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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 56 20

  2. fidder fidder Public

    Detect and erase gold fiducials in cryo-EM images

    Python 17 4

  3. mmdf mmdf Public

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

    Python 10 4

  4. imodmodel imodmodel Public

    IMOD model files as pandas dataframes in Python

    Python 13 8

  5. lil-aretomo lil-aretomo Public

    A lightweight Python API for AreTomo

    Python 8 3

  6. mdocfile mdocfile Public

    SerialEM mdoc files as pandas dataframes

    Roff 14 10

Repositories

Showing 10 of 60 repositories
  • teamtomo Public

    modular Python packages for cryo-EM and cryo-ET

    teamtomo/teamtomo's past year of commit activity
    Python 22 BSD-3-Clause 13 14 (1 issue needs help) 8 Updated Sep 9, 2026
  • teamtomo.github.io Public

    teamtomo.org website

    teamtomo/teamtomo.github.io's past year of commit activity
    Python 1 4 1 0 Updated Sep 6, 2026
  • ttsim3d Public

    Simulate a 3D scattering potentials from PDB files

    teamtomo/ttsim3d's past year of commit activity
    Python 1 BSD-3-Clause 3 2 2 Updated Sep 1, 2026
  • torch-ctf-estimation Public

    local defocus estimation in cryo-EM images

    teamtomo/torch-ctf-estimation's past year of commit activity
    Python 2 BSD-3-Clause 3 0 2 Updated Aug 16, 2026
  • torch-reconstruct-tomogram Public

    (sub-)tomogram reconstruction and subtilt extraction for cryoET.

    teamtomo/torch-reconstruct-tomogram's past year of commit activity
    Python 0 BSD-3-Clause 1 4 1 Updated Jul 31, 2026
  • torch-tilt-series Public

    everything about tilt series

    teamtomo/torch-tilt-series's past year of commit activity
    Python 0 BSD-3-Clause 1 0 1 Updated Jul 31, 2026
  • eerfile Public

    Read electron event representation (EER) files in Python

    teamtomo/eerfile's past year of commit activity
    Python 7 BSD-3-Clause 1 2 (1 issue needs help) 3 Updated Jul 20, 2026
  • membrain-seg Public

    membrane segmentation in 3D for cryo-ET

    teamtomo/membrain-seg's past year of commit activity
    Python 94 19 16 4 Updated Jul 20, 2026
  • mmdf Public

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

    teamtomo/mmdf's past year of commit activity
    Python 10 BSD-3-Clause 4 0 4 Updated Jul 20, 2026
  • etomofiles Public

    Etomo metadata IO in Python

    teamtomo/etomofiles's past year of commit activity
    Python 1 BSD-3-Clause 1 3 2 Updated Jun 30, 2026

Most used topics

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