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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 13 7

Repositories

Showing 10 of 44 repositories
  • torch-tiltxcorr Public

    Coarse tilt series alignment in PyTorch

    teamtomo/torch-tiltxcorr’s past year of commit activity
    Python 1 BSD-3-Clause 2 1 0 Updated May 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 1 1 0 Updated May 13, 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 May 13, 2025
  • eerfile Public

    Read electron event representation (EER) files in Python

    teamtomo/eerfile’s past year of commit activity
    Python 7 BSD-3-Clause 0 2 (1 issue needs help) 0 Updated May 12, 2025
  • torch-fourier-filter Public

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

    teamtomo/torch-fourier-filter’s past year of commit activity
    Python 2 BSD-3-Clause 3 0 0 Updated May 10, 2025
  • 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 1 0 Updated May 7, 2025
  • teamtomo.github.io Public

    teamtomo.org website

    teamtomo/teamtomo.github.io’s past year of commit activity
    CSS 1 2 0 0 Updated May 4, 2025
  • ttsim3d Public

    Simulate a 3D scattering potentials from PDB files

    teamtomo/ttsim3d’s past year of commit activity
    Python 1 BSD-3-Clause 2 0 0 Updated May 3, 2025
  • membrain-seg Public

    membrane segmentation in 3D for cryo-ET

    teamtomo/membrain-seg’s past year of commit activity
    Python 65 15 12 3 Updated May 1, 2025
  • torch-image-interpolation Public

    Interpolation and gridding for 2D and 3D images in PyTorch

    teamtomo/torch-image-interpolation’s past year of commit activity
    Python 5 BSD-3-Clause 3 0 0 Updated Apr 30, 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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