Výpis publikací

EŠNER, Milan, Vladimír ULMAN, Nils NORLIN, Ivana SEKANINOVÁ a Eliška JANÍČKOVÁ. ImgLib2 and BigDataViewer Hackathon Brno. 2023.

MAŠKA, Martin, Vladimír ULMAN, Pablo DELGADO-RODRIGUEZ, Estibaliz GÓMEZ-DE-MARISCAL, Tereza NEČASOVÁ, Fidel A Guerrero PEÑA, Tsang Ing REN, Elliot M MEYEROWITZ, Tim SCHERR, Katharina LÖFFLER, Ralf MIKUT, Tianqi GUO, Yin WANG, Jan P ALLEBACH, Rina BAO, Noor M AL-SHAKARJI, Gani RAHMON, Imad Eddine TOUBAL, Kannappan PALANIAPPAN, Filip LUX, Petr MATULA, Ko SUGAWARA, Klas E G MAGNUSSON, Layton AHO, Andrew R COHEN, Assaf ARBELLE, Tal BEN-HAIM, Tammy Riklin RAVIV, Fabian ISENSEE, Paul F JÄGER, Klaus H MAIER-HEIN, Yanming ZHU, Cristina EDERRA, Ainhoa URBIOLA, Erik MEIJERING, Alexandre CUNHA, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, roč. 20, č. 7, s. 1010-1020. ISSN 1548-7091. Dostupné z: https://dx.doi.org/10.1038/s41592-023-01879-y.

ULMAN, Vladimír a David WIESNER. Review of cell image synthesis for image processing. In Ninon Burgos, David Svoboda. Biomedical Image Synthesis and Simulation - Methods and Applications. 1st ed. Neuveden: Elsevier, 2022, s. 447-489. The MICCAI Society book Series. ISBN 978-0-12-824349-7. Dostupné z: https://dx.doi.org/10.1016/B978-0-12-824349-7.00028-1.

JAIN, Akanksha, Vladimír ULMAN, Argo MUKHERJEE, Mangal PRAKASH, Lokesh PIMPALE, Stefan MÜNSTER, Panfilio KRISTEN, Florian JUG, Stephan GRILL, Pavel TOMANCAK a Anastasios PAVLOPOULOS. Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation. Online. Nature Communications. Springer, 2020, roč. 11, s. 1-13. Dostupné z: https://dx.doi.org/10.1038/s41467-020-19356-x.

HANDBERG-THORSAGER, Mette, Vladimír ULMAN, Pavel TOMANČÁK, D. ARENDT a M. SCHUBERT. A Behavioral Assay to Study Effects of Retinoid Pharmacology on Nervous System Development in a Marine Annelid. In Swapan K. Ray. Retinoid and Rexinoid Signaling. Springer, 2019, s. 193-207. ISBN 978-1-4939-9584-4. Dostupné z: https://dx.doi.org/10.1007/978-1-4939-9585-1_14.

AKBAŞ, Cem Emre, Vladimír ULMAN, Martin MAŠKA, Florian JUG a Michal KOZUBEK. Automatic Fusion of Segmentation and Tracking Labels. In Laura Leal-Taixé, Stefan Roth. Computer Vision – ECCV 2018 Workshops. LNCS 11134. Switzerland: Springer Nature, 2019, s. 446-454. ISBN 978-3-030-11023-9. Dostupné z: https://dx.doi.org/10.1007/978-3-030-11024-6_34.

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://dx.doi.org/10.1109/ICIP.2019.8803721.

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://dx.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://dx.doi.org/10.1007/978-3-030-00536-8_8.

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://dx.doi.org/10.1038/nmeth.4473.

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://dx.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://dx.doi.org/10.1109/ISBI.2017.7950644.

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://dx.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://dx.doi.org/10.1002/cyto.a.23031.

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://dx.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://dx.doi.org/10.1007/978-3-319-23231-7_56.

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://dx.doi.org/10.1093/bioinformatics/btu080.

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://dx.doi.org/10.1109/ICIP.2014.7025801.

SVOBODA, David, Luděk MATYSKA a Vladimír ULMAN. CytoPacq v2.0. 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://dx.doi.org/10.1007/978-3-642-41184-7_44.

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://dx.doi.org/10.1007/978-3-642-31298-4_56.

