Publication Records

LANG, Matěj, Radoslav MRÁZ, Marek TRTÍK, Sergej STOPPEL, Jan BYŠKA and Barbora KOZLÍKOVÁ. Antarstick: Extracting Snow Height From Time-Lapse Photography. COMPUTER GRAPHICS FORUM. England: Wiley, 2024, vol. 43, No 3, p. 1-11. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.15088.

STOKLASA, Roman, Ioannis STATHOPOULOS, Efstratios KARAVASILIS, Efstathios EFSTATHOPOULOS, Marek DOSTÁL, Miloš KEŘKOVSKÝ, Michal KOZUBEK and Luigi SERIO. Brain MRI Screening Tool with Federated Learning. Online. In 2024 IEEE International Symposium on Biomedical Imaging. Athens, Greece: IEEE, 2024, p. 1-5. ISBN 979-8-3503-1333-8. Available from: https://dx.doi.org/10.1109/ISBI56570.2024.10635396.

LUX, Filip and Petr MATULA. Cell Tracking based on Integer Linear Programming and Probability Scores. In Athens, Greece, IEEE 21th International Symposium on Biomedical Imaging. Athens: IEEE 21th International Symposium on Biomedical Imaging, 2024, p. 1-5. ISBN 979-8-3503-1334-5. Available from: https://dx.doi.org/10.1109/ISBI56570.2024.10635857.

WIESNER, David, Julian SUK, Sven DUMMER, Tereza NEČASOVÁ, Ulman VLADIMÍR, David SVOBODA and Jelmer WOLTERINK. Generative modeling of living cells with SO(3)-equivariant implicit neural representations. Medical Image Analysis. Netherlands: Elsevier, 2024, vol. 2024, No 91, p. 102991-103008. ISSN 1361-8415. Available from: https://dx.doi.org/10.1016/j.media.2023.102991.

EFTIMIU, Nikomidisz Jorgosz and Michal KOZUBEK. Gravitational Cell Detection and Tracking in Fluorescence Microscopy Data (Gravitational cell detection and tracking in fluorescence microscopy data). Online. In IEEE. 24 IEEE International Symposium on Biomedical Imaging (ISBI). Athens, Greece: IEEE, 2024, p. 1-5. ISBN 979-8-3503-1334-5. Available from: https://dx.doi.org/10.1109/ISBI56570.2024.10635151.

KÉPEŠ, Erik, Jakub VRÁBEL, Tomáš BRÁZDIL, Petr HOLUB, Pavel POŘÍZKA and Jozef KAISER. Interpreting convolutional neural network classifiers applied to laser-induced breakdown optical emission spectra. Talanta. AMSTERDAM: Elsevier, 2024, vol. 266, No 124946, p. 1-11. ISSN 0039-9140. Available from: https://dx.doi.org/10.1016/j.talanta.2023.124946.

MRÁZ, Radoslav, Karel ŠTĚPKA, Matěj PEKÁR, Petr MATULA and Stanislav PEKÁR. MAPHIS-Measuring arthropod phenotypes using hierarchical image segmentations. Methods in Ecology and Evolution. HOBOKEN: WILEY, 2024, vol. 15, No 1, p. 36-42. ISSN 2041-210X. Available from: https://dx.doi.org/10.1111/2041-210X.14250.

MAIER-HEIN, Lena, Annika REINKE, Patrick GODAU, Minu D TIZABI, Florian BUETTNER, Evangelia CHRISTODOULOU, Ben GLOCKER, Fabian ISENSEE, Jens KLEESIEK, Michal KOZUBEK, Mauricio REYES, Michael A RIEGLER, Manuel WIESENFARTH, A Emre KAVUR, Carole H SUDRE, Michael BAUMGARTNER, Matthias EISENMANN, Doreen HECKMANN-NOETZEL, Tim RAEDSCH, Laura ACION, Michela ANTONELLI, Tal ARBEL, Spyridon BAKAS, Arriel BENIS, Matthew B BLASCHKO, M Jorge CARDOSO, Veronika CHEPLYGINA, Beth A CIMINI, Gary S COLLINS, Keyvan FARAHANI, Luciana FERRER, Adrian GALDRAN, van Ginneken BRAM, Robert HAASE, Daniel A HASHIMOTO, Michael M HOFFMAN, Merel HUISMAN, Pierre JANNIN, Charles E KAHN, Dagmar KAINMUELLER, Bernhard KAINZ, Alexandros KARARGYRIS, Alan KARTHIKESALINGAM, Florian KOFLER, Annette KOPP-SCHNEIDER, Anna KRESHUK, Tahsin KURC, Bennett A LANDMAN, Geert LITJENS, Amin MADANI, Klaus MAIER-HEIN, Anne L MARTEL, Peter MATTSON, Erik MEIJERING, Bjoern MENZE, Karel G M MOONS, Henning MUELLER, Brennan NICHYPORUK, Felix NICKEL, Jens PETERSEN, Nasir RAJPOOT, Nicola RIEKE, Julio SAEZ-RODRIGUEZ, Clara I SANCHEZ, Shravya SHETTY, van Smeden MAARTEN, Ronald M SUMMERS, Abdel A TAHA, Aleksei TIULPIN, Sotirios A TSAFTARIS, Van Calster BEN, Gael VAROQUAUX and Paul F JAEGER. Metrics reloaded: recommendations for image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, vol. 21, February, p. 195-212, 30 pp. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/s41592-023-02151-z.

KOPŘIVOVÁ, Tereza, Miloš KEŘKOVSKÝ, Tomáš JŮZA, Václav VYBÍHAL, Tomáš ROHAN, Michal KOZUBEK and Marek DOSTÁL. Possibilities of Using Multi-b-value Diffusion Magnetic Resonance Imaging for Classification of Brain Lesions. Academic Radiology. New York: Elsevier, 2024, vol. 31, No 1, p. 261-272. ISSN 1076-6332. Available from: https://dx.doi.org/10.1016/j.acra.2023.10.002.

REINKE, Annika, Minu D TIZABI, Michael BAUMGARTNER, Matthias EISENMANN, Doreen HECKMANN-NÖTZEL, A Emre KAVUR, Tim RÄDSCH, Carole H SUDRE, Laura ACION, Michela ANTONELLI, Tal ARBEL, Spyridon BAKAS, Arriel BENIS, Florian BUETTNER, M Jorge CARDOSO, Veronika CHEPLYGINA, Jianxu CHEN, Evangelia CHRISTODOULOU, Beth A CIMINI, Keyvan FARAHANI, Luciana FERRER, Adrian GALDRAN, Bram van GINNEKEN, Ben GLOCKER, Patrick GODAU, Daniel A HASHIMOTO, Michael M HOFFMAN, Merel HUISMAN, Fabian ISENSEE, Pierre JANNIN, Charles E KAHN, Dagmar KAINMUELLER, Bernhard KAINZ, Alexandros KARARGYRIS, Jens KLEESIEK, Florian KOFLER, Thijs KOOI, Annette KOPP-SCHNEIDER, Michal KOZUBEK, Anna KRESHUK, Tahsin KURC, Bennett A LANDMAN, Geert LITJENS, Amin MADANI, Klaus MAIER-HEIN, Anne L MARTEL, Erik MEIJERING, Bjoern MENZE, Karel GM MOONS, Henning MÜLLER, Brennan NICHYPORUK, Felix NICKEL, Jens PETERSEN, Susanne M RAFELSKI, Nasir RAJPOOT, Mauricio REYES, Michael A RIEGLER, Nicola RIEKE, Julio SAEZ-RODRIGUEZ, Clara I SÁNCHEZ, Shravya SHETTY, Ronald M SUMMERS, Abdel A TAHA, Aleksei TIULPIN, Sotirios A TSAFTARIS, Ben Van CALSTER, Gaël VAROQUAUX, Ziv R YANIV, Paul F JÄGER and Lena MAIER-HEIN. Understanding metric-related pitfalls in image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, vol. 21, February, p. 182-194, 20 pp. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/s41592-023-02150-0.

