Výpis publikací

PŘIKRYL, Matěj; Andrea ROUSOVÁ; Ivana AĆIMOVIĆ; Petr VAŇHARA; Lukáš JAN; Petr BENEŠ; Jan ŠMARDA; Michal KOZUBEK; Karel ŠTĚPKA a Jarmila NAVRÁTILOVÁ. Cell Invasion Analysis of Tumor Spheroids Using 2D Image Data. ACS Measurement Science Au. AMER CHEMICAL SOC, 2026, roč. 6, č. 1, s. 59-67. ISSN 2694-250X. Dostupné z: https://doi.org/10.1021/acsmeasuresciau.5c00121.

EFTIMIU, Nikomidisz Jorgosz a Michal KOZUBEK. Comprehensive Attention Networks for Cell Segmentation Using Numerical Integration. Online. In 2026 IEEE International Symposium on Biomedical Imaging (ISBI). London, United Kingdom: IEEE Computer Society, 2026, s. 1-5. ISBN 979-8-3315-7764-3. Dostupné z: https://doi.org/10.1109/ISBI61048.2026.11516000.

PITSMAUSOVÁ, Zuzana a David SVOBODA. Detection of Splicing in Digital Image Forgery. Online. In Proceedings on 2026 IEEE International Conference on Image Processing (ICIP). 445 Hoes Lane Piscataway, NJ 08854, USA: IEEE, 2026, s. 1-6. ISBN 979-8-3315-5151-3. Dostupné z: https://doi.org/10.1109/ICIP61757.2026.11630551.

GARCÍA-LÓPEZ-DE-HARO, Carlos; Caterina FUSTER-BARCELÓ; Curtis T. RUEDEN; Jónathan HERAS; Vladimír ULMAN; Daniel FRANCO-BARRANCO; Adrián INÉS; Kevin W. ELICEIRI; Jean-Christophe OLIVO-MARIN; Jean-Yves TINEVEZ; Daniel SAGE a Arrate MUÑOZ-BARRUTIA. SAMJ: fast image annotation on ImageJ/Fiji via segment anything model. Nature Communications. Nature Research, 2026, roč. 17, č. 1, s. 1-9. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-026-71752-x.

HRADECKÁ, Lucia a Martin MAŠKA. Shape-Aware Cell Segmentation with Global Cues. IEEE SIGNAL PROCESSING LETTERS. UNITED STATES: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2026, roč. 33, č. 2026, s. 3277-3281. ISSN 1070-9908. Dostupné z: https://doi.org/10.1109/LSP.2026.3721049.

HRADECKÁ, Lucia; Filip LUX; Samuel ŠUĽAN a Petr MATULA. Bio-Volumentations. 2025.

HRADECKÁ, Lucia; Filip LUX; Samuel ŠUĽAN a Petr MATULA. Bio-Volumentations: A Python library for augmentation of volumetric image sequences. SOFTWAREX. NETHERLANDS: ELSEVIER, 2025, roč. 30, č. 102151, s. 1-6. ISSN 2352-7110. Dostupné z: https://doi.org/10.1016/j.softx.2025.102151.

STOKLASA, Roman. CDF Normalizer (lib). 2025.

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.

AKBAS, Cem Emre; Vladimír ULMAN; Martin MAŠKA a Michal KOZUBEK. DeepFuse: A multi-rater fusion and refinement network for computing silver-standard annotations. Computers in Biology and Medicine. Elsevier, 2025, roč. 192, Part A, s. 1-11. ISSN 0010-4825. Dostupné z: https://doi.org/10.1016/j.compbiomed.2025.110186.

STOKLASA, Roman. IMAGE HARMONIZATION USING ROBUST RESTRICTED CDF MATCHING. Online. In 2025 IEEE 22ND INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI. NEW YORK: IEEE, 2025, s. 1-5. ISBN 979-8-3315-2053-3. Dostupné z: https://doi.org/10.1109/ISBI60581.2025.10981263.

MICHÁLEK, Jan a Michal MIKL. Smooth dynamic T2* mapping in fMRI based on a novel, total variation-minimizing algorithm for efficient multi-echo BOLD time series denoising with high signal-to-noise and contrast-to-noise ratios. FRONTIERS IN NEUROSCIENCE. LAUSANNE: FRONTIERS MEDIA SA, 2025, roč. 19, Oct, s. 1-21. ISSN 1662-453X. Dostupné z: https://doi.org/10.3389/fnins.2025.1544748.

BRÁZDIL, Tomáš; Vít MUSIL; Karel ŠTĚPKA; Adam KUKUČKA; Rudolf NENUTIL; Adam BAJGER a Petr HOLUB. Strojové učení v digitální patologii. Ceskoslovenska Patologie. Nakladatelske Stredisko CLSJE Purkyne, 2025, roč. 61, č. 2, s. 58-69. ISSN 0009-0611.

MELNIKOVA, Aleksandra a Petr MATULA. Study of Shape Fusion Algorithms for 3D Time-Lapse Microscopy. Online. In Proceedings - International Symposium on Biomedical Imaging. ISBI 2025: IEEE Computer Society, 2025, s. 1-5. ISBN 979-8-3315-2052-6. Dostupné z: https://doi.org/10.1109/ISBI60581.2025.10980908.

MELNIKOVA, Aleksandra; Martin MAŠKA a Petr MATULA. Topology-preserving contourwise shape fusion. Nature Scientific Reports. NATURE PUBLISHING GROUP, 2025, roč. 15, č. 10713, s. 1-12. ISSN 2045-2322. Dostupné z: https://doi.org/10.1038/s41598-025-94977-0.

