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Scopus Author ID: 56304026600
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Employment (2)

University of Zurich: Zurich, CH

Director (BioVisionCenter)
Employment
Source: Self-asserted source
Virginie Uhlmann

EMBL-EBI: Cambridge, GB

Visiting Research Group Leader
Employment
Source: Self-asserted source
Virginie Uhlmann

Works (50)

Label-free phenotyping of human microvessel networks

2024-02 | Preprint
DOI: 10.1101/2024.02.20.581133
PPR: PPR810812
Contributors: Rappez L; Akinbote A; Cherubini M; Uhlmann V; Haase K
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

2023-12 | Preprint
DOI: 10.1101/2023.12.20.572494
PPR: PPR777151
Contributors: Lee JTH; Barnett SN; Roberts K; Ashwin H; Milross L; Cho J; Huseynov A; Woodhams B; Aivazidis A; Li T et al.
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

2023-10 | Preprint
DOI: 10.1101/2023.10.25.562925
PPR: PPR749160
Contributors: Yayon N; Kedlian VR; Boehme L; Suo C; Wachter B; Beuschel RT; Amsalem O; Polanski K; Koplev S; Tuck E et al.
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Simulating structurally variable nuclear pore complexes for microscopy.

Bioinformatics (Oxford, England)
2023-10 | Journal article
DOI: 10.1093/bioinformatics/btad587
PMID: 37756700
PMC: PMC10570993
Contributors: Theiss M; Hériché JK; Russell C; Helekal D; Soppitt A; Ries J; Ellenberg J; Brazma A; Uhlmann V
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Embryo-uterine interaction coordinates mouse embryogenesis during implantation.

The EMBO journal
2023-07 | Journal article
DOI: 10.15252/embj.2022113280
PMID: 37522872
PMC: PMC10476174
Contributors: Bondarenko V; Nikolaev M; Kromm D; Belousov R; Wolny A; Blotenburg M; Zeller P; Rezakhani S; Hugger J; Uhlmann V et al.
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

PLoS biology
2023-06 | Journal article
DOI: 10.1371/journal.pbio.3002167
PMID: 37368874
PMC: PMC10298797
Contributors: Senft RA; Diaz-Rohrer B; Colarusso P; Swift L; Jamali N; Jambor H; Pengo T; Brideau C; Llopis PM; Uhlmann V et al.
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

Journal of microscopy
2023-06 | Journal article
DOI: 10.1111/jmi.13208
PMID: 37269048
Contributors: Culley S; Caballero AC; Burden JJ; Uhlmann V
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

eLife
2023-02 | Journal article
DOI: 10.7554/elife.80918
PMID: 36795088
PMC: PMC9934868
Contributors: Zinchenko V; Hugger J; Uhlmann V; Arendt D; Kreshuk A
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Temporal variability and cell mechanics control robustness in mammalian embryogenesis

2023-01 | Preprint
DOI: 10.1101/2023.01.24.525420
PPR: PPR607657
Contributors: Fabrèges D; Murtra BC; Moghe P; Kickuth A; Ichikawa T; Iwatani C; Tsukiyama T; Daniel N; Gering J; Stokkermans A et al.
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Microscopy image analysis: course materials

2022-12 | Other
DOI: 10.6019/tol.microscopyimagematerials-t.2022.00001.1
OTHER-ID:

C8138
Contributors: Lopez PC; Holinski A; Russell C; Uhlmann V; Brazma A; Swedlow J
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

[]
2022-06-16 | Preprint
DOI: 10.1101/2022.06.13.495767
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

Editorial: Methods and Tools for Bioimage Analysis

Frontiers in Computer Science
2022-05-30 | Journal article
DOI: 10.3389/fcomp.2022.931939
Part of ISSN: 2624-9898
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

LOMAR: LOcalization Microscopy Analysis in R

[]
2022-05-30 | Preprint
DOI: 10.1101/2022.05.30.493957
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

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

Bioinformatics
2022-05-26 | Journal article
DOI: 10.1093/bioinformatics/btac270
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

Simulating structurally variable Nuclear Pore Complexes for Microscopy

[]
2022-05-17 | Preprint
DOI: 10.1101/2022.05.17.492295
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

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

[]
2022-05-07 | Preprint
DOI: 10.1101/2022.05.07.490949
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

A Practical Guide to Supervised Deep Learning for Bioimage Analysis: Challenges and good practices

IEEE Signal Processing Magazine
2022-03 | Journal article
DOI: 10.1109/msp.2021.3123589
Part of ISSN: 1053-5888
Part of ISSN: 1558-0792
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