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

MRÁZ, Radoslav, Karel ŠTĚPKA, Matěj PEKÁR, Petr MATULA and Stanislav PEKÁR. MAPHIS - Measuring arthropod phenotypes using hierarchical image segmentations. 2023. Available from: https://dx.doi.org/10.1111/2041-210X.14250.

HOLUB, Petr, Heimo MÜLLER, Tomáš BÍL, Luca PIREDDU, Markus PLASS, Fabian PRASSER, Irene SCHLÜNDER, Kurt ZATLOUKAL, Rudolf NENUTIL and Tomáš BRÁZDIL. Privacy risks of whole-slide image sharing in digital pathology. Nature Communications. 2023, vol. 14, No 2577, p. 1-15. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-37991-y.

HRADECKÁ, Lucia, David WIESNER, Jakub SUMBAL, Zuzana SUMBALOVÁ KOLEDOVÁ and Martin MAŠKA. Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy. IEEE Transactions on Medical Imaging. 2023, vol. 42, No 1, p. 281-290. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2022.3210714.

GALLO, Matej, Vojtěch KRAJŇANSKÝ, Rudolf NENUTIL, Petr HOLUB and Tomáš BRÁZDIL. Shedding light on the black box of a neural network used to detect prostate cancer in whole slide images by occlusion-based explainability. NEW BIOTECHNOLOGY. NETHERLANDS: ELSEVIER, 2023, vol. 78, December, p. 52-67. ISSN 1871-6784. Available from: https://dx.doi.org/10.1016/j.nbt.2023.09.008.

WIESNER, David and Julian SUK. Spatiotemporal cell surface generator. 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 and Carlos ORTIZ-DE-SOLÓRZANO. The Cell Tracking Challenge: 10 years of objective benchmarking. Nature Methods. 2023, vol. 20, No 7, p. 1010-1020. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/s41592-023-01879-y.

EISENMANN, M., A. REINKE, V. WERU, M. D. TIZABI, F. ISENSEE, T. J. ADLER, S. ALI, V. ANDREARCZYK, M. AUBREVILLE, U. BAID, S. BAKAS, N. BALU, S. BANO, J. BERNAL, S. BODENSTEDT, A. CASELLA, V. CHEPLYGINA, M. DAUM, M. DE BRUIJNE, A. DEPEURSINGE, R. DORENT, J. EGGER, D. G. ELLIS, S. ENGELHARDT, M. GANZ, N. GHATWARY, G. GIRARD, P. GODAU, A. GUPTA, L. HANSEN, K. HARADA, M. HEINRICH, N. HELLER, A. HERING, A. HUAULME, P. JANNIN, A. E. KAVUR, O. KODYM, Michal KOZUBEK, J. LI, H. LI, J. MA, C. MARTIN-ISLA, B. MENZE, A. NOBLE, V. OREILLER, N. PADOY, S. PATI, K. PAYETTE, T. RAEDSCH, J. RAFAEL-PATINO, V. Singh BAWA, S. SPEIDEL, C. H. SUDRE, K. VAN WIJNEN, M. WAGNER, D. WEI, A. YAMLAHI, M. H. YAP, C. YUAN, M. ZENK, A. ZIA, D. ZIMMERER, D. AYDOGAN, B. BHATTARAI, L. BLOCH, R. BRUENGEL, J. CHO, C. CHOI, Q. DOU, I. EZHOV, C. M. FRIEDRICH, C. FULLER, R. R. GAIRE, A. GALDRAN, A. Garcia FAURA, M. GRAMMATIKOPOULOU, S. HONG, M. JAHANIFAR, I. JANG, A. KADKHODAMOHAMMADI, I. KANG, F. KOFLER, S. KONDO, H. KUIJF, M. LI, M. LUU, T. MARTINCIC, P. MORAIS, M. A. NASER, B. OLIVEIRA, D. OWEN, S. PANG, J. PARK, S. PARK, S. PLOTKA, E. PUYBAREAU, N. RAJPOOT, K. RYU, N. SAEED, A. SHEPHARD, P. SHI, D. STEPEC, R. SUBEDI, G. TOCHON, H. R. TORRES, H. URIEN, J. L. VILACA, K. A. WAHID, H. WANG, J. WANG, L. WANG, X. WANG, B. WIESTLER, M. WODZINSKI, F. XIA, J. XIE, Z. XIONG, S. YANG, Y. YANG, Z. ZHAO, K. MAIER-HEIN, P. F. JAEGER, A. KOPP-SCHNEIDER and L. MAIER-HEIN. Why is the winner the best?. Online. In 979-8-3503-0129-8. 2023 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR). Vancouver: IEEE COMPUTER SOC, 2023, p. 19955-19966. ISBN 979-8-3503-0129-8. Available from: https://dx.doi.org/10.1109/CVPR52729.2023.01911.

HORÁK, Jiří, Katarína FURMANOVÁ, Barbora KOZLÍKOVÁ, Tomáš BRÁZDIL, Petr HOLUB, Martin KAČENGA, Matej GALLO, Rudolf NENUTIL, Jan BYŠKA and Vít RUSŇÁK. xOpat: eXplainable Open Pathology Analysis Tool. COMPUTER GRAPHICS FORUM. England: Wiley, 2023, vol. 42, No 3, p. 63-73. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14812.

BRÁZDIL, Tomáš, Matej GALLO, Rudolf NENUTIL, Andrej KUBANDA, Martin TOUFAR and Petr HOLUB. Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining. The Journal of Pathology: Clinical Research. 2022, vol. 8, No 2, p. 129-142. ISSN 2056-4538. Available from: https://dx.doi.org/10.1002/cjp2.249.

KEŘKOVSKÝ, Miloš, Marek DOSTÁL, Tereza KOPŘIVOVÁ, Tomáš JŮZA, Václav VYBÍHAL, Eduard NEUMAN, Petr MATULA and Michal KOZUBEK. Differentiation of high grade glioma and brain metastasis using intravoxel incoherent motion MRI. In 45th ESNR Annual Meeting. 2022.

