-8. Dostupné z: https://doi.org/10.1109/ISBI.2015.7163972.

ULMAN, Vladimír; Zoltán ORÉMUŠ a David SVOBODA. TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. In Vittorio Murino, Enrico Puppo, Gianni Vernazza. Proceedings of 18th International Conference on Image Analysis and Processing. Heidelberg, Německo: Springer International Publishing, 2015, s. 623-634. ISBN 978-3-319-23230-0. Dostupné z: https://doi.org/10.1007/978-3-319-23231-7_56.

MAJTNER, Tomáš a David SVOBODA. 2D/3D Gabor Features and 2D/3D MPEG-7 EHD Features. 2015.

MAŠKA, Martin; Vladimír ULMAN; David SVOBODA; Pavel MATULA; Petr MATULA; Cristina EDERRA; Ainhoa URBIOLA; Tomás ESPAÑA; Subramanian VENKATESAN; Deepak M W BALAK; Pavel KARAS; Tereza BOLCKOVÁ; Markéta ŠTREITOVÁ; Craig CARTHEL; Stefano CORALUPPI; Nathalie HARDER; Karl ROHR; Klas E G MAGNUSSON; Joakim JALDÉN; Helen M BLAU; Oleh DZYUBACHYK; Pavel KŘÍŽEK; Guy M HAGEN; David PASTOR-ESCUREDO; Daniel JIMENEZ-CARRETERO; Maria J LEDESMA-CARBAYO; Arrate MUÑOZ-BARRUTIA; Erik MEIJERING; Michal KOZUBEK a Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics. 2014, roč. 30, č. 11, s. 1609-1617. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btu080.

WILLIAMS, Ian; Nicholas BOWRING a David SVOBODA. A performance evaluation of statistical tests for edge detection in textured images. Computer Vision and Image Understanding. Elsevier, 2014, roč. 122, May 2014, s. 115-130. ISSN 1077-3142. Dostupné z: https://doi.org/10.1016/j.cviu.2014.02.009.

MAJTNER, Tomáš a David SVOBODA. Comparison of 3D Texture-based Image Descriptors in Fluorescence Microscopy. In Reneta P. Barneva, Valentin E. Brimkov, Josef Šlapal. 16th International Workshop on Combinatorial Image Analysis (IWCIA) 2014. Switzerland: Springer International Publishing, 2014, s. 186-195. ISBN 978-3-319-07147-3. Dostupné z: https://doi.org/10.1007/978-3-319-07148-0_17.

STOKLASA, Roman; Tomáš MAJTNER a David SVOBODA. Efficient k-NN based HEp-2 cells classifier. PATTERN RECOGNITION. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2014, roč. 47, č. 7, s. 2409-2418. ISSN 0031-3203. Dostupné z: https://doi.org/10.1016/j.patcog.2013.09.021.

SVOBODA, David; Vladimír ULMAN; Luděk MATYSKA; Martin MAŠKA; Ján BELLA a Stanislav STEJSKAL. On Proper Simulation of Phenomena Influencing Image Formation in Fluorescence Microscopy. In 2014 IEEE International Conference on Image Processing. Neuveden: IEEE Signal Processing Society, 2014, s. 3944-3948. ISBN 978-1-4799-5750-7. Dostupné z: https://doi.org/10.1109/ICIP.2014.7025801.

MAJTNER, Tomáš; Roman STOKLASA a David SVOBODA. RSurf - the Efficient Texture-Based Descriptor for Fluorescence Microscopy Images of HEp-2 Cells. In 22nd International Conference on Pattern Recognition. Los Alamitos, California: IEEE Computer Society, 2014, s. 1194-1199. ISBN 978-1-4799-5208-3. Dostupné z: https://doi.org/10.1109/ICPR.2014.215.

MAJTNER, Tomáš; Roman STOKLASA a David SVOBODA. RSurf Texture Descriptor. 2014.

MAJTNER, Tomáš a David SVOBODA. Texture Analysis Using 3D Gabor Features and 3D MPEG-7 Edge Histogram Descriptor in Fluorescence Microscopy. Online. In 4th International Conference on 3D Imaging (IC3D). Los Alamitos, California: IEEE Computer Society, 2014, s. 1-7. ISBN 978-1-4799-8023-9. Dostupné z: https://doi.org/10.1109/IC3D.2014.7032576.

SVOBODA, David. The Importance of Computer Generated Data in Fluorescence Microscopy. In Advances in Molecular and Cancer Biology. 2014.