ZENK, Maximilian; Ujjwal BAID; Sarthak PATI; Akis LINARDOS; Brandon EDWARDS; Micah SHELLER; Patrick FOLEY; Alejandro ARISTIZABAL; David ZIMMERER; Alexey GRUZDEV; Jason MARTIN; Russell T SHINOHARA; Annika REINKE; Fabian ISENSEE; Santhosh PARAMPOTTUPADAM; Kaushal PAREKH; Ralf FLOCA; Hasan KASSEM; Bhakti BAHETI; Siddhesh THAKUR; Verena CHUNG; Kaisar KUSHIBAR; Karim LEKADIR; Meirui JIANG; Youtan YIN; Hongzheng YANG; Quande LIU; Cheng CHEN; Qi DOU; Pheng-Ann HENG; Xiaofan ZHANG; Shaoting ZHANG; Muhammad Irfan KHAN; Mohammad Ayyaz AZEEM; Mojtaba JAFARITADI; Esa ALHONIEMI; Elina KONTIO; Suleiman A KHAN; Leon MAECHLER; Ivan EZHOV; Florian KOFLER; Suprosanna SHIT; Johannes C PAETZOLD; Timo LOEHR; Benedikt WIESTLER; Himashi PEIRIS; Kamlesh PAWAR; Shenjun ZHONG; Zhaolin CHEN; Munawar HAYAT; Gary EGAN; Mehrtash HARANDI; Isik Polat ECE; Gorkem POLAT; Altan KOCYIGIT; Alptekin TEMIZEL; Anup TULADHAR; Lakshay TYAGI; Raissa SOUZA; Nils D FORKERT; Pauline MOUCHES; Matthias WILMS; Vishruth SHAMBHAT; Akansh MAURYA; Shubham Subhas DANANNAVAR; Rohit KALLA; Vikas Kumar ANAND; Ganapathy KRISHNAMURTHI; Sahil NALAWADE; Chandan GANESH; Ben WAGNER; Divya REDDY; Yudhajit DAS; Fang F YU; Baowei FEI; Ananth J MADHURANTHAKAM; Joseph MALDJIAN; Gaurav SINGH; Jianxun REN; Wei ZHANG; Ning AN; Qingyu HU; Youjia ZHANG; Ying ZHOU; Vasilis SIOMOS; Giacomo TARRONI; Jonathan PASSERRAT-PALMBACH; Ambrish RAWAT; Giulio ZIZZO; Swanand Ravindra KADHE; Jonathan P EPPERLEIN; Stefano BRAGHIN; Yuan WANG; Renuga KANAGAVELU; Qingsong WEI; Yechao YANG; Yong LIU; Krzysztof KOTOWSKI; Szymon ADAMSKI; Bartosz MACHURA; Wojciech MALARA; Lukasz ZARUDZKI; Jakub NALEPA; Yaying SHI; Hongjian GAO; Salman AVESTIMEHR; Yonghong YAN; Agus S AKBAR; Ekaterina KONDRATEVA; Hua YANG; Zhaopei LI; Hung-Yu WU; Johannes ROTH; Camillo SAUERESSIG; Alexandre MILESI; Quoc D NGUYEN; Nathan J GRUENHAGEN; Tsung-Ming HUANG; Jun MA; Har Shwinder H SINGH; Nai-Yu PAN; Dingwen ZHANG; Ramy A ZEINELDIN; Michal FUTREGA; Yading YUAN; Gian Marco CONTE; Xue FENG; Quan D PHAM; Yong XIA; Zhifan JIANG; Huan Minh LUU; Mariia DOBKO; Alexandre CARRE; Bair TUCHINOV; Hassan MOHY-UD-DIN; Saruar ALAM; Anup SINGH; Nameeta SHAH; Weichung WANG; Chiharu SAKO; Michel BILELLO; Satyam GHODASARA; Suyash MOHAN; Christos DAVATZIKOS; Evan CALABRESE; Jeffrey RUDIE; Javier VILLANUEVA-MEYER; Soonmee CHA; Christopher HESS; John MONGAN; Madhura INGALHALIKAR; Manali JADHAV; Umang PANDEY; Jitender SAINI; Raymond Y HUANG; Ken CHANG; Minh-Son TO; Sargam BHARDWAJ; Chee CHONG; Marc AGZARIAN; Michal KOZUBEK; Filip LUX; Jan MICHÁLEK; Petr MATULA; Miloš KEŘKOVSKÝ; Tereza KOPŘIVOVÁ; Marek DOSTÁL; Václav VYBÍHAL; Marco C PINHO; James HOLCOMB; Marie METZ; Rajan JAIN; Matthew D LEE; Yvonne W LUI; Pallavi TIWARI; Ruchika VERMA; Rohan BAREJA; Ipsa YADAV; Jonathan CHEN; Neeraj KUMAR; Yuriy GUSEV; Krithika BHUVANESHWAR; Anousheh SAYAH; Camelia BENCHEQROUN; Anas BELOUALI; Subha MADHAVAN; Rivka R COLEN; Aikaterini KOTROTSOU; Philipp VOLLMUTH; Gianluca BRUGNARA; Chandrakanth J PREETHA; Felix SAHM; Martin BENDSZUS; Wolfgang WICK; Abhishek MAHAJAN; Carmen BALANA; Jaume CAPELLADES; Josep PUIG; Yoon Seong CHOI; Seung-Koo LEE; Jong Hee CHANG; Sung Soo AHN; Hassan F SHAYKH; Alejandro HERRERA-TRUJILLO; Maria TRUJILLO; William ESCOBAR; Ana ABELLO; Jose BERNAL; Jhon GOMEZ; Pamela LAMONTAGNE; Daniel S MARCUS; Mikhail MILCHENKO; Arash NAZERI; Bennett LANDMAN; Karthik RAMADASS; Kaiwen XU; Silky CHOTAI; Lola B CHAMBLESS; Akshitkumar MISTRY; Reid C THOMPSON; Ashok SRINIVASAN; J Rajiv BAPURAJ; Arvind RAO; Nicholas WANG; Ota YOSHIAKI; Toshio MORITANI; Sevcan TURK; Joonsang LEE; Snehal PRABHUDESAI; John GARRETT; Matthew LARSON; Robert JERAJ; Hongwei LI; Tobias WEISS; Michael WELLER; Andrea BINK; Bertrand POUYMAYOU; Sonam SHARMA; Tzu-Chi TSENG; Saba ADABI; Xavier Falcao ALEXANDRE; Samuel B MARTINS; Bernardo C A TEIXEIRA; Flavia SPRENGER; David MENOTTI; Diego R LUCIO; Simone P NICLOU; Olivier KEUNEN; Ann-Christin HAU; Enrique PELAEZ; Heydy FRANCO-MALDONADO; Francis LOAYZA; Sebastian QUEVEDO; Richard MCKINLEY; Johannes SLOTBOOM; Piotr RADOJEWSKI; Raphael MEIER; Roland WIEST; Johannes TRENKLER; Josef PICHLER; Georg NECKER; Andreas HAUNSCHMIDT; Stephan MECKEL; Pamela GUEVARA; Esteban TORCHE; Cristobal MENDOZA; Vera FRANCO; Elvis RIOS; Eduardo LOPEZ; Sergio A VELASTIN; Joseph CHOI; Stephen BAEK; Yusung KIM; Heba ISMAEL; Bryan ALLEN; John M BUATTI; Peter ZAMPAKIS; Vasileios PANAGIOTOPOULOS; Panagiotis TSIGANOS; Sotiris ALEXIOU; Ilias HALIASSOS; Evangelia I ZACHARAKI; Konstantinos MOUSTAKAS; Christina KALOGEROPOULOU; Dimitrios M KARDAMAKIS; Bing LUO; Laila M POISSON; Ning WEN; Martin VALLIERES; Mahdi Ait Lhaj LOUTFI; David FORTIN; Martin LEPAGE; Fanny MORON; Jacob MANDEL; Gaurav SHUKLA; Spencer LIEM; Gregory S ALEXANDRE; Joseph LOMBARDO; Joshua D PALMER; Adam E FLANDERS; Adam P DICKER; Godwin OGBOLE; Dotun OYEKUNLE; Olubunmi ODAFE-OYIBOTHA; Babatunde OSOBU; Hikima Mustapha SHU'AIBU; Mayowa SONEYE; Farouk DAKO; Adeleye DORCAS; Derrick MURCIA; Eric FU; Rourke HAAS; John A THOMPSON; David Ryan ORMOND; Stuart CURRIE; Kavi FATANIA; Russell FROOD; Amber L SIMPSON; Jacob J PEOPLES; Ricky HU; Danielle CUTLER; Fabio Y MORAES; Anh TRAN; Mohammad HAMGHALAM; Michael A BOSS; James GIMPEL; Kattil Veettil DEEPAK; Kendall SCHMIDT; Lisa CIMINO; Cynthia PRICE; Brian BIALECKI; Sailaja MARELLA; Charles APGAR; Andras JAKAB; Marc-Andre WEBER; Errol COLAK; Jens KLEESIEK; John B FREYMANN; Justin S KIRBY; Lena MAIER-HEIN; Jake ALBRECHT; Peter MATTSON; Alexandros KARARGYRIS; Prashant SHAH; Bjoern MENZE; Klaus MAIER-HEIN a Spyridon BAKAS. Towards fair decentralized benchmarking of healthcare AI algorithms with the Federated Tumor Segmentation (FeTS) challenge. Nature communications. BERLIN: NATURE PORTFOLIO, 2025, roč. 16, č. 1, s. 1-20. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-025-60466-1.

STOKLASA, Roman a Ioannis STATHOPOULOS. Brain MRI Screening Tool. 2024.

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

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

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.

EFTIMIU, Nikomidisz Jorgosz a Michal KOZUBEK. Gravitational Cell Detection and Tracking in Fluorescence Microscopy Data. Online. In IEEE. 24 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/ISBI56570.2024.10635151.

MRÁZ, Radoslav; Karel ŠTĚPKA; Matěj PEKÁR; Petr MATULA a Stanislav PEKÁR. MAPHIS-Measuring arthropod phenotypes using hierarchical image segmentations. Methods in Ecology and Evolution. HOBOKEN: WILEY, 2024, roč. 15, č. 1, s. 36-42. ISSN 2041-210X. Dostupné z: https://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 a Paul F JAEGER. Metrics reloaded: recommendations for image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, roč. 21, February, s. 195-212, 30 s. ISSN 1548-7091. Dostupné z: https://doi.org/10.1038/s41592-023-02151-z.

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 a Lena MAIER-HEIN. Understanding metric-related pitfalls in image analysis validation. NATURE METHODS. UNITED STATES: NATURE PORTFOLIO, 2024, roč. 21, č. 2, s. 182-194, 20 s. ISSN 1548-7091. Dostupné z: https://doi.org/10.1038/s41592-023-02150-0.

HRADECKÁ, Lucia; David WIESNER; Jakub SUMBAL; Zuzana SUMBALOVÁ KOLEDOVÁ a Martin MAŠKA. Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy. IEEE Transactions on Medical Imaging. 2023, roč. 42, č. 1, s. 281-290. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2022.3210714.

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://doi.org/10.1038/s41592-023-01879-y.

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.

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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.

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://doi.org/10.1016/B978-0-12-824349-7.00028-1.

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.

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 a Jan ŠMARDA. Multimodal Imaging of 3D Cell Aggregates. In MSB 2021. 2021.

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.

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

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.