PATI, Sarthak, Ujjwal BAID, Brandon EDWARDS, Micah SHELLER, Shih-Han WANG, G Anthony REINA, Patrick FOLEY, Alexey GRUZDEV, Deepthi KARKADA, Christos DAVATZIKOS, Chiharu SAKO, Satyam GHODASARA, Michel BILELLO, Suyash MOHAN, Philipp VOLLMUTH, Gianluca BRUGNARA, Chandrakanth J PREETHA, Felix SAHM, Klaus MAIER-HEIN, Maximilian ZENK, Martin BENDSZUS, Wolfgang WICK, Evan CALABRESE, Jeffrey RUDIE, Javier VILLANUEVA-MEYER, Soonmee CHA, Madhura INGALHALIKAR, Manali JADHAV, Umang PANDEY, Jitender SAINI, John GARRETT, Matthew LARSON, Robert JERAJ, Stuart CURRIE, Russell FROOD, Kavi FATANIA, Raymond Y HUANG, Ken CHANG, Carmen Balaña QUINTERO, Jaume CAPELLADES, Josep PUIG, Johannes TRENKLER, Josef PICHLER, Georg NECKER, Andreas HAUNSCHMIDT, Stephan MECKEL, Gaurav SHUKLA, Spencer LIEM, Gregory S ALEXANDER, Joseph LOMBARDO, Joshua D PALMER, Adam E FLANDERS, Adam P DICKER, Haris I SAIR, Craig K JONES, Archana VENKATARAMAN, Meirui JIANG, Tiffany Y SO, Cheng CHEN, Pheng Ann HENG, Qi DOU, Michal KOZUBEK, Filip LUX, Jan MICHÁLEK, Petr MATULA, Miloš KEŘKOVSKÝ, Tereza KOPŘIVOVÁ, Marek DOSTÁL, Václav VYBÍHAL, Michael A VOGELBAUM, J Ross MITCHELL, Joaquim FARINHAS, Joseph A MALDJIAN, Chandan Ganesh Bangalore YOGANANDA, Marco C PINHO, Divya REDDY, James HOLCOMB, Benjamin C WAGNER, Benjamin M ELLINGSON, Timothy F CLOUGHESY, Catalina RAYMOND, Talia OUGHOURLIAN, Akifumi HAGIWARA, Chencai WANG, Minh-Son TO, Sargam BHARDWAJ, Chee CHONG, Marc AGZARIAN, Alexandre Xavier FALCÃO, Samuel B MARTINS, Bernardo C A TEIXEIRA, Flávia SPRENGER, David MENOTTI, Diego R LUCIO, Pamela LAMONTAGNE, Daniel MARCUS, Benedikt WIESTLER, Florian KOFLER, Ivan EZHOV, Marie METZ, Rajan JAIN, Matthew LEE, Yvonne W LUI, Richard MCKINLEY, Johannes SLOTBOOM, Piotr RADOJEWSKI, Raphael MEIER, Roland WIEST, Derrick MURCIA, Eric FU, Rourke HAAS, John THOMPSON, David Ryan ORMOND, Chaitra BADVE, Andrew E SLOAN, Vachan VADMAL, Kristin WAITE, Rivka R COLEN, Linmin PEI, Murat AK, Ashok SRINIVASAN, J Rajiv BAPURAJ, Arvind RAO, Nicholas WANG, Ota YOSHIAKI, Toshio MORITANI, Sevcan TURK, Joonsang LEE, Snehal PRABHUDESAI, Fanny MORÓN, Jacob MANDEL, Konstantinos KAMNITSAS, Ben GLOCKER, Luke V M DIXON, Matthew WILLIAMS, Peter ZAMPAKIS, Vasileios PANAGIOTOPOULOS, Panagiotis TSIGANOS, Sotiris ALEXIOU, Ilias HALIASSOS, Evangelia I ZACHARAKI, Konstantinos MOUSTAKAS, Christina KALOGEROPOULOU, Dimitrios M KARDAMAKIS, Yoon Seong CHOI, Seung-Koo LEE, Jong Hee CHANG, Sung Soo AHN, Bing LUO, Laila POISSON, Ning WEN, Pallavi TIWARI, Ruchika VERMA, Rohan BAREJA, Ipsa YADAV, Jonathan CHEN, Neeraj KUMAR, Marion SMITS, Sebastian R VAN DER VOORT, Ahmed ALAFANDI, Fatih INCEKARA, Maarten M J WIJNENGA, Georgios KAPSAS, Renske GAHRMANN, Joost W SCHOUTEN, Hendrikus J DUBBINK, Arnaud J P E VINCENT, Martin J VAN DEN BENT, Pim J FRENCH, Stefan KLEIN, Yading YUAN, Sonam SHARMA, Tzu-Chi TSENG, Saba ADABI, Simone P NICLOU, Olivier KEUNEN, Ann-Christin HAU, Martin VALLIÈRES, David FORTIN, Martin LEPAGE, Bennett LANDMAN, Karthik RAMADASS, Kaiwen XU, Silky CHOTAI, Lola B CHAMBLESS, Akshitkumar MISTRY, Reid C THOMPSON, Yuriy GUSEV, Krithika BHUVANESHWAR, Anousheh SAYAH, Camelia BENCHEQROUN, Anas BELOUALI, Subha MADHAVAN, Thomas C BOOTH, Alysha CHELLIAH, Marc MODAT, Haris SHUAIB, Carmen DRAGOS, Aly ABAYAZEED, Kenneth KOLODZIEJ, Michael HILL, Ahmed ABBASSY, Shady GAMAL, Mahmoud MEKHAIMAR, Mohamed QAYATI, Mauricio REYES, Ji Eun PARK, Jihye YUN, Ho Sung KIM, Abhishek MAHAJAN, Mark MUZI, Sean BENSON, Regina G H BEETS-TAN, Jonas TEUWEN, Alejandro HERRERA-TRUJILLO, Maria TRUJILLO, William ESCOBAR, Ana ABELLO, Jose BERNAL, Jhon GÓMEZ, Joseph CHOI, Stephen BAEK, Yusung KIM, Heba ISMAEL, Bryan ALLEN, John M BUATTI, Aikaterini KOTROTSOU, Hongwei LI, Tobias WEISS, Michael WELLER, Andrea BINK, Bertrand POUYMAYOU, Hassan F SHAYKH, Joel SALTZ, Prateek PRASANNA, Sampurna SHRESTHA, Kartik M MANI, David PAYNE, Tahsin KURC, Enrique PELAEZ, Heydy FRANCO-MALDONADO, Francis LOAYZA, Sebastian QUEVEDO, Pamela GUEVARA, Esteban TORCHE, Cristobal MENDOZA, Vera FRANCO, Elvis RÍOS, Eduardo LÓPEZ, Sergio A VELASTIN, Godwin OGBOLE, Mayowa SONEYE, Dotun OYEKUNLE, Olubunmi ODAFE-OYIBOTHA, Babatunde OSOBU, Mustapha SHU'AIBU, Adeleye DORCAS, Farouk DAKO, Amber L SIMPSON, Mohammad HAMGHALAM, Jacob J PEOPLES, Ricky HU, Anh TRAN, Danielle CUTLER, Fabio Y MORAES, Michael A BOSS, James GIMPEL, Deepak Kattil VEETTIL, Kendall SCHMIDT, Brian BIALECKI, Sailaja MARELLA, Cynthia PRICE, Lisa CIMINO, Charles APGAR, Prashant SHAH, Bjoern MENZE, Jill S BARNHOLTZ-SLOAN, Jason MARTIN and Spyridon BAKAS. Federated learning enables big data for rare cancer boundary detection. Nature Communications. London: Nature Publishing Group, 2022, vol. 13, No 7346, p. 1-17. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-022-33407-5.

WIESNER, David, Julian SUK, Sven DUMMER, David SVOBODA and 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, p. 58-67. ISBN 978-3-031-16439-2. Available from: https://dx.doi.org/10.1007/978-3-031-16440-8_6.

