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@teamtomo

teamtomo

teamtomo

Welcome to the TeamTomo GitHub organization.

modular Python packages the cryo-ET community can depend on

Mission

To help the cryo-ET community develop their ideas without reinventing the software stack.

Key ideas

  • packages are small, modular and easy to install
  • package scope is limited and well defined
  • APIs are Pythonic and type hinted
  • code is tested

If this seems daunting, we're here to help, please reach out by posting on image.sc)!

Development model

Because packages in teamtomo are small and well scoped it is easy to depend on only those packages relevant to your work.

teamtomo is not a place for the development of your own software projects. Your projects belong to you and the credit should be yours alone! Did you develop a small, reusable component along the way that could benefit the entire community? We would love to work with you to bring it here.

Work with us

Interested in working with us in some way? Fantastic, Welcome aboard!

Most discussion should happen on image.sc so it is easy to find when searching online.

For realtime chat we use image.sc's zulip, a chat platform open to all for discussing details about the project.

Licensing

All projects in this organisation should be licensed under the 3-Clause BSD License.

Using and Citing the Tools

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  1. starfile starfile Public

    STAR file I/O in Python

    Python 46 19

  2. fidder fidder Public

    Detect and erase gold fiducials in cryo-EM images

    Python 11 4

  3. mmdf mmdf Public

    macromolecular structure files (.pdb/.mmCIF) as pandas DataFrames

    Python 8 2

  4. imodmodel imodmodel Public

    IMOD model files as pandas dataframes in Python

    Python 9 7

  5. lil-aretomo lil-aretomo Public

    A lightweight Python API for AreTomo

    Python 7 4

  6. mdocfile mdocfile Public

    SerialEM mdoc files as pandas dataframes

    Roff 9 7

Repositories

Showing 10 of 31 repositories
  • torch-fourier-rescale Public

    Rescale 2D and 3D images by Fourier padding/cropping in PyTorch

    teamtomo/torch-fourier-rescale’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Nov 19, 2024
  • torch-cubic-spline-grids Public

    Cubic spline interpolation on multidimensional grids in PyTorch

    teamtomo/torch-cubic-spline-grids’s past year of commit activity
    Python 25 1 1 0 Updated Nov 19, 2024
  • tttsa Public

    Automated tilt-series alignment for cryo-ET in PyTorch

    teamtomo/tttsa’s past year of commit activity
    Python 1 BSD-3-Clause 1 6 1 Updated Nov 19, 2024
  • torch-fourier-slice Public

    Fourier slice extraction/insertion in PyTorch

    teamtomo/torch-fourier-slice’s past year of commit activity
    Python 1 BSD-3-Clause 4 2 3 Updated Nov 19, 2024
  • cryohub Public

    IO hub for Cryo-EM, Cryo-ET and subtomogram averaging data.

    teamtomo/cryohub’s past year of commit activity
    Python 9 5 0 1 Updated Nov 19, 2024
  • torch-subpixel-crop Public

    Crop 2D/3D images with subpixel precision in PyTorch

    teamtomo/torch-subpixel-crop’s past year of commit activity
    Python 2 BSD-3-Clause 0 1 0 Updated Nov 19, 2024
  • torch-image-lerp Public

    Linear interpolation and gridding for 2D and 3D images in PyTorch

    teamtomo/torch-image-lerp’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 0 Updated Nov 18, 2024
  • starfile Public

    STAR file I/O in Python

    teamtomo/starfile’s past year of commit activity
    Python 46 BSD-3-Clause 19 5 1 Updated Nov 18, 2024
  • torch-grid-utils Public

    Grid utilities for 2D/3D image manipulations in PyTorch

    teamtomo/torch-grid-utils’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Nov 18, 2024
  • torch-fourier-shell-correlation Public

    Calculate the Fourier shell correlation in PyTorch

    teamtomo/torch-fourier-shell-correlation’s past year of commit activity
    Python 3 BSD-3-Clause 0 1 (1 issue needs help) 0 Updated Nov 18, 2024

Most used topics

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