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 a Sébastien TOSI. BIAFLOWS: A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows. Patterns. Cell Press, 2020, roč. 1, č. 3, s. 1-10. ISSN 2666-3899. Dostupné z: https://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 a Bennett A. LANDMAN. BIAS: Transparent reporting of biomedical image analysis challenges. Medical Image Analysis. Elsevier, 2020, roč. 66, č. 101796, s. 1-7. ISSN 1361-8415. Dostupné z: https://doi.org/10.1016/j.media.2020.101796.

AKBAS, Cem Emre a 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, s. 446-450. ISBN 978-1-5386-9330-8. Dostupné z: https://doi.org/10.1109/ISBI45749.2020.9098351.

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.

PAVLATOVSKÁ, Barbora; Markéta MACHÁLKOVÁ; Petra BRISUDOVÁ; Adam PRUŠKA; Karel ŠTĚPKA; Jan MICHÁLEK; Tereza NEČASOVÁ; Petr BENEŠ; Jan ŠMARDA; Jan PREISLER; Michal KOZUBEK a 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, roč. 10, December, s. 1-18. ISSN 2234-943X. Dostupné z: https://doi.org/10.3389/fonc.2020.581365.

KOZUBEK, Michal. When Deep Learning Meets Cell Image Synthesis. Cytometry Part A. John Wiley & Sons, 2020, roč. 97, č. 3, s. 222-225. ISSN 1552-4922. Dostupné z: https://doi.org/10.1002/cyto.a.23957.

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://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://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 a 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 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.

GÓMEZ-DE-MARISCAL, Estibaliz; Martin MAŠKA; Anna KOTRBOVÁ; Vendula POSPÍCHALOVÁ; Pavel MATULA a Arrate MUÑOZ-BARRUTIA. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Scientific Reports. 2019, roč. 9, č. 13211, s. 1-10. ISSN 2045-2322. Dostupné z: https://doi.org/10.1038/s41598-019-49431-3.

LUX, Filip a 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, s. 236-239. ISBN 978-1-5386-3641-1. Dostupné z: https://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 a 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, roč. 91, č. 21, s. 13475-13484. ISSN 0003-2700. Dostupné z: https://doi.org/10.1021/acs.analchem.9b02462.

MICHÁLEK, Jan; Pavla HANZLÍKOVÁ; Tuan TRINH a Dalibor PACÍK. Fast and accurate compensation of signal offset for T2 mapping. Magnetic Resonance Materials in Physics, Biology and Medicine. Springer International Publishing, 2019, roč. 32, č. 4, s. 423-436. ISSN 0968-5243. Dostupné z: https://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 a Michal KOZUBEK. Fiducial-based semi-automatic coregistration and analysis of multimodal MALDI MS and immunofluorescent data. In Imaging Principles of Life 2019. 2019.

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.

MICHÁLEK, Jan; Karel ŠTĚPKA; Michal KOZUBEK; Jarmila NAVRÁTILOVÁ; Barbora PAVLATOVSKÁ; Markéta MACHÁLKOVÁ; Jan PREISLER a 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, roč. 25, č. 6, s. 1311-1322. ISSN 1431-9276. Dostupné z: https://doi.org/10.1017/S1431927619014983.

KOTRBOVÁ, Anna; Karel ŠTĚPKA; Martin MAŠKA; Juraj PÁLENIK; Ladislav ILKOVICS; Dobromila KLEMOVÁ; Marek KRAVEC; František HUBATKA; Zankruti DAVE; Aleš HAMPL; Vítězslav BRYJA; Pavel MATULA a 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, roč. 8, č. 1, s. 1-13. ISSN 2001-3078. Dostupné z: https://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 a Irena KOUTNÁ. The Effect of Uncoated SPIONs on hiPSC-Differentiated Endothelial Cells. International Journal of Molecular Sciences. BASEL: Molecular Diversity Preservation International, 2019, roč. 20, č. 14, s. 1-16. ISSN 1422-0067. Dostupné z: https://doi.org/10.3390/ijms20143536.

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.

PAVLATOVSKÁ, Barbora; Jarmila NAVRÁTILOVÁ; Markéta MACHÁLKOVÁ; Petra BRISUDOVÁ; Jan MICHÁLEK; Karel ŠTĚPKA; Adam PRUŠKA; Michal KOZUBEK; Petr BENEŠ; Jan ŠMARDA a 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 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.

CASTILLA, Carlos; Martin MAŠKA; Dmitry SOROKIN; Erik MEIJERING a Carlos ORTIZ-DE-SOLÓRZANO. 3-D Quantification of Filopodia in Motile Cancer Cells. IEEE Transactions on Medical Imaging. IEEE, 2019, roč. 38, č. 3, s. 862-872. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2018.2873842.

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.

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 a 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, s. 388-395. ISBN 978-3-030-00936-6. Dostupné z: https://doi.org/10.1007/978-3-030-00937-3_45.

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.

SOROKIN, Dmitry; Igor PETERLÍK; Marco TEKTONIDIS; Karl ROHR a 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, roč. 37, č. 1, s. 173-184. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2017.2734169.

DVOŘÁČKOVÁ, Martina; B. RAPOSO; Petr MATULA; J. FUCHS; V. SCHUBERT; Vratislav PEŠKA; B. DESVOYES; C. GUTIERREZ a 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, roč. 131, č. 2, s. nestránkováno, 12 s. ISSN 0021-9533. Dostupné z: https://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 a 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, roč. 27, č. 1, s. 10-22. ISSN 1547-3287. Dostupné z: https://doi.org/10.1089/scd.2017.0132.

CASTILLA, Carlos; Martin MAŠKA; Dmitry SOROKIN; Erik MEIJERING a 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, s. 413-417. ISBN 978-1-5386-3636-7. Dostupné z: https://doi.org/10.1109/ISBI.2018.8363605.

PAVLATOVSKÁ, Barbora; Jarmila NAVRÁTILOVÁ; Markéta MACHÁLKOVÁ; Adam PRUŠKA; Jan MICHÁLEK; Karel ŠTĚPKA; Michal KOZUBEK; Jan ŠMARDA a 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 a Jan PREISLER. 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 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.

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 a Annette KOPP-SCHNEIDER. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications. Nature Publishing Group, 2018, roč. 9, č. 5217, s. 1-13. ISSN 2041-1723. Dostupné z: https://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 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.

ANOSHINA, Nadezhda A.; Andrey S. KRYLOV a 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, s. 1-6. ISBN 978-1-5386-1842-4. Dostupné z: https://doi.org/10.1109/IPTA.2017.8310125.

ŠIMARA, Pavel; Lenka TESAŘOVÁ; Daniela ŘEHÁKOVÁ; Pavel MATULA; Stanislav STEJSKAL; Aleš HAMPL a Irena KRONTORÁD KOUTNÁ. DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing. Stem Cell Research & Therapy. Springer Nature, 2017, roč. 8, č. 73, s. 1-13. ISSN 1757-6512. Dostupné z: https://doi.org/10.1186/s13287-017-0522-5.

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.

TESAŘOVÁ, Lenka; Pavel ŠIMARA; Stanislav STEJSKAL a 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, roč. 19, č. 4, s. 270-284. ISSN 2152-4971. Dostupné z: https://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 a Carlos ORTIZ-DE-SOLORZANO. Characterization of three-dimensional cancer cell migration in mixed collagen-Matrigel scaffolds using microfluidics and image analysis. PLoS ONE. 2017, roč. 12, č. 2, s. 1-24. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0171417.

POPOVICI, Vlad; Eva BUDINSKÁ; Ladislav DUŠEK; Michal KOZUBEK a Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics. Oxford: Oxford University Press, 2017, roč. 33, č. 13, s. 2002-2009. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btx027.

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.

MAŠKA, Martin a 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, s. 11-17. ISBN 978-1-5386-1034-3. Dostupné z: https://doi.org/10.1109/ICCVW.2017.8.

FRANEK, Michal; Jana SUCHÁNKOVÁ; Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ; Jana KREJČÍ; Soňa LEGARTOVÁ; Stanislav KOZUBEK; J VEČEŘA; Dmitry SOROKIN a Eva BÁRTOVÁ. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. Microscopy and Microanalysis. Saarbrücken: Cambridge University Press, 2016, roč. 22, č. 2, s. 326-341. ISSN 1431-9276. Dostupné z: https://doi.org/10.1017/S1431927616000052.

ŠTĚPKA, Karel; Martin MAŠKA; Jakub Jozef PÁLENIK; Vendula POSPÍCHALOVÁ; Anna KOTRBOVÁ; Ladislav ILKOVICS; Dobromila KLEMOVÁ; Aleš HAMPL; Vítězslav BRYJA a 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, s. 318-325. ISBN 978-3-319-46603-3. Dostupné z: https://doi.org/10.1007/978-3-319-46604-0_23.