BRÁZDIL, Tomáš, David KLAŠKA, Antonín KUČERA, Vít MUSIL, Petr NOVOTNÝ and Vojtěch ŘEHÁK. On-the-fly Adaptation of Patrolling Strategies in Changing Environments. Online. In James Cussens, Kun Zhang. Proceedings of the Thirty-Eighth Conference on Uncertainty in Artificial Intelligence, UAI 2022. Neuveden: Proceedings of Machine Learning Research, 2022, p. 244-254. ISBN 978-1-7138-6329-8.

ULMAN, Vladimír and 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, p. 447-489. The MICCAI Society book Series. ISBN 978-0-12-824349-7. Available from: https://dx.doi.org/10.1016/B978-0-12-824349-7.00028-1.

PREISLER, Jan, Markéta MACHÁLKOVÁ, Barbora ADAMOVÁ, Jarmila NAVRÁTILOVÁ, Marek STIBOREK, Stanislava MELIORISOVÁ, Jiří KROUPA, Pavel HOUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Katarzyna Anna RADASZKIEWICZ, Adam PRUŠKA, Viktor KANICKÝ, Michal KOZUBEK and Jan ŠMARDA. Multimodal Imaging of 3D Cell Aggregates. In MSB 2021. 2021.

SVOBODA, David, Ninon BURGOS, Jelmer M. WOLTERINK and Can ZHAO. Simulation and Synthesis in Medical Imaging. 1st ed. Cham: Springer, 2021, 154 pp. ISBN 978-3-030-87591-6. Available from: https://dx.doi.org/10.1007/978-3-030-87592-3.

MELNIKOVA, Aleksandra and Petr MATULA. Topology Preserving Segmentation Fusion for Cells with Complex Shapes. Online. In The IEEE International Symposium on Biomedical Imaging. Nice: IEEE, 2021, p. 204-207. ISBN 978-1-6654-1246-9. Available from: https://dx.doi.org/10.1109/ISBI48211.2021.9433867.

KOZLOVSKÝ, Martin, David WIESNER and 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, p. 77-86. ISBN 978-3-030-87591-6. Available from: https://dx.doi.org/10.1007/978-3-030-87592-3_8.

FERKOVÁ, Zuzana, Petra URBANOVÁ, Dominik ČERNÝ, Marek ŽUŽI and Petr MATULA. Age and gender-based human face reconstruction from single frontal image. Multimedia Tools and Applications. Kluwer Academic Publishers, 2020, vol. 79, 5-6, p. 3217-3242. ISSN 1380-7501. Available from: https://dx.doi.org/10.1007/s11042-018-6869-5.

ŠUJAKOVÁ, Lenka, Jiří PAŘENICA, Jiří HLÁSENSKÝ, Miloš KEŘKOVSKÝ, Tomáš ANDRAŠINA, Zdeněk ŠILHART and Petr KALA. Akutní končetinová ischemie při konkomitantní systémové a plicní embolizaci (Acute limb ischemia in concomitant systemic and pulmonary embolization). Cor et Vasa Case Reports. Brno: Česká kardiologická společnost, z. s., 2020, vol. 2020, No 3, p. 73-78. ISSN 2571-0648.

RUBENS, Ulysse, Romain MORMONT, Lassi PAAVOLAINEN, Volker BÄCKER, Benjamin PAVIE, Leandro A. SCHOLZ, Gino MICHIELS, Martin MAŠKA, Devrim ÜNAY, Graeme BALL, Renaud HOYOUX, Rémy VANDAELE, Ofra GOLANI, Stefan G. STANCIU, Natasa SLADOJE, Perrine PAUL-GILLOTEAUX, Raphaël MARÉE and Sébastien TOSI. BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. Patterns. Cell Press, 2020, vol. 1, No 3, p. 1-10. ISSN 2666-3899. Available from: https://dx.doi.org/10.1016/j.patter.2020.100040.

MAIER-HEIN, Lena, Annika REINKE, Michal KOZUBEK, Anne L. MARTEL, Tal ARBEL, Matthias EISENMANN, Allan HANBURY, Pierre JANNIN, Henning MÜLLER, Sinan ONOGUR, Julio SAEZ-RODRIGUEZ, Bram VAN GINNEKEN, Annette KOPP-SCHNEIDER and Bennett A. LANDMAN. BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Analysis. Elsevier, 2020, vol. 66, No 101796, p. 1-7. ISSN 1361-8415. Available from: https://dx.doi.org/10.1016/j.media.2020.101796.

AKBAS, Cem Emre and Michal KOZUBEK. Condensed U-Net (CU-Net): An Improved U-Net Architecture for Cell Segmentation Powered by 4x4 Max-Pooling Layers. Online. In IEEE 17th International Symposium on Biomedical Imaging. Iowa: IEEE, 2020, p. 446-450. ISBN 978-1-5386-9330-8. Available from: https://dx.doi.org/10.1109/ISBI45749.2020.9098351.

ROHAN, Tomáš and Tereza KOPŘIVOVÁ. Difuzní léze jater. In 18. Valtické kurzy abdominální a gastrointestinální radiologie. 2020.

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

PAVLATOVSKÁ, Barbora, Markéta MACHÁLKOVÁ, Petra BRISUDOVÁ, Adam PRUŠKA, Karel ŠTĚPKA, Jan MICHÁLEK, Tereza NEČASOVÁ, Petr BENEŠ, Jan ŠMARDA, Jan PREISLER, Michal KOZUBEK and Jarmila NAVRÁTILOVÁ. Lactic Acidosis Interferes With Toxicity of Perifosine to Colorectal Cancer Spheroids: Multimodal Imaging Analysis. Frontiers in Oncology. Lausanne: Frontiers Media S.A., 2020, vol. 10, December, p. 1-18. ISSN 2234-943X. Available from: https://dx.doi.org/10.3389/fonc.2020.581365.

HOŘÍNKOVÁ, Jana, Elis BARTEČKŮ, Marek DOSTÁL, Miloš KEŘKOVSKÝ, Alena DAMBORSKÁ and Petra ŠTROCHOLCOVÁ. Morfologie Corpus Callosum a klinický stav u pacientů s depresivní poruchou (Corpus Callosum morphology and clinical state in patients with major depression). In Změny klimatu v české psychiatrii: Sborník příspěvků XIII. sjezdu Psychiatrické společnosti ČLS JEP 2020. 2020.

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

KOZUBEK, Michal. When Deep Learning Meets Cell Image Synthesis. Cytometry Part A. John Wiley & Sons, 2020, vol. 97, No 3, p. 222-225. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23957.

HANDBERG-THORSAGER, Mette, Vladimír ULMAN, Pavel TOMANČÁK, D. ARENDT and 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, p. 193-207. ISBN 978-1-4939-9584-4. Available from: https://dx.doi.org/10.1007/978-1-4939-9585-1_14.

AKBAŞ, Cem Emre, Vladimír ULMAN, Martin MAŠKA, Florian JUG and 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, p. 446-454. ISBN 978-3-030-11023-9. Available from: https://dx.doi.org/10.1007/978-3-030-11024-6_34.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Jan MICHÁLEK, Karel ŠTĚPKA, Adam PRUŠKA, Michal KOZUBEK, Petr BENEŠ, Jan ŠMARDA and Jan PREISLER. Combined therapy of perifosine and ABT-737 results in higher cytotoxic effect but also induces expression of EMT markers in colon cancer cell lines. In Spetses Summer School: Molecular Mechanisms in Signal Transduction and Cancer, Greece. 2019.

