ilastik Publications

How to cite: The current ilastik version (1.0 and newer) is described in this Nature Methods Perspective:

  • ilastik: interactive machine learning for (bio)image analysis
    Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N. Straehle, Bernhard X. Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy, Kemal Eren, Jaime I Cervantes, Buote Xu, Fynn Beuttenmueller, Adrian Wolny, Chong Zhang, Ullrich Koethe, Fred A. Hamprecht & Anna Kreshuk
    in: Nature Methods, (2019) Link at publisher, BibTex file
The first ilastik release (version 0.5) was described in this conference paper:
  • ilastik: Interactive Learning and Segmentation Toolkit
    C. Sommer, C. Strähle, U. Köthe, F. A. Hamprecht
    in: Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, (2011), 230-233
    Link at publisher, BibTex file, Technical Report

Reviews: Many colleagues have been so kind as to include ilastik into their reviews of image processing software. If you want to get a better idea of how ilastik compares with similar software tools in different application domains, read one of the references below:

  • Machine learning applications in cell image analysis
    Andrey Kan
    Immunology and Cell Biology, 2017
  • High-Content Screening for Quantitative Cell Biology
    Mojca Mattiazzi Usaj, Erin B. Styles, Adrian J. Verster, Helena Friesen, Charles Boone and Brenda J. Andrews
    Trends in Cell Biology, 2016
  • Exploring the third dimension: Volume electron microscopy comes of age
    C.J. Peddie, L.M. Collinson
    Micron, 2014
  • Automated Processing of Zebrafish Imaging Data: A Survey
    R. Mikut, T. Dickmeis, W. Driever, P. Geurts, F.A. Hamprecht,
    B.X. Kausler, M.J. Ledesma-Carbayo, R. Marée, K. Mikula,
    P. Pantazis, O. Ronneberger, A. Santos, R. Stotzka,
    U. Straehle, and N. Peyriéras
    Zebrafish, September 2013, 10(3): 401-421.
  • Bioimage Informatics for Systems Pharmacology
    F. Li, Z. Yin, G. Jin, H. Zhao, S.T.C. Wong
    PLoS computational biology, 2013
  • Light microscopy applications in systems biology: opportunities and challenges
    P.M.A. Antony, C. Trefois, A. Stojanovic, A.S. Baumuratov, K. Kozak
    Cell Communication and Signaling, 2013, 11:24
  • Computational methods and challenges for large-scale circuit mapping
    M. Helmstaedter, P.P. Mitra
    Current opinion in neurobiology, 2012
  • A call for bioimaging software usability
    A.E. Carpenter, L. Kamentsky, K.W. Eliceiri
    Nature methods, 2012

Applications by ilastik users: Researchers from various application domains have successfully used ilastik in their work. An almost random selection of such papers is shown below, see google scholar for the full listing.