KONDRAT'EV, Alexandr a 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, s. 326-331. ISBN 978-1-5090-4846-5. Dostupné z: https://doi.org/10.1109/ICPR.2016.7899655.

ŠIMARA, Pavel; Irena KRONTORÁD KOUTNÁ; Lenka TESAŘOVÁ; Daniela ŘEHÁKOVÁ a Pavel MATULA. DNA double strand breaks detection in pluripotent stem cells with regard to cell cycle stages. In ISSCR 2016 Annual Meeting. 2016.

KOZUBEK, Michal. Challenges and Benchmarks in Bioimage Analysis. Online. In DeVos WH, Munck S, Timmermans JP. Focus on Bio-Image Informatics. Berlin: Springer, 2016, s. 231-262. Advances in Anatomy, Embryology and Cell Biology 219. ISBN 978-3-319-28547-4. Dostupné z: https://doi.org/10.1007/978-3-319-28549-8_9.

LEGARTOVÁ, Soňa; Petra ŘEZNÍČKOVÁ-PODLOUČKOVÁ; Barbora MALYŠKOVÁ; Thomas KÜNTZIGER; Philippe COLLAS; Dušan CMARKO; Ivan RAŠKA; Dmitry SOROKIN; Stanislav KOZUBEK a 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, roč. 117, č. 11, s. 2583-2596. ISSN 0730-2312. Dostupné z: https://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 a Eugene V. SHEVAL. RNA-dependent disassembly of nuclear bodies. Journal of Cell Science. The Company of Biologists Ltd., 2016, roč. 129, č. 24, s. 4509-4520. ISSN 0021-9533. Dostupné z: https://doi.org/10.1242/jcs.189142.

STOKLASA, Roman a 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, s. 1212-1216. ISBN 978-1-4799-2350-2. Dostupné z: https://doi.org/10.1109/ISBI.2016.7493484.

TESAŘOVÁ, Lenka; Pavel ŠIMARA; Stanislav STEJSKAL a Irena KRONTORÁD KOUTNÁ. The Aberrant DNA Methylation Profile of Human Induced Pluripotent Stem Cells Is Connected to the Reprogramming Process and Is Normalized During In Vitro Culture. PLOS ONE. Public Library of Science, 2016, roč. 11, č. 6, s. nestránkováno, 16 s. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0157974.

KRATOCHVÍLOVÁ, Kateřina; Lukáš MORÁŇ; Stanislava PAĎOUROVÁ; Stanislav STEJSKAL; Lenka TESAŘOVÁ; Pavel ŠIMARA; Aleš HAMPL; Irena KRONTORÁD KOUTNÁ a Petr VAŇHARA. The role of the endoplasmic reticulum stress in stemness, pluripotency and development. European Journal of Cell Biology. Jena: Elsevier GMBH, 2016, roč. 95, 3-5, s. 115-123. ISSN 0171-9335. Dostupné z: https://doi.org/10.1016/j.ejcb.2016.02.002.

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.

STOKLASA, Roman; Lukáš BÁLEK; Pavel KREJČÍ a Petr MATULA. Automated Cell Segmentation in Phase-Contrast Images based on Classification and Region Growing. In Proceedings of 2015 IEEE International Symposium on Biomedical Imaging, 2015. Neuveden: Engineering in Medicine and Biology Society, 2015, s. 1447-1451. ISBN 978-1-4799-2374-8. Dostupné z: https://doi.org/10.1109/ISBI.2015.7164149.

STEJSKAL, Stanislav; Karel ŠTĚPKA; Lenka TESAŘOVÁ; Karel STEJSKAL; Martina MATĚJKOVÁ; Pavel ŠIMARA; Zbyněk ZDRÁHAL a Irena KRONTORÁD KOUTNÁ. Cell cycle-dependent changes in H3K56ac in human cells. Cell Cycle. Philadelphia: Taylor&Francis Inc, 2015, roč. 14, č. 24, s. 3851-3863. ISSN 1538-4101. Dostupné z: https://doi.org/10.1080/15384101.2015.1106760.

MATULA, Pavel; Martin MAŠKA; Dmitry SOROKIN; Petr MATULA; Carlos ORTIZ-DE-SOLÓRZANO a Michal KOZUBEK. Cell tracking accuracy measurement based on comparison of acyclic oriented graphs. PLoS ONE. 2015, roč. 10, č. 12, s. "e0144959", 19 s. ISSN 1932-6203. Dostupné z: https://doi.org/10.1371/journal.pone.0144959.

KARAS, Pavel; Vincent MORARD; Jan BARTOVSKÝ; Thierry GRANDPIERRE; Eva DOKLÁDALOVÁ; Petr MATULA a Petr DOKLÁDAL. GPU Implementation of Linear Morphological Openings with Arbitrary Angle. Journal of Real-Time Image Processing. Springer-Verlag, 2015, roč. 10, č. 1, s. 27-41. ISSN 1861-8200. Dostupné z: https://doi.org/10.1007/s11554-012-0248-7.

ANGUIANO, María; Carlos CASTILLA; Martin MAŠKA; Cristina EDERRA; Javier FERNÁNDEZ-MARQUÉS; Rafael PELÁEZ; Ana ROUZAUT; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Characterization of the Role of Collagen Network Structure and Composition in Cancer Cell Migration. Online. In 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Milano: IEEE, 2015, s. 8139-8142. ISBN 978-1-4244-9271-8. Dostupné z: https://doi.org/10.1109/EMBC.2015.7320283.

SOROKIN, Dmitry; Lenka STIXOVÁ; Petra SEHNALOVÁ; Soňa LEGARTOVÁ; Jana SUCHÁNKOVÁ; Pavel ŠIMARA; Stanislav KOZUBEK; Pavel MATULA; Magdalena SKALNÍKOVÁ; Ivan RAŠKA a 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, roč. 6, č. 4, s. 301-313. ISSN 1949-1034. Dostupné z: https://doi.org/10.1080/19491034.2015.1075111.

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.

ŠTĚPKA, Karel; Pavel MATULA; Petr MATULA; Stefan WOERZ; Karl ROHR a Michal KOZUBEK. Performance and Sensitivity Evaluation of 3-D Spot Detection Methods in Confocal Microscopy. Cytometry Part A. John Wiley & Sons, 2015, roč. 87A, č. 8, s. 759-772. ISSN 1552-4922. Dostupné z: https://doi.org/10.1002/cyto.a.22692.

MAŠKA, Martin; Cristina EDERRA; Javier FERNÁNDEZ-MARQUÉS; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Carlos ORTIZ-DE-SOLÓRZANO. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. Online. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015, s. 1791-1794. ISBN 978-1-4799-8339-1. Dostupné z: https://doi.org/10.1109/ICIP.2015.7351109.

ŠIMARA, Pavel; Irena KRONTORÁD KOUTNÁ; Stanislav STEJSKAL a Lenka TESAŘOVÁ. The effect of reprogramming method, source cell type and long-term cell culture on genomic stability of human induced pluripotent stem cells. In ISSCR 2015 Annual Meeting. 2015.

ORTIZ-DE-SOLÓRZANO, Carlos; Arrate MUÑOZ-BARRUTIA; Erik MEIJERING a Michal KOZUBEK. Toward a Morphodynamic Model of the Cell. IEEE Signal Processing Magazine. New York: IEEE, 2015, roč. 32, č. 1, s. 20-29. ISSN 1053-5888. Dostupné z: https://doi.org/10.1109/MSP.2014.2358263.

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.

JIANG, Yan; Saba HABIBOLLAH; Katarzyna TILGNER; Joseph COLLIN; Tomáš BÁRTA; Jumana Yousuf AL-AAMA; Lenka TESAŘOVÁ; Rafiqul HUSSAIN; Andrew TRAFFORD; Graham KIRKWOOD; Evelyne SERNAGOR; Cyril ELEFTHERIOU; Stefan PRZYBORSKI; Miodrag STOJKOVIC; Majlinda LAKO; Bernard KEAVNEY a Lyle ARMSTRONG. An induced pluripotent stem cell model of hypoplastic left heart syndrome (HLHS) reveals multiple expression and functional differences in HLHS derived cardiac myocytes. Stem cells translational medicine. 2014, roč. 3, č. 4, s. 416-423. ISSN 2157-6564. Dostupné z: https://doi.org/10.5966/sctm.2013-0105.