WIESNER, David, David SVOBODA, Martin MAŠKA and Michal KOZUBEK. CytoPacq: A web-interface for simulating multi-dimensional cell imaging. Bioinformatics. Oxford University Press, 2019, vol. 35, No 21, p. 4531-4533. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz417.

GÓMEZ-DE-MARISCAL, Estibaliz, Martin MAŠKA, Anna KOTRBOVÁ, Vendula POSPÍCHALOVÁ, Pavel MATULA and Arrate MUÑOZ-BARRUTIA. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Scientific Reports. 2019, vol. 9, No 13211, p. 1-10. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-019-49431-3.

LUX, Filip and Petr MATULA. DIC Image Segmentation of Dense Cell Populations by Combining Deep Learning and Watershed. Online. In IEEE 16th International Symposium on Biomedical Imaging. Venice, Italy, Italy: IEEE 16th International Symposium on Biomedical Imaging, 2019, p. 236-239. ISBN 978-1-5386-3641-1. Available from: https://dx.doi.org/10.1109/ISBI.2019.8759594.

MACHÁLKOVÁ, Markéta, Barbora PAVLATOVSKÁ, Jan MICHÁLEK, Adam PRUŠKA, Karel ŠTĚPKA, Tereza NEČASOVÁ, Katarzyna Anna RADASZKIEWICZ, Michal KOZUBEK, Jan ŠMARDA, Jan PREISLER and Jarmila NAVRÁTILOVÁ. Drug Penetration Analysis in 3D Cell Cultures Using Fiducial-Based Semiautomatic Coregistration of MALDI MSI and Immunofluorescence Images. Analytical Chemistry. American Chemical Society, 2019, vol. 91, No 21, p. 13475-13484. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.9b02462.

MICHÁLEK, Jan, Pavla HANZLÍKOVÁ, Tuan TRINH and Dalibor PACÍK. Fast and accurate compensation of signal offset for T2 mapping. Magnetic Resonance Materials in Physics, Biology and Medicine. Springer International Publishing, 2019, vol. 32, No 4, p. 423-436. ISSN 0968-5243. Available from: https://dx.doi.org/10.1007/s10334-019-00737-3.

NAVRÁTILOVÁ, Jarmila, Markéta MACHÁLKOVÁ, Barbora PAVLATOVSKÁ, Jan MICHÁLEK, Adam PRUŠKA, Karel ŠTĚPKA, Katarzyna Anna RADASZKIEWICZ, Jan PREISLER, Jan ŠMARDA and Michal KOZUBEK. Fiducial-based semi-automatic coregistration and analysis of multimodal MALDI MS and immunofluorescent data. In Imaging Principles of Life 2019. 2019.

FERKOVÁ, Zuzana and Petr MATULA. Multimodal Point Distribution Model for Anthropological Landmark Detection. Online. In 26th IEEE International Conference on Image Processing (ICIP2019). Taipei, Taiwan: Springer, 2019, p. 2986-2990. ISBN 978-1-5386-6249-6. Available from: https://dx.doi.org/10.1109/ICIP.2019.8803252.

WIESNER, David, Tereza NEČASOVÁ and 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, p. 672-682. ISBN 978-3-030-30644-1. Available from: https://dx.doi.org/10.1007/978-3-030-30645-8_61.

MICHÁLEK, Jan, Karel ŠTĚPKA, Michal KOZUBEK, Jarmila NAVRÁTILOVÁ, Barbora PAVLATOVSKÁ, Markéta MACHÁLKOVÁ, Jan PREISLER and Adam PRUŠKA. Quantitative Assessment of Anti-Cancer Drug Efficacy From Coregistered Mass Spectrometry and Fluorescence Microscopy Images of Multicellular Tumor Spheroids. Microscopy and Microanalysis. Cambridge University Press, 2019, vol. 25, No 6, p. 1311-1322. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927619014983.

CORTESE, Mirko, Anil KUMAR, Petr MATULA, Lars KADERALI, Pietro SCATURRO, Holger ERFLE, Eliana Gisela ACOSTA, Sandra BUEHLER, Alessia RUGGIERI, Laurent CHATEL-CHAIX, Karl ROHR and Ralf BARTENSCHLAGER. Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production. Cell Reports. CAMBRIDGE, Spojené státy americké: Cell Press, 2019, vol. 27, No 9, p. 2579-2592,"e1"-"e6", 20 pp. ISSN 2211-1247. Available from: https://dx.doi.org/10.1016/j.celrep.2019.04.105.

KOTRBOVÁ, Anna, Karel ŠTĚPKA, Martin MAŠKA, Juraj PÁLENIK, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Marek KRAVEC, František HUBATKA, Zankruti DAVE, Aleš HAMPL, Vítězslav BRYJA, Pavel MATULA and Vendula POSPÍCHALOVÁ. TEM ExosomeAnalyzer: a computer-assisted software tool for quantitative evaluation of extracellular vesicles in transmission electron microscopy images. Journal of Extracellular Vesicles. Taylor and Francis Ltd., 2019, vol. 8, No 1, p. 1-13. ISSN 2001-3078. Available from: https://dx.doi.org/10.1080/20013078.2018.1560808.

ŠALINGOVÁ, Barbara, Pavel ŠIMARA, Pavel MATULA, Lenka ZAJÍČKOVÁ, Petr SYNEK, Ondřej JAŠEK, Lenka VEVERKOVÁ, Miroslava SEDLÁČKOVÁ, Zuzana NICHTOVA and Irena KOUTNÁ. The Effect of Uncoated SPIONs on hiPSC-Differentiated Endothelial Cells. International Journal of Molecular Sciences. BASEL: Molecular Diversity Preservation International, 2019, vol. 20, No 14, p. 1-16. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms20143536.

EISELLEOVÁ, Lívia, Viktor LUKJANOV, Šimon FARKAŠ, David SVOBODA, Karel ŠTĚPKA and 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, vol. 2019, Article ID 1375807, p. 1-12. ISSN 1687-966X. Available from: https://dx.doi.org/10.1155/2019/1375807.

MAŠKA, Martin, Tereza NEČASOVÁ, David WIESNER, Dmitry SOROKIN, Igor PETERLÍK, Vladimír ULMAN and 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, p. 819-823. ISBN 978-1-5386-6249-6. Available from: https://dx.doi.org/10.1109/ICIP.2019.8803721.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Petra BRISUDOVÁ, Jan MICHÁLEK, Karel ŠTĚPKA, Adam PRUŠKA, Michal KOZUBEK, Petr BENEŠ, Jan ŠMARDA and Jan PREISLER. Tumor-specific microenvironment contributes to the perifosine resistance in 3D colorectal cancer (CRC) models. In Goodbye Flat Biology: Advancing 3D-based Models for Cancer Biology and Drug Discovery, Berlin, Germany. 2019.

NEČASOVÁ, Tereza and 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, p. 385-394. ISBN 978-3-030-11023-9. Available from: https://dx.doi.org/10.1007/978-3-030-11024-6_28.

CASTILLA, Carlos, Martin MAŠKA, Dmitry SOROKIN, Erik MEIJERING and Carlos ORTIZ-DE-SOLÓRZANO. 3-D Quantification of Filopodia in Motile Cancer Cells. IEEE Transactions on Medical Imaging. IEEE, 2019, vol. 38, No 3, p. 862-872. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2018.2873842.

