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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 51 19

  2. fidder fidder Public

    Detect and erase gold fiducials in cryo-EM images

    Python 13 3

  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 11 8

  5. lil-aretomo lil-aretomo Public

    A lightweight Python API for AreTomo

    Python 7 3

  6. mdocfile mdocfile Public

    SerialEM mdoc files as pandas dataframes

    Roff 12 7

Repositories

Showing 10 of 40 repositories
  • 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 26 4 2 0 Updated Apr 16, 2025
  • torch-tiltxcorr Public

    Coarse tilt series alignment in PyTorch

    teamtomo/torch-tiltxcorr’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Apr 14, 2025
  • torch-transform-image Public

    Real space transformations of 2D/3D images in PyTorch

    teamtomo/torch-transform-image’s past year of commit activity
    Python 2 BSD-3-Clause 2 1 0 Updated Apr 12, 2025
  • teamtomo/torch-find-peaks’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Apr 11, 2025
  • torch-affine-utils Public

    Utilities for affine transforms of 2d/3d coordinates in PyTorch

    teamtomo/torch-affine-utils’s past year of commit activity
    Python 0 BSD-3-Clause 1 0 0 Updated Apr 9, 2025
  • 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 1 1 1 Updated Apr 9, 2025
  • torch-so3 Public
    teamtomo/torch-so3’s past year of commit activity
    Python 3 BSD-3-Clause 2 0 1 Updated Apr 8, 2025
  • imodmodel Public

    IMOD model files as pandas dataframes in Python

    teamtomo/imodmodel’s past year of commit activity
    Python 11 8 4 0 Updated Apr 7, 2025
  • libtilt Public archive

    Image processing for cryo-electron microscopy in PyTorch

    teamtomo/libtilt’s past year of commit activity
    Python 14 4 13 (1 issue needs help) 2 Updated Apr 5, 2025
  • torch-fourier-shift Public

    Translate 2D/3D images by phase shifting Fourier transforms in PyTorch

    teamtomo/torch-fourier-shift’s past year of commit activity
    Python 1 BSD-3-Clause 1 0 0 Updated Apr 4, 2025

People

This organization has no public members. You must be a member to see who’s a part of this organization.

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