Publications – Uhlmann Group

Shield-4i: A Whole-mount Multiplexed Imaging Platform for Studying Multiscale Information Flow in 3D Multicellular Systems

Hornbachner R, Shamipour S, Arslan FN, Fan R, Hess M, Curvaia F, Lüthi J, Oates AC, Bedzhov I, Gilmour D, Uhlmann V, Pelkmans L.

Preprint, 2026

doi:10.64898/2026.07.01.735871.

Bridging annotated microscopy imaging data and analysis method development for scientific discovery.

Yamauchi KA, Uhlmann V.

Patterns (New York, N.Y.), 2026

doi:10.1016/j.patter.2026.101542.

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

Garcia-Alonso L, Ashcroft J, Tromans-Coia C, Kuscu N, Cohen CE, Mazin PV, Paredes A, Massalha H, Icoresi Mazzeo C, Tuck L, Sancho Serra C, Prigmore E, Armingol E, Martinez G, Li T, Binkevich A, Predeus AV, Troule K, Tomlinson E, Monteiro A, Auckburally F, Koland M, Jaciow A, Wang L, Mahbubani KT, Saeb-Parsy K, Choudhary M, Prete M, Kelava I, Davies J, Lane S, Herbert M, Uhlmann V, Williams SA, Vento-Tormo R.

Preprint, 2026

doi:10.64898/2026.06.05.730381.

Topology-aware reconstruction of cellular state landscapes from microscopy using self-supervised learning

Messori E, Taha D, Fournier L, Romero AF, Uhlmann V, Frossard P, Vincent-Cuaz C, Patani R, Luisier R.

Preprint, 2026

doi:10.64898/2026.05.30.728966.

Residual ellipticity in waveplate-compensated polarization-resolved SHG microscopy may arise from femtosecond laser spectral bandwidth

Nguyen D, Wilde JP, Uhlmann V, Smith DJ, Kusch-Wieser J, Zanrè V, Schwiedrzik J, Csúcs G.

Preprint, 2026

doi:10.64898/2026.02.24.707711.

Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows

Lüthi J, Cerrone L, Comparin T, Hess M, Hornbachner R, Tschan A, Glasner de Medeiros GQ, Repina NA, Cantoni LK, Steffen FD, Bourquin J, Liberali P, Pelkmans L, Uhlmann V.

Preprint, 2026

doi:10.64898/2026.03.05.709921.

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19.

Lee JTH, Barnett SN, Roberts K, Ashwin H, Milross L, Cho JW, Huseynov A, Woodhams B, Aivazidis A, Li T, Majo J, Chaves P, Lee M, Miranda AMA, Jablonska Z, Arena V, Hanley B, Osborn M, Uhlmann V, Xu XN, McLean GR, Teichmann SA, Randi AM, Filby A, Kaye PM, Fisher AJ, Hemberg M, Noseda M, Bayraktar OA.

Nature communications, 2025

doi:10.1038/s41467-025-56473-x.

From images to understanding: Advances in deep learning for cellular dynamics analysis.

Woodhams B, Uhlmann V.

Current opinion in cell biology, 2025

doi:10.1016/j.ceb.2025.102585.

MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis.

Zulueta-Coarasa T, Jug F, Mathur A, Moore J, Muñoz-Barrutia A, Anita L, Babalola K, Bankhead P, Gilloteaux P, Gogoberidze N, Jones ML, Kleywegt GJ, Korir P, Kreshuk A, Küpcü Yoldaş A, Marconato L, Narayan K, Norlin N, Oezdemir B, Riesterer JL, Russell C, Rzepka N, Sarkans U, Serrano-Solano B, Tischer C, Uhlmann V, Ulman V, Hartley M.

Nature methods, 2025

doi:10.1038/s41592-025-02835-8.

A nanopathology pipeline for clinical research across scales using human tissue

Burrell A, Lawson M, Ronchi P, Xiong X, Albers J, McLean A, Willicombe M, Moran L, Hounsome J, Jones M, Ross G, de Folter J, Hartley M, Uhlmann V, Strange A, Schwab Y, Duke E, Roufosse C, Collinson L.

Preprint, 2025

doi:10.1101/2025.08.29.25334660.

A neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens.

Weheliye WH, Rodriguez J, Feriani L, Javer A, Uhlmann V, Brown AEX.

PLoS computational biology, 2025

doi:10.1371/journal.pcbi.1013345.

bia-binder: a web-native cloud compute service for the bioimage analysis community.

