How to build the virtual cell with artificial intelligence: Priorities and opportunities.

Bunne C, Roohani Y, Rosen Y, Gupta A, Zhang X, Roed M, Alexandrov T, AlQuraishi M, Brennan P, Burkhardt DB, Califano A, Cool J, Dernburg AF, Ewing K, Fox EB, Haury M, Herr AE, Horvitz E, Hsu PD, Jain V, Johnson GR, Kalil T, Kelley DR, Kelley SO, Kreshuk A, Mitchison T, Otte S, Shendure J, Sofroniew NJ, Theis F, Theodoris CV, Upadhyayula S, Valer M, Wang B, Xing E, Yeung-Levy S, Zitnik M, Karaletsos T, Regev A, Lundberg E, Leskovec J, Quake SR

Cell, 2024

doi:10.1016/j.cell.2024.11.015.

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.

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, Uhlman V, Hannezo E, Hiiragi T

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

doi:10.1126/science.adh1145.

Multiplex microscopy assay for assessment of therapeutic and serum antibodies against emerging pathogens.

Sartingen N, Stürmer V, Kaltenböck M, Müller TG, Schnitzler P, Kreshuk A, Kräusslich HG, Merle U, Mücksch F, Müller B, Pape C, Laketa V

Viruses, 2024

doi:10.3390/v16091473.

Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis.

Schubert MC, Soyka SJ, Tamimi A, Maus E, Schroers J, Wißmann N, Reyhan E, Tetzlaff SK, Yang Y, Denninger R, Peretzke R, Beretta C, Drumm M, Heuer A, Buchert V, Steffens A, Walshon J, McCortney K, Heiland S, Bendszus M, Neher P, Golebiewska A, Wick W, Winkler F, Breckwoldt MO, Kreshuk A, Kuner T, Horbinski C, Kurz FT, Prevedel R, Venkataramani V

Nature communications, 2024

doi:10.1038/s41467-024-51432-4.

A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context.

Vijayan A, Mody TA, Yu Q, Wolny A, Cerrone L, Strauss S, Tsiantis M, Smith RS, Hamprecht FA, Kreshuk A, Schneitz K

Development (Cambridge, England), 2024

doi:10.1242/dev.202800.

Metrics reloaded: recommendations for image analysis validation.

Maier-Hein L, Reinke A, Godau P, Tizabi MD, Buettner F, Christodoulou E, Glocker B, Isensee F, Kleesiek J, Kozubek M, Reyes M, Riegler MA, Wiesenfarth M, Kavur AE, Sudre CH, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Rädsch T, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Blaschko MB, Cardoso MJ, Cheplygina V, Cimini BA, Collins GS, Farahani K, Ferrer L, Galdran A, van Ginneken B, Haase R, Hashimoto DA, Hoffman MM, Huisman M, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Karthikesalingam A, Kofler F, Kopp-Schneider A, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Mattson P, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rajpoot N, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, van Smeden M, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Jäger PF

Nature methods, 2024

doi:10.1038/s41592-023-02151-z.

Understanding metric-related pitfalls in image analysis validation.

Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Buettner F, Cardoso MJ, Cheplygina V, Chen J, Christodoulou E, Cimini BA, Farahani K, Ferrer L, Galdran A, van Ginneken B, Glocker B, Godau P, Hashimoto DA, Hoffman MM, Huisman M, Isensee F, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Kleesiek J, Kofler F, Kooi T, Kopp-Schneider A, Kozubek M, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Meijering E, Menze B, Moons KGM, Müller H, Nichyporuk B, Nickel F, Petersen J, Rafelski SM, Rajpoot N, Reyes M, Riegler MA, Rieke N, Saez-Rodriguez J, Sánchez CI, Shetty S, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Yaniv ZR, Jäger PF, Maier-Hein L

Nature methods, 2024

doi:10.1038/s41592-023-02150-0.

Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles.

Sitarska E, Almeida SD, Beckwith MS, Stopp J, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt M, Kreshuk A, Erzberger A, Diz-Muñoz A

Nature communications, 2023

doi:10.1038/s41467-023-41173-1.

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.

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.

MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data.

Pape C, Meechan K, Moreva E, Schorb M, Chiaruttini N, Zinchenko V, Martinez Vergara H, Mizzon G, Moore J, Arendt D, Kreshuk A, Schwab Y, Tischer C

Nature methods, 2023

doi:10.1038/s41592-023-01776-4.

Convolutional networks for supervised mining of molecular patterns within cellular context.

de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB

Nature methods, 2023

doi:10.1038/s41592-022-01746-2.

GASP, a generalized framework for agglomerative clustering of signed graphs and its application to Instance Segmentation.

Bailoni A, Pape C, Hütsch N, Wolf S, Beier T, Kreshuk A, Hamprecht FA

2022

doi:10.1109/CVPR52688.2022.01135.

Sparse object-level supervision for instance segmentation with pixel embeddings.

Wolny A, Yu Q, Pape K, Kreshuk A

IEEE, 2022

doi:10.1109/CVPR52688.2022.00436.

