DeepFuse: A multi-rater fusion and refinement network for computing silver-standard annotations.

Vladimír Ulman https://orcid.org/0000-0002-4270-7982 https://www.wikidata.org/entity/Q57528347

Cem Emre Akbas Vladimír Ulman Martin Maska Michal Kozubek 0001 DeepFuse: A multi-rater fusion and refinement network for computing silver-standard annotations. 110186 2025 192 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2025.110186 db/journals/cbm/cbm192.html#AkbasUMK25 streams/journals/cbm

Carlos Garcia-Lopez-de-Haro 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 Arrate Muñoz-Barrutia SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model. 2025 June abs/2506.02783 CoRR https://doi.org/10.48550/arXiv.2506.02783 db/journals/corr/corr2506.html#abs-2506-02783 streams/journals/corr

David Wiesner Julian Suk Sven Dummer Tereza Necasová Vladimír Ulman David Svoboda Jelmer M. Wolterink Generative modeling of living cells with SO(3)-equivariant implicit neural representations. 102991 2024 January 91 Medical Image Anal. https://doi.org/10.1016/j.media.2023.102991 db/journals/mia/mia91.html#WiesnerSDNUSW24

Timo Kaiser Vladimír Ulman Bodo Rosenhahn CHOTA: A Higher Order Accuracy Metric for Cell Tracking. 122-138 2024 ECCV Workshops (16) https://doi.org/10.1007/978-3-031-91721-9_8 conf/eccv/2024-w16 db/conf/eccv/eccv2024-w16.html#KaiserUR24 streams/conf/eccv

Timo Kaiser Vladimír Ulman Bodo Rosenhahn CHOTA: A Higher Order Accuracy Metric for Cell Tracking. 2024 abs/2408.11571 CoRR https://doi.org/10.48550/arXiv.2408.11571 db/journals/corr/corr2408.html#abs-2408-11571 streams/journals/corr

David Wiesner Julian Suk Sven Dummer Tereza Necasová Vladimír Ulman David Svoboda Jelmer M. Wolterink Generative modeling of living cells with SO(3)-equivariant implicit neural representations. 2023 abs/2304.08960 CoRR https://doi.org/10.48550/arXiv.2304.08960 db/journals/corr/corr2304.html#abs-2304-08960

Martin Maska Tereza Necasová David Wiesner Dmitry V. Sorokin Igor Peterlík Vladimír Ulman David Svoboda Toward Robust Fully 3D Filopodium Segmentation and Tracking in Time-Lapse Fluorescence Microscopy. 819-823 2019 ICIP https://doi.org/10.1109/ICIP.2019.8803721 conf/icip/2019 db/conf/icip/icip2019.html#MaskaNWSPUS19

Dmitry V. Sorokin Igor Peterlík Vladimír Ulman David Svoboda Tereza Necasová Katsiarina Morgaenko Lívia Eiselleová Lenka Tesarová Martin Maska FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells With Growing and Branching Filopodia. 2630-2641 2018 37 IEEE Trans. Medical Imaging 12 https://doi.org/10.1109/TMI.2018.2845884 https://www.wikidata.org/entity/Q89558313 db/journals/tmi/tmi37.html#SorokinPUSNMETM18

Cem Emre Akbas Vladimír Ulman Martin Maska Florian Jug Michal Kozubek 0001 Automatic Fusion of Segmentation and Tracking Labels. 446-454 2018 ECCV Workshops (6) https://doi.org/10.1007/978-3-030-11024-6_34 conf/eccv/2018w6 db/conf/eccv/eccv2018w6.html#AkbasUMJK18 Igor Peterlík David Svoboda Vladimír Ulman Dmitry V. Sorokin Martin Maska Model-Based Generation of Synthetic 3D Time-Lapse Sequences of Multiple Mutually Interacting Motile Cells with Filopodia. 71-79 2018 SASHIMI@MICCAI https://doi.org/10.1007/978-3-030-00536-8_8 conf/miccai/2018sashimi db/conf/miccai/sashimi2018.html#PeterlikSUSM18

David Svoboda Vladimír Ulman MitoGen: A Framework for Generating 3D Synthetic Time-Lapse Sequences of Cell Populations in Fluorescence Microscopy. 310-321 2017 36 IEEE Trans. Medical Imaging 1 https://doi.org/10.1109/TMI.2016.2606545 https://www.wikidata.org/entity/Q39395726 db/journals/tmi/tmi36.html#SvobodaU17

Dmitry V. Sorokin Igor Peterlík Vladimír Ulman David Svoboda Martin Maska Model-based generation of synthetic 3D time-lapse sequences of motile cells with growing filopodia. 822-826 2017 ISBI https://doi.org/10.1109/ISBI.2017.7950644 conf/isbi/2017 db/conf/isbi/isbi2017.html#SorokinPUSM17 David Svoboda Vladimír Ulman Peter Kovác Barbara Salingova Lenka Tesarová Irena K. Koutna Petr Matula Vascular network formation in silico using the extended cellular potts model. 3180-3183 2016 ICIP https://doi.org/10.1109/ICIP.2016.7532946 conf/icip/2016 db/conf/icip/icip2016.html#SvobodaUKSTKM16 Vladimír Ulman Zoltán Orémus David Svoboda TRAgen: A Tool for Generation of Synthetic Time-Lapse Image Sequences of Living Cells. 623-634 2015 ICIAP (1) https://doi.org/10.1007/978-3-319-23231-7_56 conf/iciap/2015-1 db/conf/iciap/iciap2015-1.html#UlmanOS15 David Svoboda Vladimír Ulman Igor Peterlík On proper simulation of chromatin structure in static images as well as in time-lapse sequences in fluorescence microscopy. 712-716 2015 ISBI https://doi.org/10.1109/ISBI.2015.7163972 conf/isbi/2015 db/conf/isbi/isbi2015.html#SvobodaUP15