Russell CT, Burel JM, Athar A, Li S, Sarkans U, Swedlow J, Brazma A, Hartley M, Hartley M, Uhlmann V.

Bioinformatics (Oxford, England), 2025

doi:10.1093/bioinformatics/btaf412.

2024 OME-NGFF workflows hackathon

Lüthi J, Albert M, Anita L, Babalola K, Bennett D, Bogovic JA, Cerrone L, Dornier R, Eglinger J, Galinova V, Gerber R, Gros O, Hahmann S, Hess M, Hornbachner R, Horyslavets D, Huxford R, Krentzel D, LI T, Marconato L, McCormick M, Moos F, Mroz F, Özdemir B, Pavie B, Perlman E, Schulz M, Schwarz L, Spitz HM, Stansby D, Steffen F, Stoma S, Sturzenegger F, Vierdag W, Windhager J, Yamauchi K, Zubarev I, Moore J, Rzepka N, Tischer C, Ulman V, Uhlmann V.

Preprint, 2025

doi:10.37044/osf.io/5uhwz_v2.

Bridging imaging-based in vitro methods from biomedical research to regulatory toxicology.

Piergiovanni M, Mennecozzi M, Barale-Thomas E, Danovi D, Dunst S, Egan D, Fassi A, Hartley M, Kainz P, Koch K, Le Dévédec SE, Mangas I, Miranda E, Nyffeler J, Pesenti E, Ricci F, Schmied C, Schreiner A, Stokar-Regenscheit N, Swedlow JR, Uhlmann V, Wieland FC, Wilson A, Whelan M.

Archives of toxicology, 2025

doi:10.1007/s00204-024-03922-z.

BioModels' Model of the Year 2023.

Malik Sheriff RS, Asari H, Hermjakob H, Huber W, Quail T, Santos SDM, Smith AM, Uhlmann V.

Frontiers in systems biology, 2024

doi:10.3389/fsysb.2024.1363884.

An improved neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens

Weheliye WH, Rodriguez J, Feriani L, Javer A, Uhlmann V, Uhlmann V, Brown AE.

Preprint, 2024

doi:10.1101/2024.12.20.629717.

A spatial human thymus cell atlas mapped to a continuous tissue axis.

Yayon N, Kedlian VR, Boehme L, Suo C, Wachter BT, Beuschel RT, Amsalem O, Polanski K, Koplev S, Tuck E, Dann E, Van Hulle J, Perera S, Putteman T, Predeus AV, Dabrowska M, Richardson L, Tudor C, Kreins AY, Engelbert J, Stephenson E, Kleshchevnikov V, De Rita F, Crossland D, Bosticardo M, Pala F, Prigmore E, Chipampe NJ, Prete M, Fei L, To K, Barker RA, He X, Van Nieuwerburgh F, Bayraktar OA, Patel M, Davies EG, Haniffa MA, Uhlmann V, Notarangelo LD, Germain RN, Radtke AJ, Marioni JC, Taghon T, Teichmann SA.

Nature, 2024

doi:10.1038/s41586-024-07944-6.

The crucial role of bioimage analysts in scientific research and publication.

Cimini BA, Bankhead P, D'Antuono R, Fazeli E, Fernandez-Rodriguez J, Fuster-Barceló C, Haase R, Jambor HK, Jones ML, Jug F, Klemm AH, Kreshuk A, Marcotti S, Martins GG, McArdle S, Miura K, Muñoz-Barrutia A, Murphy LC, Nelson MS, Nørrelykke SF, Paul-Gilloteaux P, Pengo T, Pylvänäinen JW, Pytowski L, Ravera A, Reinke A, Rekik Y, Strambio-De-Castillia C, Thédié D, Uhlmann V, Umney O, Wiggins L, Eliceiri KW.

Journal of cell science, 2024

doi:10.1242/jcs.262322.

Making the most of bioimaging data through interdisciplinary interactions.

Uhlmann V, Hartley M, Moore J, Weisbart E, Zaritsky A.

Journal of cell science, 2024

doi:10.1242/jcs.262139.

Temporal variability and cell mechanics control robustness in mammalian embryogenesis.

Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlmann V, Hannezo E, Hiiragi T.

Science (New York, N.Y.), 2024

doi:10.1126/science.adh1145.

Label-free phenotyping of human microvessel networks

Rappez L, Akinbote A, Cherubini M, Uhlmann V, Haase K.

Preprint, 2024

doi:10.1101/2024.02.20.581133.

