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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 44 17

  2. fidder fidder Public

    Detect and erase gold fiducials in cryo-EM images

    Python 10 3

  3. mmdf mmdf Public

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

    Python 8 1

  4. imodmodel imodmodel Public

    IMOD model files as pandas dataframes in Python

    Python 8 6

  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 6

Repositories

Showing 10 of 28 repositories
  • starfile Public

    STAR file I/O in Python

    teamtomo/starfile’s past year of commit activity
    Python 44 BSD-3-Clause 17 4 2 Updated Jul 23, 2024
  • membrain-seg Public

    membrane segmentation in 3D for cryo-ET

    teamtomo/membrain-seg’s past year of commit activity
    Python 49 12 13 5 Updated Jul 16, 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 16 0 1 4 Updated Jul 12, 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 0 0 0 Updated Jul 11, 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 0 BSD-3-Clause 0 0 0 Updated Jul 5, 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 Jun 29, 2024
  • ttmask Public

    Mask creation CLI tool for cryo-EM/ET

    teamtomo/ttmask’s past year of commit activity
    Python 1 BSD-3-Clause 1 2 0 Updated Jun 18, 2024
  • libtilt Public

    Image processing for cryo-electron microscopy in PyTorch

    teamtomo/libtilt’s past year of commit activity
    Python 14 5 13 (1 issue needs help) 2 Updated Jun 17, 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 2 BSD-3-Clause 0 0 0 Updated Jun 17, 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 1 BSD-3-Clause 0 0 0 Updated Jun 16, 2024

Most used topics

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