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Works (27)

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

2022-05 | Preprint
DOI: 10.1101/2022.05.07.490949
PPR: PPR490384
Contributors: Zinchenko V; Hugger J; Uhlmann V; Arendt D; Kreshuk A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Developing open-source software for bioimage analysis: opportunities and challenges

2021-04 | Preprint
DOI: 10.12688/f1000research.52531.1
OTHER-ID:

PPR313498
Contributors: Levet F; Carpenter AE; Eliceiri KW; Kreshuk A; Bankhead P; Haase R
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Curvature sensing steers actin-driven cell migration

2021-03 | Preprint
DOI: 10.1101/2021.03.26.437199
OTHER-ID:

PPR303858
Contributors: Sitarska E; Almeida SD; Beckwith M; Stopp J; Schwab Y; Sixt M; Kreshuk A; Erzberger A; Diz-Muñoz A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Integration of Cell Growth and Asymmetric Division During Lateral Root Initiation In Arabidopsis thaliana.

Plant & cell physiology
2021-03 | Journal article
DOI: 10.1093/pcp/pcab038
PMID: 33725093
Contributors: Schütz LM; Louveaux M; Barro AV; Bouziri S; Cerrone L; Wolny A; Kreshuk A; Hamprecht FA; Maizel A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks

Pattern Recognition42nd DAGM German Conference, DAGM GCPR 2020, Tübingen, Germany, September 28 – October 1, 2020, Proceedings
2021-03 | Journal article
PMC: PMC7972687
Contributors: Bailoni A; Pape C; Wolf S; Kreshuk A; Hamprecht F
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Unsupervised temporal consistency improvement for microscopy video segmentation with Siamese networks

2021-03 | Preprint
DOI: 10.1101/2021.03.25.436993
OTHER-ID:

PPR302833
Contributors: Shabanov A; Schichler D; Pape C; Cuylen-Haering S; Kreshuk A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

A digital 3D reference atlas reveals cellular growth patterns shaping the <i>Arabidopsis</i> ovule.

eLife
2021-01 | Journal article
DOI: 10.7554/elife.63262
PMID: 33404501
PMC: PMC7787667
Contributors: Vijayan A; Tofanelli R; Strauss S; Cerrone L; Wolny A; Strohmeier J; Kreshuk A; Hamprecht FA; Smith RS; Schneitz K
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera: A semi-quantitative, high throughput, microscopy-based assay expands existing approaches to measure SARS-CoV-2 specific antibody levels in human sera.

BioEssays : news and reviews in molecular, cellular and developmental biology
2020-12 | Journal article
DOI: 10.1002/bies.202000257
PMID: 33377226
PMC: PMC7883048
Contributors: Pape C; Remme R; Wolny A; Olberg S; Wolf S; Cerrone L; Cortese M; Klaus S; Lucic B; Ullrich S et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Deep learning enables fast and dense single-molecule localization with high accuracy

2020-10 | Preprint
DOI: 10.1101/2020.10.26.355164
OTHER-ID:

PPR230741
Contributors: Speiser A; Müller L; Matti U; Obara CJ; Legant WR; Kreshuk A; Macke JH; Ries J; Turaga SC
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Mechanical competition alters the cellular interpretation of an endogenous genetic programme

2020-10 | Preprint
DOI: 10.1101/2020.10.15.333963
OTHER-ID:

PPR226687
Contributors: Bhide S; Gombalova D; Mönke G; Stegmaier J; Zinchenko V; Zinchenko V; Kreshuk A; Belmonte JM; Leptin M
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Accurate and versatile 3D segmentation of plant tissues at cellular resolution.

eLife
2020-07 | Journal article
DOI: 10.7554/elife.57613
PMID: 32723478
PMC: PMC7447435
Contributors: Wolny A; Cerrone L; Vijayan A; Tofanelli R; Barro AV; Louveaux M; Wenzl C; Strauss S; Wilson-Sánchez D; Lymbouridou R et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Deep learning-enhanced light-field imaging with continuous validation

2020-07 | Preprint
DOI: 10.1101/2020.07.30.228924
OTHER-ID:

PPR194994
Contributors: Wagner N; Beuttenmueller F; Norlin N; Gierten J; Boffi JC; Wittbrodt J; Weigert M; Hufnagel L; Prevedel R; Kreshuk A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning.