μMatch: 3D Shape Correspondence for Biological Image Data

Frontiers in Computer Science
2022-02-15 | Journal article
DOI: 10.3389/fcomp.2022.777615
Part of ISSN: 2624-9898
Contributors: Virginie Uhlmann
Source: Self-asserted source
Virginie Uhlmann

Principled Design and Implementation of Steerable Detectors

IEEE Transactions on Image Processing
2021 | Journal article
DOI: 10.1109/tip.2021.3072499
Part of ISSN: 1057-7149
Part of ISSN: 1941-0042
Source: Self-asserted source
Virginie Uhlmann

Deep learning for bioimage analysis in developmental biology

Development
2021-09-15 | Journal article
DOI: 10.1242/dev.199616
Part of ISSN: 0950-1991
Part of ISSN: 1477-9129
Source: Self-asserted source
Virginie Uhlmann

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

Cell Systems
2021-05 | Journal article
DOI: 10.1016/j.cels.2021.04.012
Part of ISSN: 2405-4712
Source: Self-asserted source
Virginie Uhlmann

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

Nature Methods
2021-05-21 | Journal article
DOI: 10.1038/s41592-021-01166-8
Part of ISSN: 1548-7091
Part of ISSN: 1548-7105
Source: Self-asserted source
Virginie Uhlmann

Aura-Net: Robust Segmentation Of Phase-Contrast Microscopy Images with Few Annotations

2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)
2021-04-13 | Conference paper
DOI: 10.1109/isbi48211.2021.9433993
Source: Self-asserted source
Virginie Uhlmann

Splinedist: Automated Cell Segmentation With Spline Curves

2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)
2021-04-13 | Conference paper
DOI: 10.1109/isbi48211.2021.9433928
Source: Self-asserted source
Virginie Uhlmann

SplineDist: Automated Cell Segmentation With Spline Curves

2020-10 | Preprint
DOI: 10.1101/2020.10.27.357640
PPR: PPR231216
Contributors: Mandal S; Uhlmann V
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Support and approximation properties of Hermite splines.

Journal of computational and applied mathematics
2020-04 | Journal article
DOI: 10.1016/j.cam.2019.112503
PMID: 32255895
PMC: PMC6919321
Contributors: Fageot J; Aziznejad S; Unser M; Uhlmann V
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

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

2020-01 | Preprint
DOI: 10.1101/2020.01.10.901702
OTHER-ID:

PPR108489
Contributors: Mandal S; Uhlmann V
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Dictionary Learning for Two-Dimensional Kendall Shapes

SIAM Journal on Imaging Sciences
2020-01 | Journal article
DOI: 10.1137/19m126044x
Part of ISSN: 1936-4954
Source: Self-asserted source
Virginie Uhlmann

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

Biomedical optics express
2019-05 | Journal article
DOI: 10.1364/BOE.10.003041
PMID: 31259073
PMC: PMC6583328
Contributors: Nguyen D; Uhlmann V; Planchette AL; Marchand PJ; Van De Ville D; Lasser T; Radenovic A
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Gaussian and sparse processes are limits of generalized Poisson processes

Applied and Computational Harmonic Analysis
2018 | Journal article
DOI: 10.1016/j.acha.2018.10.004
Source: Self-asserted source
Virginie Uhlmann
grade
Preferred source (of 2)‎

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

Journal of Biomedical Optics
2018-11 | Journal article
DOI: 10.1117/1.JBO.24.2.021205
Source: Self-asserted source
Virginie Uhlmann

DiversePathsJ: diverse shortest paths for bioimage analysis.

Bioinformatics (Oxford, England)
2018-02 | Journal article
DOI: 10.1093/bioinformatics/btx621
PMID: 29029024
Contributors: Uhlmann V; Haubold C; Hamprecht FA; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Diverse M-Best solutions by dynamic programming

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2017 | Book
DOI: 10.1007/978-3-319-66709-6_21
EID:

2-s2.0-85029590256
Contributors: Haubold, C.; Uhlmann, V.; Unser, M.; Hamprecht, F.A.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

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

PloS one
2017 | Journal article
DOI: 10.1371/journal.pone.0173433
PMID: 28453566
PMC: PMC5409058
Contributors: Uhlmann V; Ramdya P; Delgado-Gonzalo R; Benton R; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

General surface energy for spinal cord and aorta segmentation

Proceedings - International Symposium on Biomedical Imaging
2017 | Conference paper
DOI: 10.1109/ISBI.2017.7950528
EID:

2-s2.0-85023187115
Contributors: Gupta, H.; Schmitter, D.; Uhlmann, V.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

Multiresolution Subdivision Snakes.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
2017-03 | Journal article
DOI: 10.1109/tip.2016.2644263
PMID: 28026768
Contributors: Badoual A; Schmitter D; Uhlmann V; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central
grade
Preferred source (of 2)‎

