We report webKnossos, an in-browser annotation tool for 3D electron microscopic data. webKnossos provides flight mode, a single-view egocentric reconstruction method enabling trained annotator crowds to reconstruct at a speed of 1.5 ± 0.6 mm/h for axons and 2.1 ± 0.9 mm/h for dendrites in 3D electron microscopic data from mammalian cortex. webKnossos accelerates neurite reconstruction for connectomics by 4- to 13-fold compared with current state-of-the-art tools, thus extending the range of connectomes that can realistically be mapped in the future.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

    & PLoS Biol. 2, e329 (2004).

  2. 2.

    et al. J. Microsc. 259, 114–120 (2015).

  3. 3.

    et al. Cell 162, 648–661 (2015).

  4. 4.

    Nat. Methods 10, 501–507 (2013).

  5. 5.

    , , & Bioinformatics 25, 1984–1986 (2009).

  6. 6.

    et al. eLife 5, e12059 (2016).

  7. 7.

    Lect. Notes Comput. Sci. 3579, 7 (2005).

  8. 8.

    , & Nat Neurosci 14, 1081–1088 (2011).

  9. 9.

    , & Sci. Data 3, 160100 (2016).

  10. 10.

    , , , & Nat. Neurosci. 19, 816–825 (2016).

  11. 11.

    et al. Nature 500, 168–174 (2013).

  12. 12.

    , & Neuron 87, 1193–1206 (2015).

  13. 13.

    , & Nat. Commun. 6, 7923 (2015).

  14. 14.

    & Anatomy of the cortex: statistics and geometry Vol. 18 (Springer Science & Business Media, 2013).

  15. 15.

    et al. Cereb. Cortex 25, 4450–4468 (2015).

  16. 16.

    , , & IEEE Trans. Med. Imaging 32, 1864–1877 (2013).

  17. 17.

    , , , & PLoS One 9, e87351 (2014).

  18. 18.

    et al. Preprint at (2017).

  19. 19.

    et al. Nat. Methods 14, 435–442 (2017).

  20. 20.

    & The NURBS book (Springer Science & Business Media, 2012).

  21. 21.

    , & Nature 471, 183–188 (2011).

Download references


We thank D.Y. Buckley, E. Klinger and P. Laserstein for helpful discussions and comments on the manuscript; C. Roome, F. Kaiser and C. Guggenberger for outstanding IT support; and J. Striebel, S. Mischkewitz, N. Ring, A. Motta, B. Staffler and M. Zauser for contributions to the code. We thank E. Arzt and A.M. Burgin for hosting KMB at the Instituto de Investigación en Biomedicina de Buenos Aires, Argentina. We thank J. Abramovich, D. Acay, M. Ali, S. Babl, A. Banschbach, N. Berghaus, D. Beyer, L. Bezzenberger, F. Bock, D. Boehm, A. Budco, L. Buxmann, D. Celik, H. Charif, N. Cipta, T. Decker, J. Depnering, V. Dienst, S. Dittmer, L. Dufter, J.E. Martinez, H. Feddersen, A. Feiler, L. Feist, L. Frey, K. Friedl, A. Gaebelein, L. Geiser, D. Greco, M. Groothuis, S. Gross, A. Haeusl, S. Hain, J. Hartel, M.-L. Harwardt, B. Heftrich, M. Helbig, J. Heller, S. Hermann, J. Hoeltke, T. Hoermann, M. Hofweber, R. Huelse, R. Jakob, R. Jakoby, R. Janssen, M. Karabel, S. Kempf, L. Kirchner, J. Knauer, R. Kneissl, T. Koecke, P. Koenig, M. Kolodziej, F. Kraemer, E. Kuendiger, D. Kurt, M. Kuschnereit, E. Laube, D. Laubender, M. Lehnardt, Irene Meindl, Iris Meindl, J. Meyer, P. Mueller, N. Neupaertl, M. Perschke, M. Poltermann, M. Praeve, K. Puechler, M. Reiner, T. Reimann, V. Robl, F. Ruecker, T. Ruff, F. Sahin, D. Scheliu, V. Schuhbeck, S. Seiler, I. Stasiuk, B. Stiehl, A. Strubel, R. Thieleking, K. Trares, P. Wagner, Y. Wang, J. Wastl, A. Weber, S.S. Wehrheim, C. Weiss, M. Werr, A. Weyh, and J. Wiederspohn for annotation work.