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

DVOŘÁK, Pavel, David BEDNÁŘ, Pavel VAŇÁČEK, Lukáš BÁLEK, Lívia EISELLEOVÁ, Veronika ŠTĚPÁNKOVÁ, Eva ŠEBESTOVÁ, Michaela BOSÁKOVÁ, Žaneta KONEČNÁ, Stanislav MAZURENKO, Antonín KUNKA, Tereza VÁŇOVÁ, Karolína ZOUFALOVÁ, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ, Pavel KREJČÍ, Zbyněk PROKOP, Petr DVOŘÁK and Jiří DAMBORSKÝ. Computer-assisted engineering of hyperstable fibroblast growth factor 2. Biotechnology and Bioengineering. New York: Wiley, 2018, vol. 115, No 4, p. 850-862. ISSN 0006-3592. Available from: https://dx.doi.org/10.1002/bit.26531.

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA, Tereza NEČASOVÁ, Katsiarina MORGAENKO, Lívia EISELLEOVÁ, Lenka TESAŘOVÁ and 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, vol. 37, No 12, p. 2630-2641. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2018.2845884.

REINKE, Annika, Matthias EISENMANN, Sinan ONOGUR, Marko STANKOVIC, Patrick SCHOLZ, Peter M FULL, Hrvoje BOGUNOVIC, Bennett A LANDMAN, Oskar MAIER, Bjoern MENZE, Gregory C SHARP, Korsuk SIRINUKUNWATTANA, Stefanie SPEIDEL, Fons VAN DER SOMMEN, Guoyan ZHENG, Henning MÜLLER, Michal KOZUBEK, Tal ARBEL, Andrew P BRADLEY, Pierre JANNIN, Annette KOPP-SCHNEIDER and Lena MAIER-HEIN. How to Exploit Weaknesses in Biomedical Challenge Design and Organization. In Alejandro F. Frangi, Julia A. Schnabel, Christos Davatzikos, Carlos Alberola-López, Gabor Fichtinger. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. LNCS 11073. Cham (Switzerland): Springer, 2018, p. 388-395. ISBN 978-3-030-00936-6. Available from: https://dx.doi.org/10.1007/978-3-030-00937-3_45.

PETERLÍK, Igor, David SVOBODA, Vladimír ULMAN, Dmitry SOROKIN and 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, p. 71-79. ISBN 978-3-030-00535-1. Available from: https://dx.doi.org/10.1007/978-3-030-00536-8_8.

SOROKIN, Dmitry, Igor PETERLÍK, Marco TEKTONIDIS, Karl ROHR and Pavel MATULA. Non-rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model. IEEE Transactions on Medical Imaging. IEEE, 2018, vol. 37, No 1, p. 173-184. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2017.2734169.

DVOŘÁČKOVÁ, Martina, B. RAPOSO, Petr MATULA, J. FUCHS, V. SCHUBERT, Vratislav PEŠKA, B. DESVOYES, C. GUTIERREZ and Jiří FAJKUS. Replication of ribosomal DNA in Arabidopsis occurs both inside and outside the nucleolus during S phase progression. Journal of Cell Science. Cambridge: Company of Biologists Ltd., 2018, vol. 131, No 2, p. nestránkováno, 12 pp. ISSN 0021-9533. Available from: https://dx.doi.org/10.1242/jcs.202416.

ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Šimon FARKAŠ, Barbara ŠALINGOVÁ, Kateřina KUTÁLKOVÁ, Eva VAVREČKOVÁ, Pavel MATULA, Petr MATULA, Lenka VEVERKOVÁ and Irena KRONTORÁD KOUTNÁ. Reprogramming of Adult Peripheral Blood Cells into Human Induced Pluripotent Stem Cells as a Safe and Accessible Source of Endothelial Cells. Stem Cells and Development. Mary Ann Liebert, Inc. publishers, 2018, vol. 27, No 1, p. 10-22. ISSN 1547-3287. Available from: https://dx.doi.org/10.1089/scd.2017.0132.

ŠIMARA, Pavel, Lenka TESAŘOVÁ, Daniela ŘEHÁKOVÁ, Šimon FARKAŠ, Barbara ŠALINGOVÁ, Kateřina KUTÁLKOVÁ, Eva VAVREČKOVÁ, Pavel MATULA, Petr MATULA and Irena KRONTORÁD KOUTNÁ. Reprogramming of peripheral blood cells into hiPSCs as a source of endothelial cells. In SY-Stem symposium 2018. 2018.

CASTILLA, Carlos, Martin MAŠKA, Dmitry SOROKIN, Erik MEIJERING and Carlos ORTIZ-DE-SOLORZANO. Segmentation of Actin-Stained 3D Fluorescent Cells with Filopodial Protrusions using Convolutional Neural Networks. Online. In 15th IEEE International Symposium on Biomedical Imaging. Washington: IEEE, 2018, p. 413-417. ISBN 978-1-5386-3636-7. Available from: https://dx.doi.org/10.1109/ISBI.2018.8363605.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Adam PRUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Michal KOZUBEK, Jan ŠMARDA and Jan PREISLER. The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures. In Summer School in Translational Cancer Research 2018. 2018.

PAVLATOVSKÁ, Barbora, Jarmila NAVRÁTILOVÁ, Markéta MACHÁLKOVÁ, Adam PRUŠKA, Jan MICHÁLEK, Karel ŠTĚPKA, Michal KOZUBEK, Jan ŠMARDA and Jan PREISLER. The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures. (The effect and distribution of the drug perifosine in 2D and 3D colorectal cell cultures). In XIX. Meeting of Biochemists and Molecular Biologists. 2018.

SVOBODA, David, Tereza NEČASOVÁ, Lenka TESAŘOVÁ and 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, p. 90-99. ISBN 978-3-030-00535-1. Available from: https://dx.doi.org/10.1007/978-3-030-00536-8_10.

MAIER-HEIN, Lena, Matthias EISENMANN, Annika REINKE, Sinan ONOGUR, Marko STANKOVIC, Patrick SCHOLZ, Tal ARBEL, Hrvoje BOGUNOVIC, Andrew BRADLEY, Aaron CARASS, Carolin FELDMANN, Alejandro FRANGI, Peter FULL, Bram VAN GINNEKEN, Allan HANBURY, Katrin HONAUER, Michal KOZUBEK, Bennett LANDMAN, Keno MÄRZ, Oskar MAIER, Klaus MAIER-HEIN, Bjoern MENZE, Henning MÜLLER, Peter NEHER, Wiro NIESSEN, Nasir RAJPOOT, Gregory SHARP, Korsuk SIRINUKUNWATTANA, Stefanie SPEIDEL, Christian STOCK, Danail STOYANOV, Abdel Aziz TAHA, Fons VAN DER SOMMEN, Ching-Wei WANG, Marc-André WEBER, Guoyan ZHENG, Pierre JANNIN and Annette KOPP-SCHNEIDER. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications. Nature Publishing Group, 2018, vol. 9, No 5217, p. 1-13. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-018-07619-7.

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 and Carlos ORTIZ-DE-SOLORZANO. An objective comparison of cell-tracking algorithms. Nature Methods. Macmillan Publishers Limited, part of Springer Nature, 2017, vol. 14, No 12, p. 1141-1152. ISSN 1548-7091. Available from: https://dx.doi.org/10.1038/nmeth.4473.

