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.

2023

doi:10.1101/2023.12.20.572494.

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, 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.

EMBO J, 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 Biol, 2023

doi:10.1371/journal.pbio.3002167.

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

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

J Microsc, 2023

doi:10.1111/jmi.13208.

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.

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.

2022

doi:10.1101/2022.06.13.495767.

LOMAR: LOcalization Microscopy Analysis in R

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

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.

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.

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, 2022

doi:10.1093/bioinformatics/btac270.

Deep learning for bioimage analysis in developmental biology.

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

Development, 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.

Nat Methods, 2021

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

Which image-based phenotypes are most promising for using AI to understand cellular functions and why?

Lundberg E, Funke J, Uhlmann V, Gerlich D, Walter T, Carpenter A, Coehlo LP.

Cell Syst, 2021

doi:10.1016/j.cels.2021.04.012.

Principled Design and Implementation of Steerable Detectors.

Fageot J, Uhlmann V, Puspoki Z, Beck B, Unser M, Depeursinge A.

IEEE Trans Image Process, 2021

doi:10.1109/tip.2021.3072499.

Dictionary Learning for Two-Dimensional Kendall Shapes

Song A, Uhlmann V, Fageot J, Unser M.

SIAM J Imaging Sci, 2020

doi:10.1137/19m126044x.

SplineDist: Automated Cell Segmentation With Spline Curves

Mandal S, Uhlmann V.

2020

doi:10.1101/2020.10.27.357640.

Support and approximation properties of Hermite splines.

Fageot J, Aziznejad S, Unser M, Uhlmann V.

J Comput Appl Math, 2020

doi:10.1016/j.cam.2019.112503.

A Learning-Based Formulation of Parametric Curve Fitting for Bioimage Analysis

Mandal S, Uhlmann V.

2020

doi:10.1101/2020.01.10.901702.

Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography.

Nguyen D, Uhlmann V, Planchette AL, Marchand PJ, Van De Ville D, Lasser T, Radenovic A.

Biomed Opt Express, 2019

doi:10.1364/boe.10.003041.

Multimodal imaging and high-throughput image-processing for drug screening on living organisms on-chip.

Migliozzi D, Cornaglia M, Mouchiroud L, Uhlmann V, Unser MA, Auwerx J, Gijs MAM.

J Biomed Opt, 2018

doi:10.1117/1.jbo.24.2.021205.

DiversePathsJ: diverse shortest paths for bioimage analysis.

Uhlmann V, Haubold C, Hamprecht FA, Unser M.

Bioinformatics, 2018

doi:10.1093/bioinformatics/btx621.

FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila.

Uhlmann V, Ramdya P, Delgado-Gonzalo R, Benton R, Unser M.

PLoS One, 2017

doi:10.1371/journal.pone.0173433.

Multiresolution Subdivision Snakes.

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

IEEE Trans Image Process, 2017

doi:10.1109/tip.2016.2644263.

Hermite Snakes With Control of Tangents.

Uhlmann V, Fageot J, Unser M.

IEEE Trans Image Process, 2016

doi:10.1109/tip.2016.2551363.

Maximally Localized Radial Profiles for Tight Steerable Wavelet Frames.

Pad P, Uhlmann V, Unser M.

IEEE Trans Image Process, 2016

doi:10.1109/tip.2016.2545301.

CP-CHARM: segmentation-free image classification made accessible.

Uhlmann V, Singh S, Carpenter AE.

BMC Bioinformatics, 2016

doi:10.1186/s12859-016-0895-y.

Design of Steerable Wavelets to Detect Multifold Junctions.

Püspöki Z, Uhlmann V, Vonesch C, Unser M.

IEEE Trans Image Process, 2016

doi:10.1109/tip.2015.2507981.

Efficient Shape Priors for Spline-Based Snakes.

Delgado-Gonzalo R, Schmitter D, Uhlmann V, Unser M.

IEEE Trans Image Process, 2015

doi:10.1109/tip.2015.2457335.

Automated classification of immunostaining patterns in breast tissue from the human protein atlas.

Swamidoss IN, Kårsnäs A, Uhlmann V, Ponnusamy P, Kampf C, Simonsson M, Wählby C, Strand R.

J Pathol Inform, 2013

doi:10.4103/2153-3539.109881.