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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 48 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 3

  4. imodmodel imodmodel Public

    IMOD model files as pandas dataframes in Python

    Python 10 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 10 7

Repositories

Showing 10 of 33 repositories
  • torch-fourier-filter Public

    Fourier space filters for 2D/3D data in pyTorch

    teamtomo/torch-fourier-filter’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 1 Updated Dec 23, 2024
  • ttsim3d Public

    Simulate a 3D scattering potentials from PDB files

    teamtomo/ttsim3d’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 1 Updated Dec 22, 2024
  • ttmask Public

    Mask creation CLI tool for cryo-EM/ET

    teamtomo/ttmask’s past year of commit activity
    Python 3 BSD-3-Clause 4 3 1 Updated Dec 21, 2024
  • yet-another-imod-wrapper Public

    Simple API for automated tilt-series alignment in IMOD

    teamtomo/yet-another-imod-wrapper’s past year of commit activity
    Python 6 3 1 0 Updated Dec 20, 2024
  • mmdf Public

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

    teamtomo/mmdf’s past year of commit activity
    Python 8 BSD-3-Clause 3 0 0 Updated Dec 16, 2024
  • imodmodel Public

    IMOD model files as pandas dataframes in Python

    teamtomo/imodmodel’s past year of commit activity
    Python 10 7 5 0 Updated Dec 11, 2024
  • 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 1 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 2 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 2 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 3 3 Updated Nov 19, 2024

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