Volume electron microscopy.

Peddie CJ, Genoud C, Kreshuk A, Meechan K, Micheva KD, Narayan K, Pape C, Parton RG, Schieber NL, Schwab Y, Titze B, Verkade P, Aubrey A, Collinson LM

Nature reviews. Methods primers, 2022

doi:10.1038/s43586-022-00131-9.

An ex vivo system to study cellular dynamics underlying mouse peri-implantation development.

Ichikawa T, Zhang HT, Panavaite L, Erzberger A, Fabrèges D, Snajder R, Wolny A, Korotkevich E, Tsuchida-Straeten N, Hufnagel L, Kreshuk A, Hiiragi T

Developmental cell, 2022

doi:10.1016/j.devcel.2021.12.023.

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

Levet F, Carpenter AE, Eliceiri KW, Kreshuk A, Bankhead P, Haase R

F1000Research, 2021

doi:10.12688/f1000research.52531.1.

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

Musser JM, Schippers KJ, Nickel M, Mizzon G, Kohn AB, Pape C, Ronchi P, Papadopoulos N, Tarashansky AJ, Hammel JU, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra CP, Achim K, Schieber NL, Pan L, Ruperti F, Francis WR, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider TR, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz LL, Arendt D

Science (New York, N.Y.), 2021

doi:10.1126/science.abj2949.

Mechanical competition alters the cellular interpretation of an endogenous genetic program.

Bhide S, Gombalova D, Mönke G, Stegmaier J, Zinchenko V, Kreshuk A, Belmonte JM, Leptin M

The Journal of cell biology, 2021

doi:10.1083/jcb.202104107.

The Mutex Watershed and its objective: efficient, parameter-free graph partitioning.

Wolf S, Bailoni A, Pape C, Rahaman N, Kreshuk A, Kothe U, Hamprecht FA

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2021

doi:10.1109/TPAMI.2020.2980827.

Publisher correction: deep learning enables fast and dense single-molecule localization with high accuracy.

Speiser A, Müller LR, Hoess P, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC

Nature methods, 2021

doi:10.1038/s41592-021-01305-1.

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

Speiser A, Müller LR, Hoess P, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC

Nature methods, 2021

doi:10.1038/s41592-021-01236-x.

Universal autofocus for quantitative volumetric microscopy of whole mouse brains.

Silvestri L, Müllenbroich MC, Costantini I, Di Giovanna AP, Mazzamuto G, Franceschini A, Kutra D, Kreshuk A, Checcucci C, Toresano LO, Frasconi P, Sacconi L, Pavone FS

Nature methods, 2021

doi:10.1038/s41592-021-01208-1.

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

Vergara HM, Pape C, Meechan KI, Zinchenko V, Genoud C, Wanner AA, Mutemi KN, Titze B, Templin RM, Bertucci PY, Simakov O, Dürichen W, Machado P, Savage EL, Schermelleh L, Schwab Y, Friedrich RW, Kreshuk A, Tischer C, Arendt D

Cell, 2021

doi:10.1016/j.cell.2021.07.017.

Deep learning-enhanced light-field imaging with continuous validation.

Wagner N, Beuttenmueller F, Norlin N, Gierten J, Boffi JC, Wittbrodt J, Weigert M, Hufnagel L, Prevedel R, Kreshuk A

Nature methods, 2021

doi:10.1038/s41592-021-01136-0.

Integration of cell growth and asymmetric division during lateral root initiation in Arabidopsis thaliana.

Schütz LM, Louveaux M, Barro AV, Bouziri S, Cerrone L, Wolny A, Kreshuk A, Hamprecht FA, Maizel A

Plant & cell physiology, 2021

doi:10.1093/pcp/pcab038.

A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule.

Vijayan A, Tofanelli R, Strauss S, Cerrone L, Wolny A, Strohmeier J, Kreshuk A, Hamprecht FA, Smith RS, Schneitz K

eLife, 2021

doi:10.7554/eLife.63262.

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.

Pape C, Remme R, Wolny A, Olberg S, Wolf S, Cerrone L, Cortese M, Klaus S, Lucic B, Ullrich S, Anders-Össwein M, Wolf S, Cerikan B, Neufeldt CJ, Ganter M, Schnitzler P, Merle U, Lusic M, Boulant S, Stanifer M, Bartenschlager R, Hamprecht FA, Kreshuk A, Tischer C, Kräusslich HG, Müller B, Laketa V

BioEssays : news and reviews in molecular, cellular and developmental biology, 2020

doi:10.1002/bies.202000257.

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

Wolny A, Cerrone L, Vijayan A, Tofanelli R, Barro AV, Louveaux M, Wenzl C, Strauss S, Wilson-Sánchez D, Lymbouridou R, Steigleder S, Pape C, Bailoni A, Duran-Nebreda S, Bassel G, Lohmann JU, Tsiantis M, Hamprecht F, Schneitz K, Maizel A, Kreshuk A

eLife, 2020

doi:10.7554/eLife.57613.