Martin Maska Vladimír Ulman David Svoboda Pavel Matula Petr Matula Cristina Ederra Ainhoa Urbiola Tomás España Subramanian Venkatesan 0001 Deepak M. W. Balak Pavel Karas Tereza Bolcková Markéta Streitová Craig Carthel Stefano Coraluppi Nathalie Harder Karl Rohr Klas E. G. Magnusson Joakim Jaldén Helen M. Blau Oleh Dzyubachyk Pavel Krízek Guy M. Hagen David Pastor-Escuredo Daniel Jimenez-Carretero María J. Ledesma-Carbayo Arrate Muñoz-Barrutia Erik Meijering Michal Kozubek 0001 Carlos Ortiz-de-Solorzano A benchmark for comparison of cell tracking algorithms. 1609-1617 2014 30 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btu080 https://www.wikidata.org/entity/Q30578553 db/journals/bioinformatics/bioinformatics30.html#MaskaUSMMEUEVBKBSCCHRMJBDKHPJLMMKO14

David Svoboda Vladimír Ulman Ludek Matyska Martin Maska Jan Bella Stanislav Stejskal On proper simulation of phenomena influencing image formation in fluorescence microscopy. 3944-3948 2014 ICIP https://doi.org/10.1109/ICIP.2014.7025801 conf/icip/2014 db/conf/icip/icip2014.html#SvobodaUMMBS14 David Svoboda Vladimír Ulman Towards a Realistic Distribution of Cells in Synthetically Generated 3D Cell Populations. 429-438 2013 ICIAP (2) https://doi.org/10.1007/978-3-642-41184-7_44 conf/iciap/2013-2 db/conf/iciap/iciap2013-2.html#SvobodaU13 David Svoboda Vladimír Ulman Generation of Synthetic Image Datasets for Time-Lapse Fluorescence Microscopy. 473-482 2012 ICIAR (2) https://doi.org/10.1007/978-3-642-31298-4_56 conf/iciar/2012-2 db/conf/iciar/iciar2012-2.html#SvobodaU12

Vladimír Ulman Boundary Treatment for Young-van Vliet Recursive Zero-Mean Gabor Filtering. 2011 2011 EURASIP J. Adv. Signal Process. https://doi.org/10.1155/2011/234090 https://www.wikidata.org/entity/Q59266954 db/journals/ejasp/ejasp2011.html#Ulman11

Vladimír Ulman Improving Accuracy of Optical Flow of Heeger's Original Method on Biomedical Images. 263-273 2010 ICIAR (1) https://doi.org/10.1007/978-3-642-13772-3_27 conf/iciar/2010-1 db/conf/iciar/iciar2010-1.html#Ulman10 Vladimír Ulman Jan Hubený On generating ground-truth time-lapse image sequences and flow fields. 234-239 2007 conf/icinco/2007ra1 ICINCO-RA (1) db/conf/icinco/icinco2007-ra1.html#UlmanH07 Vladimír Ulman Jan Hubený Pseudo-real Image Sequence Generator for Optical Flow Computations. 976-985 2007 conf/scia/2007 SCIA https://doi.org/10.1007/978-3-540-73040-8_99 db/conf/scia/scia2007.html#UlmanH07 Jan Hubený Vladimír Ulman Pavel Matula Estimating large local motion in live-cell imaging using variational optical flow - towards motion tracking in live cell imaging using optical flow. 542-548 2007 conf/visapp/2007-2 VISAPP (2) db/conf/visapp/visapp2007-2.html#HubenyUM07 Cem Emre Akbas Deepak M. W. Balak Jan Bella Helen M. Blau Tereza Bolcková Craig Carthel Stefano Coraluppi Sven Dummer Oleh Dzyubachyk Cristina Ederra Lívia Eiselleová Kevin W. Eliceiri Tomás España Daniel Franco-Barranco Caterina Fuster-Barceló Carlos Garcia-Lopez-de-Haro Guy M. Hagen Nathalie Harder Jónathan Heras Jan Hubený Adrián Inés Joakim Jaldén Daniel Jimenez-Carretero Florian Jug Timo Kaiser Pavel Karas Irena K. Koutna Peter Kovác Michal Kozubek 0001 Pavel Krízek María J. Ledesma-Carbayo Klas E. G. Magnusson Martin Maska Pavel Matula Petr Matula Ludek Matyska Erik Meijering Katsiarina Morgaenko Arrate Muñoz-Barrutia Tereza Necasová Jean-Christophe Olivo-Marin Zoltán Orémus Carlos Ortiz-de-Solorzano David Pastor-Escuredo Igor Peterlík Karl Rohr Bodo Rosenhahn Curtis RuedenCurtis T. Rueden Daniel Sage Barbara Salingova Dmitry V. Sorokin Stanislav Stejskal Markéta Streitová Julian Suk David Svoboda Lenka Tesarová Jean-Yves Tinevez Ainhoa Urbiola Subramanian Venkatesan 0001 David Wiesner Jelmer M. Wolterink