KARAS, Pavel a David SVOBODA. Algorithms for Efficient Computation of Convolution. In Design and Architectures for Digital Signal Processing. 1st ed. Rijeka (CRO): InTech, 2013, s. 179-208. ISBN 978-953-51-0874-0. Dostupné z: https://doi.org/10.5772/3456.

SVOBODA, David; Luděk MATYSKA a Vladimír ULMAN. CytoPacq v2.0. 2013.

KARAS, Pavel; Michal KUDERJAVÝ a David SVOBODA. Deconvolution of huge 3-D images: Parallelization strategies on a multi-GPU system. In Kołodziej, Joanna and Martino, Beniamino and Talia, Domenico and Xiong, Kaiqi. Algorithms and Architectures for Parallel Processing. Neuveden: Springer International Publishing, 2013, s. 279-290. ISBN 978-3-319-03858-2. Dostupné z: https://doi.org/10.1007/978-3-319-03859-9_24.

SVOBODA, David. On generating benchmark datasets for evaluation of segmentation and tracking algorithms in fluorescence microscopy. In SPlab workshop. 2013.

SVOBODA, David a Vladimír ULMAN. Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. In Alfredo Petrosino. 17th International Conference on Image Analysis and Processing - ICIAP 2013. LNCS 8157, Part II. Berlin, Heidelberg: Springer-Verlag, 2013, s. 429-438. ISBN 978-3-642-41183-0. Dostupné z: https://doi.org/10.1007/978-3-642-41184-7_44.

MAJTNER, Tomáš a David SVOBODA. Extension of Tamura Texture Features for 3D Fluorescence Microscopy. In 2012 Second Joint 3DIM/3DPVT Conference: 3D Imaging, Modeling, Processing, Visualization & Transmission. Los Alamitos, CA, USA: IEEE Computer Society, 2012, s. 301-307. ISBN 978-0-7695-4873-9.

SVOBODA, David a Vladimír ULMAN. Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In Campilho, Aurélio; Kamel, Mohamed. Proceedings of 9th International Conference on Image Analysis and Recognition. LNCS 7325, Part II. Heidelberg: Springer-Verlag, 2012, s. 473-482. ISBN 978-3-642-31297-7. Dostupné z: https://doi.org/10.1007/978-3-642-31298-4_56.

KARAS, Pavel; David SVOBODA a Pavel ZEMČÍK. GPU Optimization of Convolution for Large 3-D Real Images. In Blanc-Talon, Jacques and Philips, Wilfried and Popescu, Dan and Scheunders, Paul and Zemcík, Pavel. Proceedings of the International Conference on Advanced Concepts for Intelligent Vision Systems (ACIVS’12). Neuveden: Springer Berlin / Heidelberg, 2012, s. 59-71. ISBN 978-3-642-33139-8. Dostupné z: https://doi.org/10.1007/978-3-642-33140-4_6.

STOKLASA, Roman; Tomáš MAJTNER; David SVOBODA a Michal BATKO. HEp-2 Cells Classifier. 2012.

KARAS, Pavel a David SVOBODA. Convolution of Large 3D Images on GPU and its Decomposition. EURASIP Journal on Advances in Signal Processing. NEW YORK (USA): HINDAWI PUBLISHING CORPORATION, 2011, roč. 2011, č. 120, s. 1-12. ISSN 1687-6172. Dostupné z: https://doi.org/10.1186/1687-6180-2011-120.

SVOBODA, David. Efficient Computation of Convolution of Huge Images. In Giuseppe Maino; Gian Luca Foresti. Image Analysis and Processing - ICIAP 2011. LNCS 6978, Part I. Berlin, Heidelberg: Springer-Verlag, 2011, s. 453-462. ISBN 978-3-642-24084-3.

SVOBODA, David; Ondřej HOMOLA a Stanislav STEJSKAL. Generation of 3D Digital Phantoms of Colon Tissue. In M. Kamel and A. Campilho. Proceedings of 8th International Conference on Image Analysis and Recognition. LNCS 6754, Part II. Berlin, Heidelberg: Springer-Verlag, 2011, s. 31-39. ISBN 978-3-642-21595-7. Dostupné z: https://doi.org/10.1007/978-3-642-21596-4_4.

ULMAN, Vladimír a David SVOBODA. Tool for Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. In 11th European Light Microscopy Initiative (ELMI) meeting. 2011.

WILLIAMS, Ian; David SVOBODA a Nicholas BOWRING. A Novel Performance Metric For Grey-Scale Edge Detection. In Proceedings of the International Conference on Computer Vision Theory and Applications. Vol. 1. Portugal: Institute for Systems and Technologies of Information, Control and Communication, 2010, s. 91-97. ISBN 978-989-674-028-3.