Machine learning: advanced image segmentation using ilastik.

Kreshuk A, Zhang C

Methods in molecular biology (Clifton, N.J.), 2019

doi:10.1007/978-1-4939-9686-5_21.

QUINT: Workflow for quantification and spatial analysis of features in histological images from rodent brain.

Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU, Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG

Frontiers in neuroinformatics, 2019

doi:10.3389/fninf.2019.00075.

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

Berg S, Kutra D, Kroeger T, Straehle CN, Kausler BX, Haubold C, Schiegg M, Ales J, Beier T, Rudy M, Eren K, Cervantes JI, Xu B, Beuttenmueller F, Wolny A, Koethe U, Zhang C, Kreshuk A, Hamprecht FA

Nature methods, 2019

doi:10.1038/s41592-019-0582-9.

Neuron Segmentation With High-Level Biological Priors.

Krasowski NE, Beier T, Knott GW, Kothe U, Hamprecht FA, Kreshuk A

IEEE transactions on medical imaging, 2018

doi:10.1109/TMI.2017.2712360.

Solving large Multicut problems for connectomics via domain decomposition

Constantin Pape, Thorsten Beier, Peter Li, Viren Jain, Davi D. Bock, and Anna Kreshuk

2017

doi:.

Multicut brings automated neurite segmentation closer to human performance.

Beier T, Pape C, Rahaman N, Prange T, Berg S, Bock DD, Cardona A, Knott GW, Plaza SM, Scheffer LK, Koethe U, Kreshuk A, Hamprecht FA

Nature methods, 2017

doi:10.1038/nmeth.4151.

Segmenting and Tracking Multiple Dividing Targets Using ilastik.

Haubold C, Schiegg M, Kreshuk A, Berg S, Koethe U, Hamprecht FA

Advances in anatomy, embryology, and cell biology, 2016

doi:10.1007/978-3-319-28549-8_8.

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

Calì C, Baghabra J, Boges DJ, Holst GR, Kreshuk A, Hamprecht FA, Srinivasan M, Lehväslaiho H, Magistretti PJ

The Journal of comparative neurology, 2016

doi:10.1002/cne.23852.

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

Kreshuk A, Walecki R, Koethe U, Gierthmuehlen M, Plachta D, Genoud C, Haastert-Talini K, Hamprecht FA

Journal of microscopy, 2015

doi:10.1111/jmi.12266.

Who Is Talking to Whom: Synaptic Partner Detection in Anisotropic Volumes of Insect Brain

Anna Kreshuk, Jan Funke, Albert Cardona, Fred A. Hamprecht

2015

doi:.

Improving 3D EM data segmentation by joint optimization over boundary evidence and biological priors

Krasowski, N, Beier, T, Knott, GW, Köthe, U, Hamprecht, FA, Kreshuk, A

2015

doi:.

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

Maco B, Cantoni M, Holtmaat A, Kreshuk A, Hamprecht FA, Knott GW

Nature protocols, 2014

doi:10.1038/nprot.2014.101.

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

Kreshuk A, Koethe U, Pax E, Bock DD, Hamprecht FA

PloS one, 2014

doi:10.1371/journal.pone.0087351.

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

Maco B, Holtmaat A, Cantoni M, Kreshuk A, Straehle CN, Hamprecht FA, Knott GW

PloS one, 2013

doi:10.1371/journal.pone.0057405.

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

Kreshuk A, Straehle CN, Sommer C, Koethe U, Cantoni M, Knott G, Hamprecht FA

PloS one, 2011

doi:10.1371/journal.pone.0024899.

Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon

Kreshuk A, Stankiewicz M, Lou XH, Kirchner M, Hamprecht FA, Mayer MP

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 2011

doi:10.1016/j.ijms.2010.08.025.

Automated segmentation of synapses in 3D EM data

Kreshuk, A, Strähle, C, Sommer, C, Köthe, U, Knott, G, Hamprecht, FA

2011

doi:.

ROOT - A C++ framework for petabyte data storage, statistical analysis and visualization

Antcheva I, Ballintijn M, Bellenot B, Biskup M, Brun R, Buncic N, Canal P, Casadei D, Couet O, Fine V, Franco L, Ganis G, Gheata A, Maline DG, Goto M, Iwaszkiewicz J, Kreshuk A, Segura DM, Maunder R, Moneta L, Naumann A, Offermann E, Onuchin V, Panacek S, Rademakers F, Russo R, Tadel M

COMPUTER PHYSICS COMMUNICATIONS, 2009

doi:10.1016/j.cpc.2009.08.005.

Developments in ROOT I/O and Trees

R Brun, P Canal, M Frank, A Kreshuk, S Linev, P Russo and F Rademakers

2008

doi:.

ROOT Statistical Software

Moneta L, Antcheva I, Brun R, and Kreshuk A

2007

doi:.

Statistics in ROOT

René Brun, Anna Kreshuk, Lorenzo Moneta

2006

doi:.