TeamTomo

TeamTomo is a set of modular Python package for cryo-EM and cryo-ET for the modern scientific computing environment.

This unified repository contains the core TeamTomo data processing functionality under a single umbrella for better maintainability and cross-package development. File I/O packages are distributed separately and can be found under the organizations repositories.

Getting Started

If you want to contribute to TeamTomo, please look through the CONTRIBUTING guide for more info on adding, migrating, or updating packages. If you're just looking to use TeamTomo for your work, follow the installation instructions below.

Package Installation

The development workspace depends on the uv tool for Python environment/package management.

For general users

If you're not looking to contribute to the monorepo, cloning the repo is the preferred way to go:

git clone https://github.com/teamtomo/teamtomo.git
cd teamtomo

For contributing developers

We strongly recommend making your own fork of the monorepo if you plan on contributing changes. Code should be edited in your repo (origin) and pull requests made into the TeamTomo repo (upstream).

First, fork the repository on GitHub (button near top-right of the repo home page), and then clone your fork locally:

git clone https://github.com/YOUR_USERNAME/teamtomo.git
cd teamtomo

Then, add the TeamTomo repository as an upstream remote to keep your fork up to date:

git remote add upstream https://github.com/teamtomo/teamtomo.git
git remote -v
# Verify remote setup looks like this
# origin        https://github.com/YOUR_USERNAME/teamtomo.git (fetch)
# origin        https://github.com/YOUR_USERNAME/teamtomo.git (push)
# upstream      https://github.com/teamtomo/teamtomo.git (fetch)
# upstream      https://github.com/teamtomo/teamtomo.git (push)

Package setting up via uv

Then, create and activate a new virtual environment:

uv venv
source .venv/bin/activate

And finally sync with the repository to install packages

uv sync --all-extras --all-packages

Note that the --all-extras and --all-packages flags install the development and testing requirements for all sub-packages. More granular install options are possible, if your system requires it.

List of Packages

🚧 Coming Soon 🚧