Introduction

The aim in high-resolution connectomics is to reconstruct complete neuronal connectivity in a tissue. Currently, the only technology capable of resolving the smallest neuronal processes is electron microscopy (EM). Thus, a common approach to network reconstruction is to perform (error-prone) automatic segmentation of EM images, followed by manual proofreading by experts to fix errors. We have developed an algorithm and software library to not only improve the accuracy of the initial automatic segmentation, but also point out the image coordinates where it is likely to have made errors. Our software, called gala (graph-based active learning of agglomeration), improves the state of the art in agglomerative image segmentation. It is implemented in Python and makes extensive use of the scientific Python stack (numpy, scipy, networkx, scikit-learn, scikit-image, and others). We present here the software architecture of the gala library, and discuss several designs that we consider would be generally useful for other segmentation packages. We also discuss the current limitations of the gala library and how we intend to address them.

Publications

  1. Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages.
    Cite this
    Nunez-Iglesias J, Kennedy R, Plaza SM, Chakraborty A, Katz WT, 2014-01-01 - Frontiers in neuroinformatics
  2. Machine learning of hierarchical clustering to segment 2D and 3D images.
    Cite this
    Nunez-Iglesias J, Kennedy R, Parag T, Shi J, Chklovskii DB, 2013-01-01 - PloS one

Credits

  1. Juan Nunez-Iglesias
    Developer

    FlyEM Project, HHMI Ashburn, United States of America

  2. Ryan Kennedy
    Developer

    FlyEM Project, HHMI Ashburn, United States of America

  3. Stephen M Plaza
    Developer

    FlyEM Project, HHMI Ashburn, United States of America

  4. Anirban Chakraborty
    Developer

    Video Computing Group, Department of Electrical Engineering, United States of America

  5. William T Katz
    Investigator

    FlyEM Project, HHMI Ashburn, United States of America

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Summary
AccessionBT006766
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByWilliam T Katz