ULMAN, Vladimír. Boundary Treatment for Young-van Vliet Recursive Zero-Mean Gabor Filtering. EURASIP Journal on Advances in Signal Processing. NEW YORK (USA): HINDAWI PUBLISHING CORPORATION, 2011, roč. 2011, ID 234090, s. 1-9. ISSN 1687-6172. Dostupné z: https://dx.doi.org/10.1155/2011/234090.

ULMAN, Vladimír. Fast Anisotropic Filtering and Performance Evaluation Tool for Optical Flow in Biomedical Image Analysis. Brno: Masarykova Univerzita, 2011, 210 s.

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.

ULMAN, Vladimír. Filtering with Anisotropic 3D Gabor Filter Bank Efficiently Computed with 1D Convolutions without Interpolation. In Proceedings of the Seventh IASTED International Conference on Signal Processing, Pattern Recognition and Applications. Calgary: ACTA Press, 2010, s. 33-42. ISBN 978-0-88986-823-6.

ULMAN, Vladimír. Improving Accuracy of Optical Flow of Heeger's Original Method on Biomedical Images. In Proceedings of the 7th International Conference on Image Analysis and Recognition, ICIAR 2010. Povoa de Varzim (Portugal): Springer, 2010, s. 263-273. ISBN 978-3-642-13771-6. Dostupné z: https://dx.doi.org/10.1007/978-3-642-13772-3_27.

VAŘECHA, Miroslav, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. In Analytical Cytometry V. 2009. ISBN 978-80-254-2561-9.

VAŘECHA, Miroslav, Michal ZIMMERMANN, Jana AMRICHOVÁ, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. Journal of Biomedical Science. BioMed website: BioMed Central, London, England, 2009, roč. 16, č. 59, s. 1-14. ISSN 1021-7770.

ULMAN, Vladimír. Arbitrarily-Oriented Anisotropic 3D Gaussian Filtering Computed with 1D Convolutions without Interpolation. In Proceedings of 8th WSEAS International Conference on Signal Processing, Computational Geometry and Artificial Vision. Ateny: WSEAS, 2008, s. 56-62. ISBN 978-960-6766-95-4.

ZIMMERMANN, Michal, Miroslav VAŘECHA, Jana AMRICHOVÁ, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Bioinformatic prediction, molecular modelling and image analysis of localization and interactions of apoptotic proteins endonuclease G, AIF, and AMID. In Apoptosis World 2008. 2008.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN a Michal KOZUBEK. Image analysis of localization and translocation of apoptotic proteins in living cells. In European Light Microscopy Initiative. 2008.

VAŘECHA, Miroslav, Michal ZIMMERMANN, Jana AMRICHOVÁ, Vladimír ULMAN a Michal KOZUBEK. Interactions of apoptotic proteins AIF and endonuclease G analyzed by bioinformatic predictions, molecular docking, and fluorescent microscopy. In 16th Euroconference on Apoptosis an 5th Swiss Apoptosis Meeting. 2008.

FEIT, Josef, Luděk MATYSKA, Vladimír ULMAN, Lukáš HEJTMÁNEK, Hana JEDLIČKOVÁ, Marta JEŽOVÁ, Mojmír MOULIS a Věra FEITOVÁ. Virtual microscope interface to high resolution histological images. In Diagnostic Pathology. (3)Suppl 1). http://www.diagnosticpathology.org: 2006 Kayser; licensee BioMed Central Ltd., 2008, s. NA, 1 s.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Emilie LUKÁŠOVÁ a Michal KOZUBEK. Bioinformatic and image analyses of cellular localization of apoptotic proteins endonuclease G, AIF, and AMID. In Symposium "Structure and Function of Cell Nucleus". 2007.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Emilie LUKÁŠOVÁ a Michal KOZUBEK. Bioinformatic and image analyses of the cellular localization of the apoptotic proteins endonuclease G, AIF, and AMID during apoptosis in human cells. Apoptosis. USA: Springer Science, 2007, roč. 12, č. 7, s. 1155-1171. ISSN 1360-8185.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Pavel MATULA a Michal KOZUBEK. Bioinformatic predictions and image analysis of localization and interactions of endonuclease G, AIF, and AMID in human cells. In Book of Abstracts for 15th Euroconference on Apoptosis. 2007.