BÁRTOVÁ, Eva; Veronika FOLTÁNKOVÁ; Soňa LEGARTOVÁ; Petra SEHNALOVÁ; Dmitry SOROKIN; Jana SUCHÁNKOVÁ a Stanislav KOZUBEK. Coilin is rapidly recruited to UVA-induced DNA lesions and gamma-radiation affects localized movement of Cajal bodies. Nucleus. Landes Bioscience, 2014, roč. 5, č. 3, s. 269-277. ISSN 1949-1034. Dostupné z: https://doi.org/10.4161/nucl.29229.

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.

TESAŘOVÁ, Lenka; Stanislav STEJSKAL a Irena KRONTORÁD KOUTNÁ. Driven hematopoietic differentiation of embryonic stem cells: Epigenetic perspectives. CURRENT PHARMACEUTICAL DESIGN. SHARJAH: BENTHAM SCIENCE PUBL LTD, 2014, roč. 20, č. 11, s. 1674-1686. ISSN 1381-6128. Dostupné z: https://doi.org/10.2174/13816128113199990524.

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.

ŠALINGOVÁ, Barbara; Martina MADARÁSOVÁ; Stanislav STEJSKAL; Lenka TESAŘOVÁ; Pavel ŠIMARA a Irena KRONTORÁD KOUTNÁ. From Endothelial Progenitor Cells to Tissue Engineering: How Far Have We Come? Journal of Stem Cell Research & Therapy. 5716 Corsa Ave, Los Angeles, USA: OMICS group, 2014, roč. 4, č. 3, s. 185-195. ISSN 2157-7633. Dostupné z: https://doi.org/10.4172/2157-7633.1000185.

ŠIMARA, Pavel; Lenka TESAŘOVÁ; Stanislava PAĎOUROVÁ a Irena KRONTORÁD KOUTNÁ. Generation of Human Induced Pluripotent Stem Cells Using Genome Integrating or Non-integrating Methods. Folia Biologica. Praha: Univerzita Karlova, 2014, roč. 60, S1, s. 85-89. ISSN 0015-5500.

TESAŘOVÁ, Lenka; Pavel ŠIMARA; Stanislav STEJSKAL a Irena KRONTORÁD KOUTNÁ. Haematopoietic developmental potential of human pluripotent stem cell lines. Folia biologica. Praha: Univerzita Karlova, 2014, roč. 60, č. 1, s. 90-94. ISSN 0015-5500.

STIXOVÁ, Lenka; Petra SEHNALOVÁ; Soňa LEGARTOVÁ; Jana SUCHÁNKOVÁ; Tereza HRUŠKOVÁ; Stanislav KOZUBEK; Dmitry SOROKIN; Pavel MATULA; Ivan RAŠKA; Aleš KOVAŘÍK; Jaroslav FULNEČEK a Eva BÁRTOVÁ. HP1B-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs. Epigenetics & Chromatin. BioMed Central, 2014, roč. 7, č. 39, s. 1-17. ISSN 1756-8935. Dostupné z: https://doi.org/10.1186/1756-8935-7-39.

ŠTĚPKA, Karel a Martin FALK. Image Analysis of Gene Locus Positions within Chromosome Territories in Human Lymphocytes. In Petr Hliněný, Zdeněk Dvořák, Jiří Jaroš, Jan Kofroň, Jan Kořenek, Petr Matula, Karel Pala. Mathematical and Engineering Methods in Computer Science : Volume 8934 of the series Lecture Notes in Computer Science. Neuveden: Springer International Publishing, 2014, s. 125-134. ISBN 978-3-319-14895-3. Dostupné z: https://doi.org/10.1007/978-3-319-14896-0_11.

RUČKA, Zdeněk; Irena KRONTORÁD KOUTNÁ; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Stanislav STEJSKAL; Pavel ŠIMARA; Petr VAŇHARA; Jan DOLEŽEL; Václav ZVONÍČEK; Oldřich COUFAL a Ivan ČAPOV. Intravenous insulin therapy during lung resection does not affect lung function or surfactant proteins. BMC Pulmonary Medicine. London, United Kingdom: BIOMED CENTRAL LTD, 2014, roč. 14, č. 1, s. 155-163. ISSN 1471-2466. Dostupné z: https://doi.org/10.1186/1471-2466-14-155.

SOROKIN, Dmitry; Marco TEKTONIDIS; Karl ROHR a 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, s. 746-749. ISBN 978-1-4673-1959-1. Dostupné z: https://doi.org/10.1109/ISBI.2014.6867978.

CHENOUARD, Nicolas; Ihor SMAL; Fabrice DE CHAUMONT; Martin MAŠKA; Ivo F SBALZARINI; Yuanhao GONG; Janick CARDINALE; Craig CARTHEL; Stefano CORALUPPI; Mark WINTER; Andrew R COHEN; William J GODINEZ; Karl ROHR; Yannis KALAIDZIDIS; Liang LIANG; James DUNCAN; Hongying SHEN; Yingke XU; Klas E G MAGNUSSON; Joakim JALDÉN; Helen M BLAU; Perrine PAUL-GILLOTEAUX; Philippe ROUDOT; Charles KERVRANN; François WAHARTE; Jean-Yves TINEVEZ; Spencer L SHORTE; Joost WILLEMSE; Katherine CELLER; Gilles P VAN WEZEL; Han-Wei DAN; Yuh-Show TSAI; Carlos ORTIZ-DE-SOLÓRZANO; Jean-Christophe OLIVO-MARIN a Erik MEIJERING. Objective Comparison of Particle Tracking Methods. Nature Methods. 2014, roč. 11, č. 3, s. 281-289. ISSN 1548-7091. Dostupné z: https://doi.org/10.1038/nmeth.2808.

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.

SUCHÁNKOVÁ, Jana; Soňa LEGARTOVÁ; Petra SEHNALOVÁ; Stanislav KOZUBEK; Sergio VALENTE; Donatella LABELLA; Antonello MAI; Carmen ECKERICH; Frank O. FACKELMAYER; Dmitry SOROKIN a 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, roč. 58, č. 2, s. 139-151. ISSN 1121-760X. Dostupné z: https://doi.org/10.4081/ejh.2014.2389.

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.

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

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.

ŠIMARA, Pavel; Stanislav STEJSKAL; Irena KRONTORÁD KOUTNÁ; David POTĚŠIL; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Zbyněk ZDRÁHAL a Jiří MAYER. Apoptosis in chronic myeloid leukemia cells transiently treated with imatinib or dasatinib is caused by residual BCR-ABL kinase inhibition. American Journal of Hematology. NJ 07030-577 United States: John Wiley & Sons, 2013, roč. 88, č. 5, s. 385-393. ISSN 0361-8609. Dostupné z: https://doi.org/10.1002/ajh.23419.

ŠTĚPKA, Karel. Automated Cell Counting in Bürker Chamber. In J.-K. Kamarainen and M. Koskela. 18th Scandinavian Conference on Image Analysis, SCIA 2013. Espoo (Finland): Springer, 2013, s. 236-245. ISBN 978-3-642-38885-9. Dostupné z: https://doi.org/10.1007/978-3-642-38886-6_23.

MAŠKA, Martin; Xabier MORALES; Arrate MUÑOZ-BARRUTIA; Ana ROUZAUT a Carlos ORTIZ-DE-SOLÓRZANO. Automatic Quantification of Filopodia-Based Cell Migration. Online. In 10th IEEE International Symposium on Biomedical Imaging. San Francisco: IEEE, 2013, s. 668-671. ISBN 978-1-4673-6454-6. Dostupné z: https://doi.org/10.1109/ISBI.2013.6556563.

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.

RUČKA, Zdeněk; Petr VAŇHARA; Irena KRONTORÁD KOUTNÁ; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Stanislav STEJSKAL; Pavel ŠIMARA; Jan DOLEŽEL; Václav ZVONÍČEK; Oldřich COUFAL a Ivan ČAPOV. Differential effects of insulin and dexamethasone on pulmonary surfactant-associated genes and proteins in A549 and H441 cells and lung tissue. INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE. UNITED STATES: SPANDIDOS PUBL LTD, 2013, roč. 32, č. 1, s. 211-218. ISSN 1107-3756. Dostupné z: https://doi.org/10.3892/ijmm.2013.1363.

FOLTÁNKOVÁ, Veronika; Pavel MATULA; Dmitry SOROKIN; Stanislav KOZUBEK a 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, s. 360-369. ISSN 1431-9276. Dostupné z: https://doi.org/10.1017/S1431927612014353.

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

ŠIMARA, Pavel; Jason MOTL a Dan KAUFMAN. Pluripotent stem cells and gene therapy. Translational Research. 2013, roč. 161, č. 4, s. 284-292. ISSN 1931-5244. Dostupné z: https://doi.org/10.1016/j.trsl.2013.01.001.

