Crowdsourcing the creation of image segmentation algorithms for connectomics

Ignacio Arganda Carreras, Srinivas C. Turaga, Daniel R. Berger, Dan Cire San, Alessandro Giusti, Luca M. Gambardella, Jürgen Schmidhuber, Dmitry Laptev, Sarvesh Dwivedi, Joachim M. Buhmann, Ting Liu, Mojtaba Seyedhosseini, Tolga Tasdizen, Lee Kamentsky, Radim Burget, Vaclav Uher, Xiao Tan, Changming Sun, Tuan D. Pham, Erhan BasMustafa G. Uzunbas, Albert Cardona, Johannes Schindelin, Hyunjune Sebastian Seung

Research output: Contribution to journalArticle

99 Scopus citations

Abstract

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic(EM) images of the brain. Participants submitted boundary map spredicted for a test set of images, and were scored based on their agreement with a on sensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deeplearning” approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from co-operation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test data set. Retrospective evaluation of the challenges coring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.

Original languageEnglish (US)
Article numberA142
Pages (from-to)1-13
Number of pages13
JournalFrontiers in Neuroanatomy
Volume9
Issue numberNovember
DOIs
StatePublished - Sep 5 2015

All Science Journal Classification (ASJC) codes

  • Anatomy
  • Neuroscience (miscellaneous)
  • Cellular and Molecular Neuroscience

Keywords

  • Connectomics
  • Electron microscopy
  • Image segmentation
  • Machine learning
  • Reconstruction

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  • Cite this

    Carreras, I. A., Turaga, S. C., Berger, D. R., San, D. C., Giusti, A., Gambardella, L. M., Schmidhuber, J., Laptev, D., Dwivedi, S., Buhmann, J. M., Liu, T., Seyedhosseini, M., Tasdizen, T., Kamentsky, L., Burget, R., Uher, V., Tan, X., Sun, C., Pham, T. D., ... Seung, H. S. (2015). Crowdsourcing the creation of image segmentation algorithms for connectomics. Frontiers in Neuroanatomy, 9(November), 1-13. [A142]. https://doi.org/10.3389/fnana.2015.00142