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Supported Applications

DeepEMhancer

  • Description

    (Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

  • Usage

    To list all executables provided by DeepEMhancer, run: $ sbgrid-list deepemhancer Copy to clipboard

  • Usage Notes

    Known Issues:
    Users have reported issues when loading the models obtained using the --download flag with DeepEMhancer. If you have errors running the application, try adding this flag

    --deepLearningModelPath /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints

    to your deepemhancer command. This will use the local models which are known to work with the versions of DeepEMhancer in SBGrid.

  • Installation

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

  • Primary Citation*

    R. Sanchez-Garcia, J. Gomez-Blanco, A. Cuervo, J. M. Carazo, C. O. S. Sorzano, and J. Vargas. 2021. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Communications Biology. 4(1): 874.


    • *Full citation information available through

  • Webinars

    DeepEMhancer

    Topic: DeepEMhancer: exploiting previous knowledge to enhance map visualization
    Presenter: Rubén Sánchez Garcia, Ph.D., The National Centre for Biotechnolgy, Spanish National Research Council


    Host: Pete Meyer
    Recorded on January 26, 2021

  • Keywords

    Electron Microscopy

  • Default Versions

    Linux 64:  20220530_cu10 (3.6 GB)

  • Other Versions

      Linux 64:

      0.16 (5.7 GB) , 20200909 (4.3 GB) , 20210511 (5.5 GB) , 20220530_cu11 (4.5 GB) , 202309_cu10 (3.7 GB) , 202309_cu11 (6.0 GB)
    • Common files size: 2.6 GB

  • Developers

    Javier Vargas, Ruben Sanchez-Garcia

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