MAŠKA, Martin; Ondřej DANĚK; Saray GARASA; Ana ROUZAUT; Arrate MUÑOZ-BARRUTIA a Carlos ORTIZ-DE-SOLÓRZANO. Segmentation and Shape Tracking of Whole Fluorescent Cells Based on the Chan-Vese Model. IEEE Transactions on Medical Imaging. 2013, roč. 32, č. 6, s. 995-1006. ISSN 0278-0062. Dostupné z: https://doi.org/10.1109/TMI.2013.2243463.

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.

ŠIMARA, Pavel; Stanislav STEJSKAL; Irena KRONTORÁD KOUTNÁ; David POTĚŠIL; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Zbyněk ZDRÁHAL a Jiří MAYER. Apoptosis in Chronic Myeloid Leukemia Cells Transiently Treated with Imatinib or Dasatinib Is Caused by Residual BCR-ABL Kinase Inhibition. In 54th ASH Annual Meeting and Exposition. 2012. ISSN 1528-0020.

ŠIMARA, Pavel; Martina PETERKOVÁ; Stanislav STEJSKAL; Michaela POTĚŠILOVÁ; Irena KRONTORÁD KOUTNÁ; Zdeněk RÁČIL; Filip RÁZGA; Tomáš JURČEK; Dana DVOŘÁKOVÁ a Jiří MAYER. BCR-ABL activity measured by 50% inhibitory concentration for imatinib, p-CrkL/CrkL ratio or p-CrkL ratio in CD34+ cells of patients with chronic myeloid leukemia does not predict treatment response. Leukemia & lymphoma. England: Informa Healthcare, 2012, roč. 53, č. 8, s. 1627-1629. ISSN 1042-8194. Dostupné z: https://doi.org/10.3109/10428194.2012.656104.

VAŘECHA, Miroslav; Michaela POTĚŠILOVÁ; Pavel MATULA a Michal KOZUBEK. Endonuclease G interacts with histone H2B and DNA topoisomerase II alpha during apoptosis. Mol Cell Biochem. 2012, roč. 363, 1-2, s. 301-307. ISSN 0300-8177. Dostupné z: https://doi.org/10.1007/s11010-011-1182-x.

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.

MAŠKA, Martin; Arrate MUÑOZ-BARRUTIA a Carlos ORTIZ-DE-SOLÓRZANO. Fast Tracking of Fluorescent Cells Based on the Chan-Vese Model. Online. In 9th IEEE International Symposium on Biomedical Imaging. Barcelona: IEEE, 2012, s. 1316–1319. ISBN 978-1-4577-1857-1.

KRONTORÁD KOUTNÁ, Irena; Pavel ŠIMARA; Petra ONDRÁČKOVÁ a Lenka TESAŘOVÁ. Flow Cytometry Analysis of Intracelular Protein. Online. In Ingrid Schmid, University of California, Los Angeles. Flow Cytometry , Recent Perspectives. Rijeka, Croatia: InTech, 2012, s. 421-438. Open science/open minds. ISBN 978-953-51-0626-5. Dostupné z: https://doi.org/10.5772/38400.

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.

TESAŘOVÁ, Lenka; Irena KRONTORÁD KOUTNÁ; Magdaléna DVOŘÁKOVÁ a Martin KLABUSAY. Relative expression of gammadelta T-cell receptor gene families detected by RT–PCR and capillary electrophoresis. International Journal of immunogenetics. Blackwell Publishing Ltd, 2012, roč. 39, č. 5, s. 381-388. ISSN 1744-3121. Dostupné z: https://doi.org/10.1111/j.1744-313X.2012.01114.x.

DANĚK, Ondřej; Pavel MATULA; Martin MAŠKA a Michal KOZUBEK. Smooth Chan-Vese Segmentation via Graph Cuts. Pattern recognition letters : an official publication of the International Association for Pattern Recognition. Amsterdam: Elsevier, 2012, roč. 33, č. 10, s. 1405-1410. ISSN 0167-8655. Dostupné z: https://doi.org/10.1016/j.patrec.2012.03.013.

DANĚK, Ondřej a Martin MAŠKA. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. Online. In Sixth Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (Selected Papers). Saarbrücken, Warden: Schloss Dagstuhl Publishing, 2011, s. 19-25. ISBN 978-3-939897-22-4.

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://doi.org/10.1155/2011/234090.

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.

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

MAŠKA, Martin; Pavel MATULA; Arrate MUÑOZ-BARRUTIA a Carlos ORTIZ-DE-SOLÓRZANO. Fast Tracking Algorithm of GFP-Transfected Living Cells Based on the Chan-Vese Model. 2011.

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.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Image Division Technique in Pre-acquisition Analysis of Information Content for Automated Microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2011, roč. 242, č. 3, s. 279-289. ISSN 0022-2720. Dostupné z: https://doi.org/10.1111/j.1365-2818.2010.03465.x.

STAIER, Florian; Heinz EIPEL; Petr MATULA; Alexei V EVSIKOV; Michal KOZUBEK; Christoph CREMER a Michael HAUSMANN. Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. Rev. Sci. Instrum. USA: American Institute of Physica, 2011, roč. 82, č. 9, s. "093701-1"-"093701-8", 8 s. ISSN 0034-6748.

TESAŘOVÁ, Lenka; Irena KRONTORÁD KOUTNÁ; Zdeněk KOŘÍSTEK a Martin KLABUSAY. Multiple myeloma patients at peripheral blood stem cell harvest: restricted usage of TCR beta variable families. Clinical Immunology. Elsevier, 2011, roč. 138, č. 1, s. 67-76. ISSN 1521-6616. Dostupné z: https://doi.org/10.1016/j.clim.2010.09.007.

KRONTORÁD KOUTNÁ, Irena; Martina PETERKOVÁ; Pavel ŠIMARA; Stanislav STEJSKAL; Lenka TESAŘOVÁ a Michal KOZUBEK. Proliferation and differentiation potential of CD133+ and CD34+ populations from the bone marrow and mobilized peripheral blood. Annals of hematology. Germany: Springer, 2011, roč. 90, (2), s. 127-137. ISSN 0939-5555.

PELLICANO, Francesca; Pavel ŠIMARA; Amy SINCLAIR; Gudmundur Vignir HELGASON; Mhairi COPLAND; Steven GRANT a Tessa HOLYOAKE. The MEK inhibitor PD184352 enhances BMS-214662-induced apoptosis in CD34+ CML stem/progenitor cells. Leukemia. London: Nature Publishing Group, 2011, roč. 25, č. 7, s. 1159-1167. ISSN 0887-6924. Dostupné z: https://doi.org/10.1038/leu.2011.67.

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.

MAŠKA, Martin; Pavel MATULA; Ondřej DANĚK a Michal KOZUBEK. A Fast Level Set-Like Algorithm for Region-Based Active Contours. Online. In 6th International Symposium on Visual Computing. Berlin, Heidelberg: Springer-Verlag, 2010, s. 387-396. ISBN 978-3-642-17276-2. Dostupné z: https://doi.org/10.1007/978-3-642-17277-9_40.

DANĚK, Ondřej a Martin MAŠKA. A Simple Topology Preserving Max-Flow Algorithm for Graph Cut Based Image Segmentation. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010, s. 45-52. ISBN 978-80-87342-10-7.

TESAŘOVÁ, Lenka; Martina PETERKOVÁ; Stanislav STEJSKAL; Michaela POTĚŠILOVÁ a Irena KRONTORÁD KOUTNÁ. Application of reverse transcription PCR and capillary electrophoresis in the analysis of T-cell receptor beta variable repertoire. In Advances in Molecular and Cancer Biology, 2010. Brno, Česká republika: muni PRESS, 2010, s. 46-51. ISBN 978-80-210-5312-0.

RUČKA, Zdeněk; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Stanislav STEJSKAL; Irena KRONTORÁD KOUTNÁ; Petr VAŇHARA a Jan DOLEŽEL. Dexamethasone and Insulin Affecting SFTPA1 and SFTPA2 mRNA Levels. In Advances in Molecular and Cancer Biology, 2010. Brno, Česká republika: muni PRESS, 2010, s. 36-38. ISBN 978-80-210-5312-0.

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://doi.org/10.1007/978-3-642-13772-3_27.

MAŠKA, Martin; Pavel MATULA a Michal KOZUBEK. Simultaneous Tracking of Multiple Objects Using Fast Level Set-Like Algorithm. In 6th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science. Brno: NOVPRESS, 2010, s. 117-125. ISBN 978-80-87342-10-7.