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

Lee JTH, Barnett SN, Roberts K, Ashwin H, Milross L, Cho J, Huseynov A, Woodhams B, Aivazidis A, Li T, Majo J, Guerrero PC, Lee M, Miranda AMA, Jablonska Z, Arena V, Hanley B, Osborn M, Uhlmann V, Xu X, McLean GR, Teichmann SA, Randi AM, Filby A, Kaye PM, Fisher AJ, Hemberg M, Noseda M, Bayraktar OA.

Preprint, 2023

doi:10.1101/2023.12.20.572494.

Author Correction: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.

Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R.

Nature genetics, 2023

doi:10.1038/s41588-022-01287-6.

Made to measure: An introduction to quantifying microscopy data in the life sciences.

Culley S, Caballero AC, Burden JJ, Uhlmann V.

Journal of microscopy, 2023

doi:10.1111/jmi.13208.

Simulating structurally variable nuclear pore complexes for microscopy.

Theiss M, Hériché JK, Russell C, Helekal D, Soppitt A, Ries J, Ellenberg J, Brazma A, Uhlmann V.

Bioinformatics (Oxford, England), 2023

doi:10.1093/bioinformatics/btad587.

Embryo-uterine interaction coordinates mouse embryogenesis during implantation.

Bondarenko V, Nikolaev M, Kromm D, Belousov R, Wolny A, Blotenburg M, Zeller P, Rezakhani S, Hugger J, Uhlmann V, Hufnagel L, Kreshuk A, Ellenberg J, van Oudenaarden A, Erzberger A, Lutolf MP, Hiiragi T.

The EMBO journal, 2023

doi:10.15252/embj.2022113280.

A biologist's guide to planning and performing quantitative bioimaging experiments.

Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, Cimini BA.

PLoS biology, 2023

doi:10.1371/journal.pbio.3002167.

MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy.

Zinchenko V, Hugger J, Uhlmann V, Arendt D, Kreshuk A.

eLife, 2023

doi:10.7554/elife.80918.

Temporal variability and cell mechanics control robustness in mammalian embryogenesis

Fabrèges D, Murtra BC, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlmann V, Hannezo E, Hiiragi T.

Preprint, 2023

doi:10.1101/2023.01.24.525420.

Microscopy image analysis: course materials

Lopez PC, Holinski A, Russell C, Uhlmann V, Brazma A, Swedlow J.

2022

doi:10.6019/tol.microscopyimagematerials-t.2022.00001.1.

Coordination Between Embryo Growth and Trophoblast Migration Upon Implantation Delineates Mouse Embryogenesis

Bondarenko V, Nikolaev M, Kromm D, Belousov R, Wolny A, Rezakhani S, Hugger J, Uhlmann V, Hufnagel L, Kreshuk A, Ellenberg J, Erzberger A, Lutolf M, Hiiragi T.

Preprint, 2022

doi:10.1101/2022.06.13.495767.

LOMAR: LOcalization Microscopy Analysis in R

Theiss M, Brazma A, Uhlmann V, Hériché J.

Preprint, 2022

doi:10.1101/2022.05.30.493957.

Simulating structurally variable Nuclear Pore Complexes for Microscopy

Theiss M, Hériché J, Russell C, Helekal D, Soppitt A, Ries J, Ellenberg J, Brazma A, Uhlmann V.

Preprint, 2022

doi:10.1101/2022.05.17.492295.

MorphoFeatures: unsupervised exploration of cell types, tissues and organs in volume electron microscopy

Zinchenko V, Hugger J, Uhlmann V, Arendt D, Kreshuk A.

Preprint, 2022

doi:10.1101/2022.05.07.490949.

Steer'n'Detect: fast 2D template detection with accurate orientation estimation.

Uhlmann V, Püspöki Z, Depeursinge A, Unser M, Sage D, Fageot J.

Bioinformatics (Oxford, England), 2022

doi:10.1093/bioinformatics/btac270.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.

Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R.

Nature genetics, 2021

doi:10.1038/s41588-021-00972-2.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Garcia-Alonso L, Handfield L, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park J, Jimenez-Linan M, Campos L, Kiselev V, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R.

Preprint, 2021

doi:10.1101/2021.01.02.425073.

Deep learning for bioimage analysis in developmental biology.

Hallou A, Yevick HG, Dumitrascu B, Uhlmann V.

Development (Cambridge, England), 2021

doi:10.1242/dev.199616.

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.

Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A.

Nature methods, 2021

doi:10.1038/s41592-021-01166-8.