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Topaz

  • Description

    a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz includes methods for micrograph denoising using deep denoising models.

  • Usage

    To list all executables provided by Topaz, run: $ sbgrid-list topaz Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install topaz Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    T. Bepler, A. Morin, M. Rapp, J. Brasch, L. Shapiro, and A. J. N. &. B. Berger. 2019. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods. 16: 1153-1160.


    • *Full citation information available through

  • Webinars

    Topaz

    Topic: Topaz: particle picking with positive-unlabeled learning
    Speaker: Tristan Bepler, MIT

    Host: Jason Key
    Recorded on Feb 26, 2019

  • Keywords

    Electron Microscopy

  • Default Versions

    Linux 64:  0.3.7 (6.2 GB)

  • Other Versions

      Linux 64:

      0.2.4 (2.5 GB) , 0.2.5 (3.8 GB) , 0.2.5-2 (3.8 GB) , 0.2.5a (5.7 GB) , 0.2.5a_cu11.3_py36 (5.9 GB) , 0.2.5_cu11 (5.6 GB) , 0.2.5_cu11.2 (5.7 GB) , 0.3.10 (5.6 GB) , 0.3.11 (6.6 GB) , 0.3.12 (5.6 GB) , 0.3.13 (5.6 GB) , 0.3.14 (5.6 GB) , 0.3.16 (5.6 GB) , 0.3.6 (5.5 GB) , 0.3.8 (2.4 GB) , 0.3.9 (5.7 GB)

  • Developers

    Tristan Bepler, Alex J. Noble

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