STEJSKAL, Stanislav; Irena KRONTORÁD KOUTNÁ; Pavel MATULA; Zdeněk RUČKA; Ondřej DANĚK; Martin MAŠKA a Michal KOZUBEK. The role of chromatin condensation during granulopoiesis in the regulation of gene cluster expression. Epigenetics. USA: Landes Bioscience, 2010, roč. 5, č. 8, s. 759-767. ISSN 1559-2294. Dostupné z: https://doi.org/10.4161/epi.5.8.13183.

POTĚŠILOVÁ, Michaela; Miroslav VAŘECHA; Lenka TESAŘOVÁ a Irena KRONTORÁD KOUTNÁ. Time lapse living cells microscopy for studying CML: Preparation of Abl1- and Bcr/Abl - fluorescent protein vectors using Gateway technology. In Advances in Molecular and Cancer Biology, 2010. Brno: muni PRESS, 2010, s. 31-35. ISBN 978-80-210-5312-0.

MAŠKA, Martin a Pavel MATULA. A Fast Level Set-Like Algorithm with Topology Preserving Constraint. Online. In 13th International Conference on Computer Analysis of Images and Patterns. Berlin, Heidelberg: Springer-Verlag, 2009, s. 930-938. ISBN 978-3-642-03766-5. Dostupné z: https://doi.org/10.1007/978-3-642-03767-2_113.

MAŠKA, Martin; Ondřej DANĚK; Carlos ORTIZ-DE-SOLÓRZANO; Arrate MUÑOZ-BARRUTIA; Michal KOZUBEK a Ignacio FERNÁNDEZ GARCÍA. A Two-Phase Segmentation of Cell Nuclei Using Fast Level Set-Like Algorithms. Online. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 390-399. ISBN 978-3-642-02229-6. Dostupné z: https://doi.org/10.1007/978-3-642-02230-2_40.

MATULA, Pavel; Martin MAŠKA; Ondřej DANĚK; Petr MATULA a Michal KOZUBEK. Acquiarium: Free Software for the Acquisition and Analysis of 3D Images of Cells in Fluorescence Microscopy. Online. In IEEE International Symposium on Biomedical Imaging. Boston: IEEE, 2009, s. 1138-1141. ISBN 978-1-4244-3932-4.

ŠIMARA, Pavel; Irena KOUTNÁ; Stanislav STEJSKAL; Petr KRONTORÁD; Zdeněk RUČKA; Martina PETERKOVÁ a Michal KOZUBEK. Combination of mRNA and protein microarray analysis in complex cell profiling. Neoplasma. Bratislava, Slovensko: AEPress, s.r.o., 2009, roč. 2/2009, č. 56, s. 141-149. ISSN 0028-2685.

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.

BRÁZDILOVÁ, Silvie Luisa a Michal KOZUBEK. Information Content Analysis in Automated Microscopy Imaging using an Adaptive Autofocus Algorithm for Multimodal Functions. Journal of Microscopy. Oxford: Blackwell Science, 2009, roč. 236, č. 3, s. 194-202. ISSN 0022-2720. Dostupné z: https://doi.org/10.1111/j.1365-2818.2009.03280.x.

RUČKA, Zdeněk; Petr VAŇHARA; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Stanislav STEJSKAL; Jan DOLEŽEL a Irena KOUTNÁ. Insulin Decreases Transcription of Three Proteins Associated with Lung Surfactant. 2009. vyd. Posters@Technologynetworks.net, 2009. The Online Journal of Scientific Posters.

PETERKOVÁ, Martina; Irena KOUTNÁ; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Michal KOZUBEK; Viera HRABČÁKOVÁ; Martin KLABUSAY; Michael DOUBEK a Jiří MAYER. Microarray analysis using limited amount of cells. Folia Biologica (Praha). 2009, roč. 2009, č. 55, s. 53-60. ISSN 0015-5500.

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.

TESAŘOVÁ, Lenka; Irena KOUTNÁ; Martina PETERKOVÁ; Michaela POTĚŠILOVÁ; Magdaléna DVOŘÁKOVÁ a Stanislav STEJSKAL. Representation of T-cell receptor V beta families detected by reverse transcription PCR and capillary electrophoresis. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA: Elsevier, 2009, s. 72. ISSN 0301-472X.

DANĚK, Ondřej; Pavel MATULA; Carlos ORTIZ-DE-SOLÓRZANO; Arrate MUÑOZ-BARRUTIA; Martin MAŠKA a Michal KOZUBEK. Segmentation of Touching Cell Nuclei using a Two-Stage Graph Cut Model. In 16th Scandinavian Conference on Image Analysis. Berlin, Heidelberg: Springer-Verlag, 2009, s. 410-419. ISBN 978-3-642-02229-6. Dostupné z: https://doi.org/10.1007/978-3-642-02230-2_42.

PETERKOVÁ, Martina; Irena KOUTNÁ; Pavel ŠIMARA; Stanislav STEJSKAL a Lenka TESAŘOVÁ. The in vitro proliferation potential and proportion of CD133+ versus CD34+ hematopoietic stem cells. In Experimental Hematology, Volume 37, Number 9. University of Nevada, USA: Elsevier, 2009, s. 35-36. ISSN 0301-472X.

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.

PETERKOVÁ, Martina; Irena KOUTNÁ; Lenka TESAŘOVÁ; Michaela POTĚŠILOVÁ; Zdeněk RUČKA; Viera HRABČÁKOVÁ a Martin KLABUSAY. cDNA Microarray: Gene Expression Profiling of Small Cell Populations. 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.

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.

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.

KOUTNÁ, Irena; Lenka TESAŘOVÁ; Martin KLABUSAY; Petr KROTORÁD; Michal STREHOVSKÝ; Martina PETERKOVÁ a Viera HRABČÁKOVÁ. Expression Profiling of CD34+ of Peripheral Blood of Patients with Lymphoma During ex vivo Granulocytic Differentiation. 2007.

KOUTNÁ, Irena; Petr KRONTORÁD; Zbyněk SVOBODA; Eva BÁRTOVÁ; Michal KOZUBEK a Stanislav KOZUBEK. New insights into gene positional clustering and its properties supported by large-scale analysis of various differentiation pathways. Genomics. United States: Elsevier Science Inc, 2007, roč. 89, č. 1, s. 81-88. ISSN 0888-7543.

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.

KOZUBEK, Michal. Automated analysis of multi-dimensional biomedical image data acquired using optical microscopy. Ed. R. Lechnerová, I. Saxl, V. Beneš. In Proceedings of the 6th International Conference on Stereology, Spatial Statistics and Stochastic Geometry. Prague: Union of Czech Mathematicians and Physicists, 2006, s. 465-476. ISBN 80-7015-037-8.

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.

JANSOVÁ, Eva; Irena KOUTNÁ; Petr KRONTORÁD; Zbyněk SVOBODA; Silvie KŘIVÁNKOVÁ; Jan ŽALOUDÍK; Michal KOZUBEK a Stanislav KOZUBEK. Comparative transcriptome maps: a new approach to the diagnosis of colorectal carcinoma patients using cDNA microarrays. Clinical Genetics. Denmark: Blackwell Munksgaard, 2006, roč. 69, č. 3, s. 218-227. ISSN 0009-9163.

KOUTNÁ, Irena; Martin KLABUSAY; Viera HRABČÁKOVÁ; Petr KRONTORÁD; Zbyněk SVOBODA; Michal KOZUBEK a Jiří MAYER. Evaluation of CD34+ - and Lin- -selected cells from peripheral blood stem cell grafts of patients with lymphoma during differentiation in culture ex vivo using a cDNA microarray technique. Experimental hematology. Netherlands: Elsevier Science Inc, 2006, roč. 34, č. 7, s. 832-840, 10 s. ISSN 0301-472X.

MATULA, Petr; Pavel MATULA; Michal KOZUBEK a Vladimír DVOŘÁK. Fast Point-Based 3D Alignment of Live Cells. IEEE Transactions on Image Processing. 2006, roč. 15, č. 8, s. 2388-2396. ISSN 1057-7149.

HUBENÝ, Jan; Pavel MATULA; Petr MATULA a Michal KOZUBEK. Improved 3D Reconstruction of Interphase Chromosomes Based on Nonlinear Diffusion Filtering. In Proceedings of PDE-Based Image Processing and Related Inverse Problems. Berlin: Springer-Verlag, 2006, s. 163-173, 10 s. ISBN 3-540-33266-9.