  • High-avidity IgA protects the intestine by enchaining growing bacteria
    Kathrin Moor, Médéric Diard, Mikael E. Sellin, Boas Felmy, Sandra Y. Wotzka, Albulena Toska, Erik Bakkeren, Markus Arnoldini, Florence Bansept, Alma Dal Co, Tom Völler, Andrea Minola, Blanca Fernandez-Rodriguez, Gloria Agatic, Sonia Barbieri, Luca Piccoli, Costanza Casiraghi, Davide Corti, Antonio Lanzavecchia, Roland R. Regoes, Claude Loverdo, Roman Stocker, Douglas R. Brumley, Wolf-Dietrich Hardt, Emma Slack
    Nature (2017), Vol. 544
  • Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER
    Jonathon Nixon-Abell, Christopher J. Obara, Aubrey V. Weigel, Dong Li, Wesley R. Legant, C. Shan Xu, H. Amalia Pasolli, Kirsten Harvey, Harald F. Hess, Eric Betzig, Craig Blackstone, Jennifer Lippincott-Schwartz
    Science (2016), Vol. 354, Issue 6311
  • Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes
    Nicolas Renier, Eliza L. Adams, Christoph Kirst, Zhuhao Wu, Ricardo Azevedo, Johannes Kohl, Anita E. Autry, Lolahon Kadiri, Kannan Umadevi Venkataraju, Yu Zhou, Victoria X. Wang, Cheuk Y. Tang, Olav Olsen, Catherine Dulac, Pavel Osten, Marc Tessier-Lavigne
    Cell (2016), Volume 165, Issue 7
  • High-throughput estimation of incident light, light interception and radiation-use efficiency of thousands of plants in a phenotyping platform
    Llorenc Cabrera-Bosquet, Christian Fournier, Nicolas Brichet, Claude Welcker, Benoit Suard and Francois Tardieu
    New Phytologist (2016)
  • Static Clathrin Assemblies at the Peripheral Vacuole—Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia
    Jon Paulin Zumthor, Lenka Cernikova, Samuel Rout, Andres Kaech, Carmen Faso, Adrian B. Hehl
    PLoS Pathogens (2016)
  • PIK3CAH1047R induces multipotency and multi-lineage mammary tumours
    Shany Koren, Linsey Reavie, Joana Pinto Couto, Duvini De Silva, Michael B. Stadler, Tim Roloff, Adrian Britschgi, Tobias Eichlisberger, Hubertus Kohler, Olulanu Aina, Robert D. Cardiff & Mohamed Bentires-Alj
    Nature (2015), 525, 114–118
  • Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass
    William Menegas, Joseph F. Bergan, Sachie K. Ogawa, Yoh Isogai, Kannan Umadevi Venkataraju, Pavel Osten, Naoshige Uchida and Mitsuko Watabe-Uchida
    Elife (2015)
  • Spatial constraints control cell proliferation in tissues
    Sebastian J. Streichan, Christian R. Hoerner, Tatjana Schneidt, Daniela Holzer and Lars Hufnagel
    PNAS (2014), vol. 111 no. 15
  • Fast and robust optical flow for time-lapse microscopy using super-voxels
    F. Amat, E.W. Myers, P.J. Keller
    Bioinformatics (2013) 29 (3): 373-380
  • Tubular endocytosis drives remodelling of the apical surface during epithelial morphogenesis in Drosophila
    P. Fabrowski, A.S. Necakov, S. Mumbauer, E. Loeser, A. Reversi, S. Streichan, J.A.G. Briggs, S. De Renzis
    Nature Communications 4 (2013), Article number: 2244
  • Analyzing the footprints of near-surface aqueous turbulence: An image processing-based approach
    J. Schnieders, C.S. Garbe, W.L. Peirson, G.B. Smith, C.J. Zappa
    Journal of Geophysical Research: Oceans (2013), Vol 118 Issue 3
  • Drop swarm analysis in dispersions with incident-light and transmitted-light illumination
    M. Mickler, B. Boecker, H.-J. Bart
    Flow Measurement and Instrumentation (2013), Vol. 30
  • Heterogeneous Nanoscale Morphology in Cross-Sections of Bulk Heterojunction
    Polymer Solar Cells Visualized by Analytical Electron Microscopy
    Harald Flügge,Martin Pfannmöller, Gerd Benner, Irene Wacker, Hans Schmidt,
    Torsten Rabe, Rasmus R. Schröder, Wolfgang Kowalsky
    Energy Procedia, Volume 31, (2012), 46–59
  • Minimizing Manual Image Segmentation Turn-Around Time for Neuronal Reconstruction by Embracing Uncertainty
    S.M. Plaza, L.K. Scheffer, M. Saunders
    PLoS ONE 7(9): e44448. (2013) doi:10.1371/journal.pone.0044448
  • Efficient fluorescence image normalization for time lapse movies
    M. Schwarzfischer,C. Marr,J. Krumsiek,P. Hoppe,T. Schroeder,F. Theis
    In Proc. Microscopic Image Analysis with Applications in Biology (2011)
  • Mechanical stiffness as an improved single-cell indicator of osteoblastic human
    mesenchymal stem cell differentiation
    T. Bongiorno, J. Kazlow, R. Mezencev, S. Griffiths, R. Olivares-Navarrete, J.F. McDonald, Z. Schwartz,
    B.D. Boyan, T.C. McDevitt, T. Sulchek
    Journal of Biomechanics (2013), in press
  • Optimized Signal Separation for 3D-Polarized Light Imaging
    J. Dammers, L. Breuer, G. Tabbì, M. Axer
    Functional Brain Mapping and the Endeavor to Understand the Working Brain, (2013)
  • The Flavonoid Isoquercitrin Promotes Neurite Elongation by Reducing RhoA Activity
    G. Palazzolo, P. Horvath, M. Zenobi-Wong
    PLoS ONE 7(11): e49979. (2011)

Applications by ilastik developers: Our developers themselves use ilastik in the course of their research and try their best to build their new algorithms into ilastik to make them available to non-experts. Some of their ilastik-related work is listed below, grouped by the application field:

Neuroscience
  • Automated Detection of Synapses in Serial Section Transmission Electron Microscopy Image Stacks
    A. Kreshuk, U. Köthe, E. Pax, D. D. Bock, F. A. Hamprecht
    PLoS ONE, in press, (2014)
  • Learning to Segment Neurons with Non-local Quality Measures
    T. Kröger, S. Mikula, W. Denk, U. Köthe, F. A. Hamprecht
    in: MICCAI 2013. Proceedings, part II, Springer(2013) 8150, 419-427
  • Correlative in vivo 2 photon and focused ion beam scanning electron microscopy of cortical neurons
    B. Maco, A. Holtmaat, M. Cantoni, A. Kreshuk, C. N. Straehle, F. A. Hamprecht, G. W. Knott
    PloS ONE, (2013) 8 (2)
  • Globally Optimal Closed-Surface Segmentation for Connectomics
    B. Andres, T. Kröger, K. L. Briggmann, W. Denk, N. Norogod, G. Knott, U. Köthe, F. A. Hamprecht
    in: ECCV 2012. Proceedings, Part 3, (2012), 778-791
  • 3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries
    B. Andres, U. Köthe, T. Kröger, M. Helmstaedter, K.L. Briggman, W. Denk, F. A. Hamprecht
    Medical Image Analysis, (2012) 16 (2012), 796-805
  • Seeded watershed cut uncertainty estimators for guided interactive segmentation
    C. Straehle, U. Köthe, K. Briggman, W. Denk, F.A. Hamprecht
    in: CVPR 2012. Proceedings, (2012), 765 - 772
  • Automated Detection and Segmentation of Synaptic Contacts in Nearly Isotropic Serial Electron Microscopy Images
    A. Kreshuk, C. N. Straehle, C. Sommer, U. Köthe, M. Cantoni, G. Knott, F. A. Hamprecht
    PLoS ONE, (2011) 6 (10)
  • Carving: Scalable Interactive Segmentation of Neural Volume Electron Microscopy Images
    C. N. Straehle, U. Köthe, G. Knott, F. A. Hamprecht
    in: MICCAI 2011, Proceedings., Springer(2011) 6891, 653-660
  • Automated Segmentation of Synapses in 3D EM Data
    A. Kreshuk, C. Strähle, C. Sommer, U. Köthe, G. Knott, F. A. Hamprecht
    in: Eighth IEEE International Symposium on Biomedical Imaging (ISBI). Proceedings, (2011), 220-223
Cell Tracking
  • Conservation Tracking
    M. Schiegg, P. Hanslovsky, B. X. Kausler, L. Hufnagel, F. A. Hamprecht
    in: ICCV 2013. Proceedings, (2013), 2928--2935
  • A Discrete Chain Graph Model for 3d+t Cell Tracking with High Misdetection Robustness
    B. X. Kausler, M. Schiegg, B. Andres, M. Lindner, U. Köthe, H. Leitte, J. Wittbrodt, L. Hufnagel, F. A. Hamprecht
    in: ECCV 2012. Proceedings, Part 3, (2012) 7574, 144-157
Counting w/o detection
  • Learning to Count with Regression Forest and Structured Labels
    L. Fiaschi, R. Nair, U. Köthe, F. A. Hamprecht
    ICPR 2012. Proceedings, (2012), 2685-2688
Cell detection
  • Yeast Cell Detection and Segmentation in Bright Field Microscopy
    C. Zhang, F. Huber, M. Knop, F. A. Hamprecht
    in: ISBI 2014. Proceedings, in press, (2014)
  • Learning-based Mitotic Cell Detection in Histopathological Images
    C. Sommer, L. Fiaschi, F. A. Hamprecht, D. Gerlich
    ICPR 2012. Proceedings, (2012), 2306-2309
  • Keeping count: Leveraging temporal context to count heavily overlapping objects
    L. Fiaschi, G. Konstantin, B. Afonso, M. Zlatic,F.A. Hamprecht
    ISBI 2013.Proceedings, (2013), 656-659
Other
  • Visualizing a homogeneous blend in bulk heterojunction polymer solar cells by analytical electron microscopy
    M. Pfannmöller, H. Flügge, G. Benner, I. Wacker, C. Sommer, M. Hanselmann, S. Schmale,
    H. Schmidt, F. A. Hamprecht, T. Rabe, W. Kowalsky, R. Schröder
    Nano Letters, (2011) 11, 3099-3107