KOZUBEK, Michal; David SVOBODA a Stanislav STEJSKAL. CytoPacq: A web-based toolbox for simulation of 3D cell imaging and quality control of related image analysis. In Mikroskopie 2010. 2010.

SVOBODA, David; Michal KOZUBEK a Jaromír COUFAL. CytoPacq. 2009.

SVOBODA, David a Michal KOZUBEK. CytoPacq – On-line Framework for Simulating Fluorescence Microscopy Images. In Hands-on Image Processing, Robotiker-Tecnalia, Bilbao, Spain. 2009.

SVOBODA, David; Michal KOZUBEK a Stanislav STEJSKAL. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A. John Wiley & Sons, Inc., 2009, roč. 75A, č. 6, s. 494-509. ISSN 1552-4922. Dostupné z: https://doi.org/10.1002/cyto.a.20714.

SVOBODA, David; Michal KOZUBEK a Stanislav STEJSKAL. Towards Proper Evaluation of Image Analysis Methods Used in Biomedical Research. In Analytical Cytometry V, International Conference. 2009. ISBN 978-80-254-2561-5.

KOZUBEK, Michal; David SVOBODA; Marek KAŠÍK; Martin MAŠKA; Jan HUBENÝ; Stanislav STEJSKAL; Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D image cytometry. In XXIV International Congress of International Society for Analytical Cytology. 2008.

KOZUBEK, Michal; David SVOBODA; Marek KAŠÍK; Martin MAŠKA; Jan HUBENÝ; Stanislav STEJSKAL; Michal SEEMAN a Pavel ZEMČÍK. Simulation of fluorescence image formation in 3D light microscopy. In 8th Meeting of European Light Microscopy Initiative. 2008.

WILLIAMS, Ian; David SVOBODA; Nicholas BOWRING a Elizabeth GUEST. Statistical Edge Detection of Concealed Weapons Using Artificial Neural Networks. In Proceedings of SPIE-IS&T Electronic Imaging. Vol. 6812. Bellingham, Washington: SPIE, 2008, s. 68121J-1-12, 12 s. ISBN 978-0-8194-6984-7.

SVOBODA, David; Martin MAŠKA; Jan SKALICKÝ; Michal KOZUBEK a Stanislav STEJSKAL. 3D AcquiGen 0.2. 2008.

SVOBODA, David; Martin MAŠKA; Jan SKALICKÝ; Michal KOZUBEK a Stanislav STEJSKAL. 3D CytoGen 0.2. 2008.

SVOBODA, David; Martin MAŠKA; Jan SKALICKÝ; Michal KOZUBEK a Stanislav STEJSKAL. 3D OptiGen 0.2. 2008.

MAŠKA, Martin; Jan HUBENÝ; David SVOBODA a Michal KOZUBEK. A Comparison of Fast Level Set-Like Algorithms for Image Segmentation in Fluorescence Microscopy. Online. In 3rd International Symposium on Visual Computing. Berlin, Heidelberg: Spinger-Verlag, 2007, s. 571-581. ISBN 978-3-540-76855-5.

SKALNÍKOVÁ, Magdalena; Eva BÁRTOVÁ; Vladimír ULMAN; Petr MATULA; David SVOBODA; Andrea HARNIČAROVÁ; Michal KOZUBEK a Stanislav KOZUBEK. Distinct patterns of histone methylation and acetylation in human interphase nuclei. Physiological Research. Prague: Czech Academy of Sciences, 2007, roč. 56, č. 6, s. 797-806. ISSN 0862-8408.

SVOBODA, David; Marek KAŠÍK; Martin MAŠKA; Jan HUBENÝ; Stanislav STEJSKAL a Michal ZIMMERMANN. On Simulating 3D Fluorescent Microscope Images. In Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2007, s. 309-316. ISBN 978-3-540-74271-5.

SVOBODA, David; Martin MAŠKA; Marek KAŠÍK; Jan HUBENÝ; Michal KOZUBEK; Michal ZIMMERMANN a Stanislav STEJSKAL. 3D AcquiGen 0.1. 2007.

SVOBODA, David; Martin MAŠKA; Marek KAŠÍK; Jan HUBENÝ; Michal KOZUBEK; Michal ZIMMERMANN a Stanislav STEJSKAL. 3D CytoGen 0.1. 2007.