USER-friendly image-based segmentation and analysis of chromosomes

Proceedings - International Symposium on Biomedical Imaging
2016 | Conference paper
DOI: 10.1109/ISBI.2016.7493291
EID:

2-s2.0-84978412129
Contributors: Uhlmann, V.; Delgado-Gonzalo, R.; Unser, M.; Michel, P.O.; Baldi, L.; Wurm, F.M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

FlyLimbTracker: an active contour based approach for leg segment tracking in unmarked, freely behaving <i>Drosophila</i>

2016-11 | Preprint
DOI: 10.1101/089714
PPR: PPR27097
Contributors: Uhlmann V; Ramdya P; Delgado-Gonzalo R; Benton R; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Maximally Localized Radial Profiles for Tight Steerable Wavelet Frames.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
2016-05 | Journal article
DOI: 10.1109/tip.2016.2545301
PMID: 28113854
Contributors: Pad P; Uhlmann V; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central
grade
Preferred source (of 2)‎

Hermite Snakes with Control of Tangents.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
2016-04 | Journal article
PMID: 27071167
Contributors: Uhlmann V; Fageot J; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central
grade
Preferred source (of 3)‎

Design of Steerable Wavelets to Detect Multifold Junctions.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
2016-02 | Journal article
DOI: 10.1109/tip.2015.2507981
PMID: 26685237
Contributors: Püspöki Z; Uhlmann V; Vonesch C; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central
grade
Preferred source (of 2)‎

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

BMC bioinformatics
2016-01 | Journal article
DOI: 10.1186/s12859-016-0895-y
PMID: 26817459
PMC: PMC4729047
Contributors: Uhlmann V; Singh S; Carpenter AE
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Snakes on a Plane: A perfect snap for bioimage

IEEE Signal Processing Magazine
2015 | Journal article
DOI: 10.1109/MSP.2014.2344552
EID:

2-s2.0-85032751680
Contributors: Delgado-Gonzalo, R.; Uhlmann, V.; Schmitter, D.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

Statistical optimality of Hermite splines

2015 International Conference on Sampling Theory and Applications, SampTA 2015
2015 | Conference paper
DOI: 10.1109/SAMPTA.2015.7148885
EID:

2-s2.0-84941080252
Contributors: Uhlmann, V.; Fageot, J.; Gupta, H.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

Tip-seeking active contours for bioimage segmentation

Proceedings - International Symposium on Biomedical Imaging
2015 | Conference paper
DOI: 10.1109/ISBI.2015.7163931
EID:

2-s2.0-84944328162
Contributors: Uhlmann, V.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

Efficient Shape Priors for Spline-Based Snakes.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society
2015-11 | Journal article
DOI: 10.1109/tip.2015.2457335
PMID: 26353353
Contributors: Delgado-Gonzalo R; Schmitter D; Uhlmann V; Unser M
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central
grade
Preferred source (of 2)‎

Exponential Hermite splines for the analysis of biomedical images

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
2014 | Conference paper
DOI: 10.1109/ICASSP.2014.6853874
EID:

2-s2.0-84905261984
Contributors: Uhlmann, V.; Delgado-Gonzalo, R.; Conti, C.; Romani, L.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

Snakes with tangent-based control and energies for bioimage analysis

2014 IEEE 11th International Symposium on Biomedical Imaging, ISBI 2014
2014 | Conference paper
EID:

2-s2.0-84927933220
Contributors: Uhlmann, V.; Delgado-Gonzalo, R.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

VOW: Variance-optimal wavelets for the steerable pyramid

2014 IEEE International Conference on Image Processing, ICIP 2014
2014 | Conference paper
DOI: 10.1109/ICIP.2014.7025601
EID:

2-s2.0-84944331481
Contributors: Pad, P.; Uhlmann, V.; Unser, M.
Source: Self-asserted source
Virginie Uhlmann via Scopus - Elsevier

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

Journal of pathology informatics
2013 | Journal article
DOI: 10.4103/2153-3539.109881
PMID: 23766936
PMC: PMC3678740
Contributors: Swamidoss IN; Kårsnäs A; Uhlmann V; Ponnusamy P; Kampf C; Simonsson M; Wählby C; Strand R
Source: Self-asserted source
Virginie Uhlmann via Europe PubMed Central

Peer review (6 reviews for 5 publications/grants)

Review activity for BMC bioinformatics (2)
Review activity for F1000Research. (1)
Review activity for Nature computational science. (1)
Review activity for Nature methods. (1)
Review activity for PLoS computational biology. (1)
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