KONDRATĚV, Alexandr and Dmitry SOROKIN. Automatic detection of laser-induced structures in live cell fluorescent microscopy images using snakes with geometric constraints. In 23rd International Conference on Pattern Recognition, ICPR 2016. Cancun, Mexico: Institute of Electrical and Electronics Engineers Inc., 2017, p. 331-336. ISBN 978-1-5090-4847-2. Available from: https://dx.doi.org/10.1109/ICPR.2016.7899655.

ANOSHINA, Nadezhda A., Andrey S. KRYLOV and Dmitry SOROKIN. Correlation-based 2D Registration Method for Single Particle Cryo-EM Images. Online. In Seventh International Conference on Image Processing Theory, Tools and Applications (IPTA), 2017. Montreal: IEEE, 2017, p. 1-6. ISBN 978-1-5386-1842-4. Available from: https://dx.doi.org/10.1109/IPTA.2017.8310125.

SEČKÁŘ, Petr and David SVOBODA. FTutor: An Interactive Guide to the Fundamentals of Frequency Analysis. Computer Applications in Engineering Education. Wiley, 2017, vol. 25, No 3, p. 508-520. ISSN 1061-3773. Available from: https://dx.doi.org/10.1002/cae.21817.

TESAŘOVÁ, Lenka, Pavel ŠIMARA, Stanislav STEJSKAL and Irena KRONTORÁD KOUTNÁ. 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. Cellular Reprogramming. 2017, vol. 19, No 4, p. 270-284. ISSN 2152-4971. Available from: https://dx.doi.org/10.1089/cell.2016.0042.

ANGUIANO, María, Carlos CASTILLA, Martin MAŠKA, Cristina EDERRA, Rafael PELÁEZ, Xabier MORALES, Gorka MUÑOZ-ARRIETA, Maite MUJIKA, Michal KOZUBEK, Arrate MUÑOZ-BARRUTIA, Ana ROUZAUT, Sergio ARANA, José Manuel GARCIA-AZNAR and Carlos ORTIZ-DE-SOLORZANO. Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis. PLoS ONE. 2017, vol. 12, No 2, p. 1-24. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0171417.

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK and Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 13, p. 2002-2009. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx027.

SVOBODA, David and 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, vol. 36, No 1, p. 310-321. ISSN 0278-0062. Available from: https://dx.doi.org/10.1109/TMI.2016.2606545.

SOROKIN, Dmitry, Igor PETERLÍK, Vladimír ULMAN, David SVOBODA and 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, p. 822-826. ISBN 978-1-5090-1172-8. Available from: https://dx.doi.org/10.1109/ISBI.2017.7950644.

SVOBODA, David and 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, p. 89-98. ISBN 978-3-319-68126-9. Available from: https://dx.doi.org/10.1007/978-3-319-68127-6_10.

MASKOVA, P., B. RADOCHOVA, Z. LHOTAKOVA, Jan MICHÁLEK and H. LIPAVSKA. Nonstructural carbohydrate-balance response to long-term elevated CO2 exposure in European beech and Norway spruce mixed cultures: biochemical and ultrastructural responses. Canadian journal of forest research. Ottawa: The national research council, 2017, vol. 47, No 11, p. 1488-1494. ISSN 0045-5067. Available from: https://dx.doi.org/10.1139/cjfr-2017-0083.

MAŠKA, Martin and Pavel MATULA. Particle Tracking Accuracy Measurement Based on Comparison of Linear Oriented Forests. Online. In 16th IEEE International Conference on Computer Vision Workshops. Venice: IEEE, 2017, p. 11-17. ISBN 978-1-5386-1034-3. Available from: https://dx.doi.org/10.1109/ICCVW.2017.8.

ŠIMARA, Pavel, Irena KRONTORÁD KOUTNÁ, Lenka TESAŘOVÁ and Šimon FARKAŠ. POTENTIAL OF hiPSCs DERIVED FROM DIFFERENT CELL TYPES TO DIFFERENTIATE INTO FUNCTIONAL ENDOTHELIAL CELLS. In ISSCR 2017 Annual Meeting. 2017.

HAMPL, Aleš, Hana KOTASOVÁ, Zuzana GARLÍKOVÁ and Irena KRONTORÁD KOUTNÁ. Self-Renewing Early Lung Epithelial Progenitor Cells Differentiated From Human Embryonic Stem Cells. In ISSCR 2017 Annual Meeting, Boston, USA, 14.-17.6.2017. 2017.

FERKOVÁ, Zuzana, Marek ŽUŽI, Petra URBANOVÁ and Petr MATULA. Single image reconstruction of human faces using database of depth images. Online. In 9th International Conference on Virtual Worlds and Games for Serious Applications (VS-Games 2017). Athens, Greece: IEEE Computer Society, 2017, p. 109-116. ISBN 978-1-5090-5812-9. Available from: https://dx.doi.org/10.1109/VS-GAMES.2017.8056578.

ŘEHÁKOVÁ, Daniela, Kateřina KUTÁLKOVÁ and Irena KRONTORÁD KOUTNÁ. Standardized hiPSCs culture – vitronectin coating for cGMP compliant protocol. Online. Olomouc: Univerzita Palackého, 2017, p. 25-28, 57 pp. ISSN 1804-7521.

FRANEK, Michal, Jana SUCHÁNKOVÁ, Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ, Jana KREJČÍ, Soňa LEGARTOVÁ, Stanislav KOZUBEK, J VEČEŘA, Dmitry SOROKIN and Eva BÁRTOVÁ. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. Microscopy and Microanalysis. Saarbrücken: Cambridge University Press, 2016, vol. 22, No 2, p. 326-341. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927616000052.

ŠTĚPKA, Karel, Martin MAŠKA, Jakub Jozef PÁLENIK, Vendula POSPÍCHALOVÁ, Anna KOTRBOVÁ, Ladislav ILKOVICS, Dobromila KLEMOVÁ, Aleš HAMPL, Vítězslav BRYJA and Pavel MATULA. Automatic Detection and Segmentation of Exosomes in Transmission Electron Microscopy. In Gang Hua, Hervé Jégou. Computer Vision -- ECCV 2016 Workshops: Amsterdam, The Netherlands, October 8-10 and 15-16, 2016, Proceedings, Part I. Cham, Switzerland: Springer International Publishing, 2016, p. 318-325. ISBN 978-3-319-46603-3. Available from: https://dx.doi.org/10.1007/978-3-319-46604-0_23.

KONDRAT'EV, Alexandr and Dmitry SOROKIN. Automatic Detection of Laser-Induced Structures in Live Cell Fluorescent Microscopy Images Using Snakes with Geometric Constraints. Online. In IEEE 23rd International Conference on Pattern Recognition (ICPR). Not specified: IEEE, 2016, p. 326-331. ISBN 978-1-5090-4846-5. Available from: https://dx.doi.org/10.1109/ICPR.2016.7899655.

LEGARTOVÁ, Soňa, Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ, Barbora MALYŠKOVÁ, Thomas KÜNTZIGER, Philippe COLLAS, Dušan CMARKO, Ivan RAŠKA, Dmitry SOROKIN, Stanislav KOZUBEK and Eva BÁRTOVÁ. Localized Movement and Levels of 53BP1 Protein Are Changed by gamma-irradiation in PML Deficient Cells. Journal of Cellular Biochemistry [IF=2.778 (1990)]. Wiley-Liss, 2016, vol. 117, No 11, p. 2583-2596. ISSN 0730-2312. Available from: https://dx.doi.org/10.1002/jcb.25551.