TASLEROVÁ, Renata; Stanislav KOZUBEK; Eva BÁRTOVÁ; Pavla GAJDUŠKOVÁ; Roman KODET a Michal KOZUBEK. Localization of genetic elements of intact and derivative chromosome 11 and 22 territories in nuclei of Ewing sarcoma cells. Journal of Structural Biology. San Diego,USA: Academic Press, 2006, roč. 155, č. 3, s. 493-504. ISSN 1047-8477.

KOUTNÁ, Irena; Petr KRONTORÁD; Lenka TESAŘOVÁ; Martin KLABUSAY; Viera HRABČÁKOVÁ a Michal KOZUBEK. Transcription density map as a new tool for evaluation of various expression profiles: Ex vivo differentiation of CD34+ cells. In ISREC Conference on Cancer Research. 2006.

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.

KOUTNÁ, Irena; Eva JANSOVÁ; Petr KRONTORÁD; Zbyněk SVOBODA; Michal KOZUBEK a Stanislav KOZUBEK. cDNA Microarray Technology as a Tool for Better Understanding of Progress of Malignant Diseases. In Prague Post Genome Technology Workshop. Prague, Czech Republic: Czech Pattern Recognition Society, 2005, s. 69-72. ISBN 80-01-03239-6.

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.

KOZUBEK, Michal; Petr MATULA; Pavel MATULA a Stanislav KOZUBEK. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. Microscopy research and technique. USA: Wiley-Liss, 2004, roč. 64, č. 2, s. 164-175. ISSN 1059-910X.

KOZUBEK, Michal; Petr MATULA a Pavel MATULA. Automated confocal microscopy: The way of achieving both quality and quantity in 3D image cytometry. In International Symposium on Biomedical Imaging. Arlington, USA: IEEE, 2004, s. 69-72. ISBN 0-7803-8389-3.

TASLEROVÁ, Renata; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Pavla JIRSOVÁ; Eva BÁRTOVÁ a Michal KOZUBEK. Arrangement of chromosome 11 and 22 territories, EWSR1 and FLI-1 genes, and other genetic elements of these chromosomes in human lymphocytes and Ewing sarcoma cells. Human Genetics. 2003, roč. 112, č. 2, s. 143-155. ISSN 0340-6717.

AMRICHOVÁ, Jana; Emilie LUKÁŠOVÁ; Stanislav KOZUBEK a Michal KOZUBEK. Nuclear and territorial topography of chromosome telomeres in human lymphocytes. Experimental Cell Research. Elsevier Science, USA, 2003, roč. 289, č. 1, s. 11-26. ISSN 0014-4827.

MATULA, Petr; Michal KOZUBEK; Florian STAIER a Michael HAUSMANN. Precise 3D image alignment in micro-axial tomography. Journal of Microscopy. Oxford: Blackwell Science, 2003, roč. 209, č. 2, s. 126-142. ISSN 0022-2720.

KOZUBEK, Michal; Magdalena SKALNÍKOVÁ; Petr MATULA; Eva BÁRTOVÁ; Joachim RAUCH; Friedrich NEUHAUS; Heinz EIPEL a Michael HAUSMANN. Automated micro axial tomography of cell nuclei after specific labelling by fluorescence in situ hybridisation. Micron. Amsterdam: Elsevier, 2002, roč. 33, č. 7, s. 655-665. ISSN 0968-4328.

KOZUBEK, Stanislav; Emilie LUKÁŠOVÁ; Pavla JIRSOVÁ; Irena KOUTNÁ; Michal KOZUBEK; Alena GAŇOVÁ; Eva BÁRTOVÁ; Martin FALK a Renata TASLEROVÁ. 3D Structure of the human genome: Order in randomness. Chromosoma. Berlin: Springer-Verlag, 2002, roč. 111, č. 5, s. 321-331. ISSN 0009-5915.

KOZUBEK, Michal; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Eva BÁRTOVÁ; Magdalena SKALNÍKOVÁ; Pavel MATULA; Petr MATULA; Pavla JIRSOVÁ; Alena GAŇOVÁ a Irena KOUTNÁ. Combined confocal and wide-field high-resolution cytometry of FISH-stained cells. Cytometry. New York: International Society for Analytical Cyt, 2001, roč. 45, č. 1, s. 1-12. ISSN 0196-4763.

KOZUBEK, Michal. Theoretical versus experimental resolution in optical microscopy. Microscopy research and technique. USA: Wiley-Liss, 2001, roč. 53, č. 2, s. 157-166. ISSN 1059-910X. Dostupné z: https://doi.org/10.1002/jemt.1080.

KOZUBEK, Michal a Petr MATULA. An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy. Journal of Microscopy. Oxford: Blackwell Science, 2000, roč. 200, č. 3, s. 206-217. ISSN 0022-2720.

SKALNÍKOVÁ, Magdalena; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Eva BÁRTOVÁ; Pavla JIRSOVÁ; Alena CAFOURKOVÁ; Irena KOUTNÁ a Michal KOZUBEK. Spatial arrangement of genes, centromeres and chromosomes in human blood cell nuclei and its changes during the cell cycle, differentiation and after irradiation. Chromosome Research. Dordrecht: Kluwer Academic, 2000, roč. 8, č. 6, s. 487-499. ISSN 0967-3849.

KOUTNÁ, Irena; Stanislav KOZUBEK; Jan ŽALOUDÍK; Michal KOZUBEK; Emilie LUKÁŠOVÁ; Pavel MATULA; Eva BÁRTOVÁ; Magdalena SKALNÍKOVÁ; Alena CAFOURKOVÁ a Pavla JIRSOVÁ. Topography of genetic loci in tissue samples: towards new diagnostic tool using interphase FISH and high-resolution image analysis techniques. Analytical Cellular Pathology. Amsterdam: IOS Press, 2000, roč. 20, č. 4, s. 173-185. ISSN 0921-8912.

KOZUBEK, Michal; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Leonard RÝZNAR; Andrea LIŠKOVÁ; Jana AMRICHOVÁ a Gerda HORNECK. Advances in computer analysis of radiation-induced changes in human genome. edited by C.Baumstark-Khan, S.Kozubek, G.Horneck. In Fundamentals for the assesment of risks from environmental radiation. Dordrecht: Kluwer Academic Publishers, 1999, s. 243-248. ISBN 0-7923-5667-5.

KOZUBEK, Michal; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Andrea MAREČKOVÁ; Eva BÁRTOVÁ; Magdalena SKALNÍKOVÁ a Adriana JERGOVÁ. High-resolution cytometry of FISH dots in interphase cell nuclei. Cytometry. New York: International Society for Analytical Cyt, 1999, roč. 36, č. 4, s. 279-293. ISSN 0196-4763.

KOZUBEK, Michal; Stanislav KOZUBEK; Emilie LUKÁŠOVÁ; Jana AMRICHOVÁ; Leonard RÝZNAR a Andrea LIŠKOVÁ. Semi-automated FISH-stained interphase nuclei analysis in human genome studies. edited by J.Slavík. In Fluorescence Microscopy and Fluorescent Probes. vol.2. New York: Plenum, 1998, s. 173-179. ISBN 0-306-46021-1.

KOZUBEK, Stanislav; Emilie LUKÁŠOVÁ; Leonard RÝZNAR; Michal KOZUBEK; Raisa GOVORUN; Evgenij KRASAVIN a Gerda HORNECK. Distribution of ABL and BCR genes in cell nuclei of normal and irradiated lymphocytes. Blood. 1997, roč. 89, č. 12, s. 4537-4545. ISSN 0006-4971.

LUKÁŠOVÁ, Emilie; Stanislav KOZUBEK; Michal KOZUBEK; Jana KJERONSKÁ; Leonard RÝZNAR; Jana HORÁKOVÁ; Eva KRAHULCOVÁ a Gerda HORNECK. Localisation and distance between ABL and BCR genes in interphase nuclei of bone marrow cells of control donors and patients with chronic myeloid leukemia. Human Genetics. 1997, roč. 100, 5/6, s. 525-535. ISSN 0340-6717.

SCHRADER, Martin; Michal KOZUBEK; Stefan HELL a Tony WILSON. Optical transfer functions of 4Pi confocal microscopes : theory and experiment. Optics Letters. 1997, roč. 22, č. 7, s. 436-438. ISSN 0146-9592.

WILSON, Tony; Rimas JUŠKAITIS; Mark NEIL a Michal KOZUBEK. Confocal microscopy by aperture correlation. Optics Letters. 1996, roč. 21, č. 23, s. 1879-1881. ISSN 0146-9592.

JUŠKAITIS, Rimas; Tony WILSON; Mark NEIL a Michal KOZUBEK. Efficient real-time confocal microscopy with white light sources. Nature. 1996, roč. 383, č. 6603, s. 804-806. ISSN 0028-0836.