Author information

Author notes

    • Kevin M Boergens
    •  & Manuel Berning

    These authors contributed equally to this work.


  1. Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany.

    • Kevin M Boergens
    • , Manuel Berning
    • , Florian Drawitsch
    • , Heiko Wissler
    •  & Moritz Helmstaedter
  2. Scalable minds UG (haftungsbeschränkt) & Co. KG, Potsdam, Germany.

    • Tom Bocklisch
    • , Dominic Bräunlein
    • , Johannes Frohnhofen
    • , Tom Herold
    • , Philipp Otto
    • , Norman Rzepka
    • , Thomas Werkmeister
    • , Daniel Werner
    •  & Georg Wiese


  1. Search for Kevin M Boergens in:

  2. Search for Manuel Berning in:

  3. Search for Tom Bocklisch in:

  4. Search for Dominic Bräunlein in:

  5. Search for Florian Drawitsch in:

  6. Search for Johannes Frohnhofen in:

  7. Search for Tom Herold in:

  8. Search for Philipp Otto in:

  9. Search for Norman Rzepka in:

  10. Search for Thomas Werkmeister in:

  11. Search for Daniel Werner in:

  12. Search for Georg Wiese in:

  13. Search for Heiko Wissler in:

  14. Search for Moritz Helmstaedter in:


M.H. initiated and supervised the project; K.M.B., M.B., T.B., N.R., T.W. and M.H. developed specifications and conceptual design with contributions by H.W.; T.B., D.B., J.F., T.H., P.O., N.R., T.W., D.W., G.W. and K.M.B. implemented the software; H.W., M.B., K.M.B. and F.D. provided data; K.M.B., M.H., H.W. and M.B. analyzed the data; M.H., K.M.B. and M.B. wrote the manuscript with contributions by all authors.

Competing interests

T.B., T.H. and N.R. own scalable minds UG (haftungsbeschränkt) & Co. KG, which offers IT consulting services–among these, the installation and usage of webKnossos. D.B., J.F., P.O., D.W. and G.W. are employees of this company. T.W. is a former employee and does not hold any shares of this company. All other authors declare no competing financial interests.

Corresponding authors

Correspondence to Kevin M Boergens or Moritz Helmstaedter.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–2

Zip files

  1. 1.

    Supplementary Software 1

    MATLAB code for automated detection of open branch points and first nodes with degree 1 in skeleton reconstructions (Fig. 1k-n, see Methods page 11, see detectopenBP.m). MATLAB code for measurement of skeleton path length and skeleton path smoothing using NURBS (Fig. 1 h-o, Suppl. Fig. 1 f-g, see pathLengthNURBS.m). MATLAB code for preparing axon skeletons for flight mode synapse annotation (see Methods page 16, see linearizeSkeletons.m). MATLAB scripts to attach spine annotations to dendrite tracings and for evaluating spine attachment performance (Fig. 2 a-b, Suppl. Fig. 2a, see attachSpines.m). Note these scripts require the skeleton data in Supplementary Software 2 and 3

  2. 2.

    Supplementary Software 2

    Skeleton data for scripts in Supplementary Software 1; part 1

  3. 3.

    Supplementary Software 3

    Skeleton data for scripts in Supplementary Software 1; part 2

  4. 4.

    Supplementary Software 4

    Python library for interfacing with the webKnossos API for measuring task completion times and automate task and project creation (for randomized assignment of tracing tasks to annotators, Fig. 1 h-o)

  5. 5.

    Supplementary Software 5

    All code and installation instructions for installing webKnossos independently on a web server. The source code is licensed under AGPLv3. The code is also available as a public GitHub repository at https://github.com/scalableminds/webknossos upon publication.


  1. 1.

    webKnossos Flight mode example, Expert tracing; Axon in Cortex; average speed: 1.7 mm/h

    Video demonstrating flight mode, including the creation and annotation of branchpoints. Note that the annotator encounters a branch point at 12”, inspects this location briefly, then presses “b” for branch point creation at 18”, and jumps back to this location after reaching the end of the dataset at 44”.

  2. 2.

    Brief instruction for testing webKnossos

    Brief introductory video for using the webKnossos demo site at https://demo.webknossos.brain.mpg.de

About this article

Publication history






Further reading