MUSINOVA, Yana R., Olga M. LISITSYNA, Dmitry SOROKIN, Eugene A. ARIFULIN, Tatiana A. SMIRNOVA, Roman A. ZINOVKIN, Daria M. POTASHNIKOVA, Yegor S. VASSETZKY and Eugene V. SHEVAL. RNA-dependent disassembly of nuclear bodies. Journal of Cell Science. The Company of Biologists Ltd., 2016, vol. 129, No 24, p. 4509-4520. ISSN 0021-9533. Available from: https://dx.doi.org/10.1242/jcs.189142.

STOKLASA, Roman and Tomáš MAJTNER. Texture Analysis of 3D Fluorescence Microscopy Images Using RSurf 3D Features. Online. In International Symposium on Biomedical Imaging (ISBI'16). Los Alamitos, California: IEEE Computer Society, 2016, p. 1212-1216. ISBN 978-1-4799-2350-2. Available from: https://dx.doi.org/10.1109/ISBI.2016.7493484.

SVOBODA, David, Vladimír ULMAN, Peter KOVÁČ, Barbara ŠALINGOVÁ, Lenka TESAŘOVÁ, Irena KRONTORÁD KOUTNÁ and 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, p. 3180-3183. ISBN 978-1-4673-9961-6. Available from: https://dx.doi.org/10.1109/ICIP.2016.7532946.

ULMAN, Vladimír, David SVOBODA, Matti NYKTER, Michal KOZUBEK and Pekka RUUSUVUORI. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry Part A. John Wiley & Sons, 2016, 89A, No 12, p. 1057-1072. ISSN 1552-4922. Available from: https://dx.doi.org/10.1002/cyto.a.23031.

MATULA, Pavel, Martin MAŠKA, Dmitry SOROKIN, Petr MATULA, Carlos ORTIZ-DE-SOLÓRZANO and Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, vol. 10, No 12, p. "e0144959", 19 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0144959.

SOROKIN, Dmitry, Lenka STIXOVÁ, Petra SEHNALOVÁ, Soňa LEGARTOVÁ, Jana SUCHÁNKOVÁ, Pavel ŠIMARA, Stanislav KOZUBEK, Pavel MATULA, Magdalena SKALNÍKOVÁ, Ivan RAŠKA and Eva BÁRTOVÁ. Localized movement and morphology of UBF1-positive nucleolar regions are changed by gamma-irradiation in G2 phase of the cell cycle. Nucleus. 2015, vol. 6, No 4, p. 301-313. ISSN 1949-1034. Available from: https://dx.doi.org/10.1080/19491034.2015.1075111.

SVOBODA, David, Vladimír ULMAN and 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, p. 712-716. ISBN 978-1-4799-2374-8. Available from: https://dx.doi.org/10.1109/ISBI.2015.7163972.

ULMAN, Vladimír, Zoltán ORÉMUŠ and 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, p. 623-634. ISBN 978-3-319-23230-0. Available from: 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 and Carlos ORTIZ-DE-SOLORZANO. A Benchmark for Comparison of Cell Tracking Algorithms. Bioinformatics. 2014, vol. 30, No 11, p. 1609-1617. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btu080.

BÁRTOVÁ, Eva, Veronika FOLTÁNKOVÁ, Soňa LEGARTOVÁ, Petra SEHNALOVÁ, Dmitry SOROKIN, Jana SUCHÁNKOVÁ and Stanislav KOZUBEK. Coilin is rapidly recruited to UVA-induced DNA lesions and gamma-radiation affects localized movement of Cajal bodies. Nucleus. Landes Bioscience, 2014, vol. 5, No 3, p. 269-277. ISSN 1949-1034. Available from: https://dx.doi.org/10.4161/nucl.29229.

STIXOVÁ, Lenka, Petra SEHNALOVÁ, Soňa LEGARTOVÁ, Jana SUCHÁNKOVÁ, Tereza HRUŠKOVÁ, Stanislav KOZUBEK, Dmitry SOROKIN, Pavel MATULA, Ivan RAŠKA, Aleš KOVAŘÍK, Jaroslav FULNEČEK and Eva BÁRTOVÁ. HP1B-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs (HP1B-dependent recruitment of UBF1 to 3 irradiated chromatin occurs simultaneously with 4 CPDs). Epigenetics & Chromatin. BioMed Central, 2014, vol. 7, No 39, p. 1-17. ISSN 1756-8935. Available from: https://dx.doi.org/10.1186/1756-8935-7-39.

SOROKIN, Dmitry, Marco TEKTONIDIS, Karl ROHR and Pavel MATULA. NON-RIGID CONTOUR-BASED TEMPORAL REGISTRATION OF 2D CELL NUCLEI IMAGES USING THE NAVIER EQUATION. Online. In IEEE International Symposium on Biomedical Imaging: Nano to Macro. Beijing: IEEE, 2014, p. 746-749. ISBN 978-1-4673-1959-1. Available from: https://dx.doi.org/10.1109/ISBI.2014.6867978.

SVOBODA, David, Vladimír ULMAN, Luděk MATYSKA, Martin MAŠKA, Ján BELLA and 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, p. 3944-3948. ISBN 978-1-4799-5750-7. Available from: https://dx.doi.org/10.1109/ICIP.2014.7025801.

SUCHÁNKOVÁ, Jana, Soňa LEGARTOVÁ, Petra SEHNALOVÁ, Stanislav KOZUBEK, Sergio VALENTE, Donatella LABELLA, Antonello MAI, Carmen ECKERICH, Frank O. FACKELMAYER, Dmitry SOROKIN and Eva BÁRTOVÁ. PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage. European Journal of Histochemistry. Pavia, Italy: PAGEPress, 2014, vol. 58, No 2, p. 139-151. ISSN 1121-760X. Available from: https://dx.doi.org/10.4081/ejh.2014.2389.

SOROKIN, Dmitry, Jana SUCHÁNKOVÁ, Eva BÁRTOVÁ and Pavel MATULA. Visualizing Stable Features in Live Cell Nucleus for Evaluation of the Cell Global Motion Compensation. Folia biologica. Univerzita Karlova, 2014, vol. 60, (Suppl 1), p. 45-49. ISSN 0015-5500.

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

FOLTÁNKOVÁ, Veronika, Pavel MATULA, Dmitry SOROKIN, Stanislav KOZUBEK and Eva BÁRTOVÁ. Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body co-localization in DNA lesions. Microscopy and Microanalysis. Saarbrücken: Cambridge University Press, 2013, Volume 19, Issue 2, p. 360-369. ISSN 1431-9276. Available from: https://dx.doi.org/10.1017/S1431927612014353.

SVOBODA, David and 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, p. 429-438. ISBN 978-3-642-41183-0. Available from: https://dx.doi.org/10.1007/978-3-642-41184-7_44.

SVOBODA, David and 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, p. 473-482. ISBN 978-3-642-31297-7. Available from: 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, vol. 2011, ID 234090, p. 1-9. ISSN 1687-6172. Available from: 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 pp.

ULMAN, Vladimír and 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, p. 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, p. 263-273. ISBN 978-3-642-13771-6. Available from: https://dx.doi.org/10.1007/978-3-642-13772-3_27.

VAŘECHA, Miroslav, Vladimír ULMAN, Pavel MATULA and 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 and Michal KOZUBEK. Prediction of localization and interactions of apoptotic proteins. Journal of Biomedical Science. BioMed website: BioMed Central, London, England, 2009, vol. 16, No 59, p. 1-14. ISSN 1021-7770.