IEEE transactions on pattern analysis and machine intelligence
2020-03 | Journal article
DOI: 10.1109/tpami.2020.2980827
PMID: 32175858
Contributors: Wolf S; Bailoni A; Pape C; Rahaman N; Kreshuk A; Kothe U; Hamprecht FA
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Whole-body integration of gene expression and single-cell morphology

2020-02 | Preprint
DOI: 10.1101/2020.02.26.961037
OTHER-ID:

PPR115105
Contributors: Vergara HM; Pape C; Meechan KI; Zinchenko V; Genoud C; Wanner AA; Titze B; Templin RM; Bertucci PY; Simakov O et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain.

Frontiers in neuroinformatics
2019-12 | Journal article
DOI: 10.3389/fninf.2019.00075
PMID: 31849633
PMC: PMC6901597
Contributors: Yates SC; Groeneboom NE; Coello C; Lichtenthaler SF; Kuhn PH; Demuth HU; Hartlage-Rübsamen M; Roßner S; Leergaard T; Kreshuk A et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

ilastik: interactive machine learning for (bio)image analysis.

Nature methods
2019-09 | Journal article
PMID: 31570887
Contributors: Berg S; Kutra D; Kroeger T; Straehle CN; Kausler BX; Haubold C; Schiegg M; Ales J; Beier T; Rudy M et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

2019-09 | Preprint
DOI: 10.1101/758276
OTHER-ID:

PPR91135
Contributors: Musser JM; Schippers KJ; Nickel M; Mizzon G; Kohn AB; Pape C; Hammel JU; Wolf F; Liang C; Hernández-Plaza A et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Machine Learning: Advanced Image Segmentation Using ilastik.

Methods in molecular biology (Clifton, N.J.)
2019-01 | Journal article
DOI: 10.1007/978-1-4939-9686-5_21
PMID: 31432492
Contributors: Kreshuk A; Zhang C
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Neuron Segmentation With High-Level Biological Priors.

IEEE transactions on medical imaging
2017-06 | Journal article
DOI: 10.1109/tmi.2017.2712360
PMID: 28600240
Contributors: Krasowski NE; Beier T; Knott GW; Kothe U; Hamprecht FA; Kreshuk A
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Multicut brings automated neurite segmentation closer to human performance.

Nature methods
2017-01 | Journal article
DOI: 10.1038/nmeth.4151
PMID: 28139671
Contributors: Beier T; Pape C; Rahaman N; Prange T; Berg S; Bock DD; Cardona A; Knott GW; Plaza SM; Scheffer LK et al.
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Segmenting and Tracking Multiple Dividing Targets Using ilastik.

Advances in anatomy, embryology, and cell biology
2016-01 | Journal article
DOI: 10.1007/978-3-319-28549-8_8
PMID: 27207368
Contributors: Haubold C; Schiegg M; Kreshuk A; Berg S; Koethe U; Hamprecht FA
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues.

The Journal of comparative neurology
2015-08 | Journal article
DOI: 10.1002/cne.23852
PMID: 26179415
PMC: PMC5042088
Contributors: Calì C; Baghabra J; Boges DJ; Holst GR; Kreshuk A; Hamprecht FA; Srinivasan M; Lehväslaiho H; Magistretti PJ
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Automated tracing of myelinated axons and detection of the nodes of Ranvier in serial images of peripheral nerves.

Journal of microscopy
2015-06 | Journal article
DOI: 10.1111/jmi.12266
PMID: 26191646
Contributors: Kreshuk A; Walecki R; Koethe U; Gierthmuehlen M; Plachta D; Genoud C; Haastert-Talini K; Hamprecht FA
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Semiautomated correlative 3D electron microscopy of in vivo-imaged axons and dendrites.

Nature protocols
2014-05 | Journal article
DOI: 10.1038/nprot.2014.101
PMID: 24833174
Contributors: Maco B; Cantoni M; Holtmaat A; Kreshuk A; Hamprecht FA; Knott GW
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Automated detection of synapses in serial section transmission electron microscopy image stacks.

PloS one
2014-02 | Journal article
DOI: 10.1371/journal.pone.0087351
PMID: 24516550
PMC: PMC3916342
Contributors: Kreshuk A; Koethe U; Pax E; Bock DD; Hamprecht FA
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons.

PloS one
2013-02 | Journal article
DOI: 10.1371/journal.pone.0057405
PMID: 23468982
PMC: PMC3585404
Contributors: Maco B; Holtmaat A; Cantoni M; Kreshuk A; Straehle CN; Hamprecht FA; Knott GW
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central

Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images.

PloS one
2011-10 | Journal article
DOI: 10.1371/journal.pone.0024899
PMID: 22031814
PMC: PMC3198725
Contributors: Kreshuk A; Straehle CN; Sommer C; Koethe U; Cantoni M; Knott G; Hamprecht FA
Source: Self-asserted source
Anna Kreshuk via Europe PubMed Central
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