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Uhlmann Group

From images to biological knowledge

Publications

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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.

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 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.

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.

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<i>in vivo</i>and<i>in vitro</i>

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.

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.

Multiresolution Subdivision Snakes.

Badoual A, Schmitter D, Uhlmann V, Unser M.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 2016

doi:10.1109/tip.2016.2644263.

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