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. (2020)

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

Elife 9 doi: 10.7554/eLife.57613
Europe PMC | doi

Kreshuk A, Zhang C. (2019)

Machine learning: advanced image segmentation using ilastik.

Methods Mol Biol 2040:449-463. doi: 10.1007/978-1-4939-9686-5_21
Europe PMC | doi

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. (2019)

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

Front Neuroinform 13 doi: 10.3389/fninf.2019.00075
Europe PMC | doi

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. (2019)

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

Nat. Methods 16(12):1226-1232. doi: 10.1038/s41592-019-0582-9
Europe PMC | doi

Krasowski NE, Beier T, Knott GW, Kothe U, Hamprecht FA, Kreshuk A. (2018)

Neuron Segmentation With High-Level Biological Priors.

IEEE Trans Med Imaging 37(4):829-839. doi: 10.1109/TMI.2017.2712360
Europe PMC | doi

Constantin Pape, Thorsten Beier, Peter Li, Viren Jain, Davi D. Bock, and Anna Kreshuk. (2017)

Solving large Multicut problems for connectomics via domain decomposition

In: Lisa O’Conner, Computer Vision Workshop (ICCVW), 2017 IEEE International Conference on.

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. (2017)

Multicut brings automated neurite segmentation closer to human performance.

Nat Methods 14(2):101-102. doi: 10.1038/nmeth.4151
Europe PMC | doi

Haubold C, Schiegg M, Kreshuk A, Berg S, Koethe U, Hamprecht FA. (2016)

Segmenting and Tracking Multiple Dividing Targets Using ilastik.

Adv Anat Embryol Cell Biol 219:199-229. doi: 10.1007/978-3-319-28549-8_8
Europe PMC | doi

Calì C, Baghabra J, Boges DJ, Holst GR, Kreshuk A, Hamprecht FA, Srinivasan M, Lehväslaiho H, Magistretti PJ. (2016)

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

J Comp Neurol 524(1):23-38. doi: 10.1002/cne.23852
Europe PMC | doi

Kreshuk A, Walecki R, Koethe U, Gierthmuehlen M, Plachta D, Genoud C, Haastert-Talini K, Hamprecht FA. (2015)

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

J Microsc 259(2):143-54. doi: 10.1111/jmi.12266
Europe PMC | doi

Anna Kreshuk, Jan Funke, Albert Cardona, Fred A. Hamprecht. (2015)

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

In: Nassir Navab et al., Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015.

Krasowski, N, Beier, T, Knott, GW, Köthe, U, Hamprecht, FA, Kreshuk, A. (2015)

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

Maco B, Cantoni M, Holtmaat A, Kreshuk A, Hamprecht FA, Knott GW. (2014)

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

Nat Protoc 9(6):1354-66. doi: 10.1038/nprot.2014.101
Europe PMC | doi

Kreshuk A, Koethe U, Pax E, Bock DD, Hamprecht FA. (2014)

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

PLoS One 9(2) doi: 10.1371/journal.pone.0087351
Europe PMC | doi

Maco B, Holtmaat A, Cantoni M, Kreshuk A, Straehle CN, Hamprecht FA, Knott GW. (2013)

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

PLoS One 8(2) doi: 10.1371/journal.pone.0057405
Europe PMC | doi

Kreshuk A, Straehle CN, Sommer C, Koethe U, Cantoni M, Knott G, Hamprecht FA. (2011)

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

PLoS One 6(10) doi: 10.1371/journal.pone.0024899
Europe PMC | doi

Kreshuk A, Stankiewicz M, Lou XH, Kirchner M, Hamprecht FA, Mayer MP. (2011)

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

INT J MASS SPECTROM 302(1-3):125-131. doi: 10.1016/j.ijms.2010.08.025
doi

Kreshuk, A, Strähle, C, Sommer, C, Köthe, U, Knott, G, Hamprecht, FA. (2011)

Automated segmentation of synapses in 3D EM data

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. (2009)

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

Comput Phys Commun 180(12):2499-2512. doi: 10.1016/j.cpc.2009.08.005
doi

R Brun, P Canal, M Frank, A Kreshuk, S Linev, P Russo and F Rademakers. (2008)

Developments in ROOT I/O and Trees

Moneta L, Antcheva I, Brun R, and Kreshuk A. (2007)

ROOT Statistical Software

René Brun, Anna Kreshuk, Lorenzo Moneta. (2006)

Statistics in ROOT