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.

HUBENÝ, Jan, Vladimír ULMAN a Pavel MATULA. Estimating Large Local Motion in Live-Cell Imaging Using Variational Optical Flow. In VISAPP 2007 Second International Conference On Computer Vision Theory And Applications, Proceedings. Portugal: INSTICC PRESS, 2007, s. 542-548. ISBN 978-972-8865-74-0.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Marek KAŠÍK a Michal KOZUBEK. Fluorescent microscopy of living cells. In Analytical Cytometry IV: Book of Abstracts. 2007. ISBN 978-80-239-9591-6.

FEIT, Josef, Lukáš HEJTMÁNEK, Luděk MATYSKA, Vladimír ULMAN, Marta JEŽOVÁ, Mojmír MOULIS, Věra FEITOVÁ, Sylva HOTÁRKOVÁ, Ondřej SOUČEK, Katarína MÚČKOVÁ a Pavel VLAŠÍN. Hypertextové atlasy patologie 2007. In MEFANET 2007. Brno: MSD, 2007. ISBN 978-80-739-2007-4.

ULMAN, Vladimír a Jan HUBENÝ. On Generating Ground-truth Time-lapse Image Sequences and Flow Fields. In Proceedings of the Fourth International Conference on Informatics in Control, Automation and Robotics. RA-1. Angers: INSTICC, 2007, s. 234-239. ISBN 978-972-8865-83-2.

ULMAN, Vladimír a Jan HUBENÝ. Pseudo-real Image Sequence Generator for Optical Flow Computations. In Proceedings of 15th Scandinavian Conference on Image Analysis. LNCS 4522. Heidelberg: Springer, 2007, s. 976-985. ISBN 978-3-540-73039-2.

FEIT, Josef, Luděk MATYSKA, Hana JEDLIČKOVÁ, Věra FEITOVÁ a Vladimír ULMAN. Rozhraní virtuálního mikroskopu pro přístup k histologickým obrazům o velmi vysokém rozlišení. In MEDSOFT 2007. Praha: Agentura Action M, 2007, s. 33-37, 4 s. ISBN 978-80-867-4200-7.

ULMAN, Vladimír. Automatic Detection of Histones on Chromosome X in Images of Cell Nuclei. Clinician and Technology (Lékař a technika). Praha: Czech Medical Association J.E.Purkyne, 2006, roč. 36, č. 2, s. 160-164. ISSN 0301-5491.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Michal ZIMMERMANN, Vladimír ULMAN, Pavel MATULA, Petr MATULA a Michal KOZUBEK. Single-cell image analysis of cellular localization and colocalization of endonuclease G, AIF and AMID in living cells. In Book of Abstracts for 14th Euroconference on Apoptosis. 2006.

VAŘECHA, Miroslav, Jana AMRICHOVÁ, Vladan ONDŘEJ, Emilie LUKÁŠOVÁ, Vladimír ULMAN, Petr MATULA, Michal KOZUBEK a Stanislav KOZUBEK. Imaging of mitochondrial apoptogenic proteins released during apoptosis in living and fixed cells. In Book of Abstracts for 13th Euroconference on Apoptosis. 2005. ISBN 963-219-273-7.

ULMAN, Vladimír. Mosaicking of High-resolution Biomedical Images Acquired from Wide-field Optical Microscope. In Proceedings of the 3rd European Medical and Biological Engineering Conference EMBEC'05. Praha: IFMBE Proceedings Series, vol. 11, 2005, s. 1-5. ISSN 1727-1983.

ULMAN, Vladimír. Mosaicking of High-resolution Biomedical Images Acquired from Wide-field Optical Microscope. Znojmo: 1st Doctoral Workshop on Mathematical and Engeneering methods in Computer Science, 2005.

ULMAN, Vladimír. Quantitative Analysis of Intracellular Processes in Living Cells. In Proceedings of the 1st International Summer School on Computational Biology. Brno: Masarykova universita, 2005, s. 84-94. ISBN 80-210-3907-8.

FEIT, Josef, Vladimír ULMAN, Werner KEMPF a Hana JEDLIČKOVÁ. Pořizování obrazů o velmi vysokém rozlišení metodou skládání. Čes-slov. Patologie. 2004, roč. 40, č. 2, s. 78-82. ISSN 1210-7875.