SVOBODA, David; Martin MAŠKA; Marek KAŠÍK; Jan HUBENÝ; Michal KOZUBEK; Michal ZIMMERMANN a Stanislav STEJSKAL. 3D OptiGen 0.1. 2007.

WILLIAMS, Ian; David SVOBODA; Nicholas BOWRING a Elizabeth GUEST. Improved statistical edge detection through neural networks. In 10th Conference on Medical Image Understanding and Analysis. Manchester: BMVA, 2006, s. 56-60. ISBN 1-901727-31-9.

SVOBODA, David; Ian WILLIAMS; Nicholas BOWRING a Elizabeth GUEST. Statistical techniques for edge detection in histological images. In First International Conference on Computer Vision Theory and Applications. Portugalsko: INSTICC Press, 2006, s. 457-462. ISBN 972-8865-40-6.

KOZUBEK, Michal; Pavel MATULA; Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In 1st International Summer School on Computational Biology. 2005.

KOZUBEK, Michal; Pavel MATULA; Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In DUŠEK, Ladislav; Jiří HŘEBÍČEK a Jiří JARKOVSKÝ. Proceedings of the 1st International Summer School on Computational Biology. Brno: Masaryk University, 2005, s. 21-28. ISBN 80-210-3907-8.

KOZUBEK, Michal; Pavel MATULA; Petr MATULA a David SVOBODA. Analysis of biomedical image data acquired using optical microscopy. In Prague Post Genome Technology Workshop. Prague, Czech Republic: Czech Pattern Recognition Society, 2005, s. 24-27. ISBN 80-01-03239-6.

JANSOVÁ, Eva; Petr KRONTORÁD; Irena KOUTNÁ; Stanislav STEJSKAL; Petr MATULA; David SVOBODA; Michal KOZUBEK a Stanislav KOZUBEK. Combination of cDNA microarray technology and fluorescence leads to better understanding of relationships between gene expression and epigenetic regulation. In MGED8 Abstract book. 2005.

HUBENÝ, Jan; David SVOBODA; Pavel MATULA a Michal KOZUBEK. Využití deformabilních modelů v obrazové cytometrii. 2005.

KOZUBEK, Michal; Petr MATULA; Pavel MATULA; David SVOBODA; Jan HUBENÝ a Petr KRONTORÁD. Automated image analysis in fluorescence microscopy: From isolated cells to tissues and microarray images. In Biophysics of the Genome. First Edition 2004. Brno: Masaryk University, 2004, s. 44-46. ISBN 80-210-3560-9.

SVOBODA, David. Towards a Fully Automated Tissue Cell Segmentation Method. In Visualization, Imaging, and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2004, s. 430-434. ISBN 0-88986-454-3.

SVOBODA, David a Pavel MATULA. Multilevel Adaptive Thresholding and Dual Simplex Mesh Deformation as a Tool for Tissue Reconstruction. In Visualization, Imaging, and Image Processing. Anaheim, Calgary, Zurich: ACTA Press, 2003, s. 499-503. ISBN 0-88986-382-2.

MATULA, Pavel a David SVOBODA. Spherical Object Reconstruction Using Simplex Meshes from Sparse Data. In Discrete Geometry for Computer Imagery. Berlin Heidelberg New York: Springer-Verlag, 2003, s. 524-533. ISBN 3-540-20499-7.

SVOBODA, David a Pavel MATULA. Tissue image reconstruction: Localization of nuclei markers and segmentation based on deformable models. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 67-70. ISBN 80-210-3226-X.

SVOBODA, David a Pavel MATULA. Tissue Reconstruction Based on Deformation of Dual Simplex Meshes. In Discrete Geometry for Computer Imagery. Berlin, Heidelberg, New York: Springer, 2003, s. 514-523. ISBN 3-540-20499-7.

MATULA, Pavel a David SVOBODA. 3D Object reconstructions in image cytometry. In Biophysics of the Genome. Brno: Masaryk University, 2003, s. 49-50. ISBN 80-210-3226-X.

MATULA, Pavel a David SVOBODA. Cell Nuclei Segmentation Using Star-Shaped Simplex Meshes. In Biophysics of the Genome and Its Interactions. Brno: Masaryk University, 2002, s. 74-76. ISBN 80-210-2853-X.

MATULA, Pavel a David SVOBODA. Spherical Object Reconstruction Using Star-Shaped Simplex Meshes. In Energy Minimization Methods in Computer Vision and Pattern Recognition. Berlin, Heidelberg, New York: Springer-Verlag, 2001, s. 608-620. ISBN 3-540-42523-3.