tomo_toolshed

A small, growing collection of lightweight cryo-ET file/CLI tools — etomo and WarpTools helpers, segmentation curation, and more to come — all installed at once and exposed as subcommands of a single tomo_toolshed command. Every tool here is intentionally lightweight (file/CLI editors, no heavy or GPU deps), so one install gets you everything.

Install

git clone https://github.com/hamid13r/tomo_toolshed.git
cd tomo_toolshed
pip install -e .

This installs the tomo_toolshed command. List the available tools with:

tomo_toolshed --help

Prefer conda/micromamba? A merged environment is provided:

micromamba create -f environment.yml -y
micromamba activate tomo-toolshed
pip install -e .

Tools

Development

pip install -e ".[test]"
pytest

Adding a tool

The layout is designed so a new lightweight tool is easy to drop in. Convention:

1. Create a subpackage under src/tomo_toolshed/<your_tool>/ with a cli.py exposing a click command (split heavier logic into a core.py, like skipped_views/ does). Keep any GUI/matplotlib imports lazy so the package stays headless-import-safe.
2. Register it in src/tomo_toolshed/cli.py: import the command and add it to the group with tomo_toolshed.add_command(<cmd>, name="<subcommand>"). Also add a one-line entry to the group docstring so tomo_toolshed --help reads as a useful index.
3. Add any new dependencies to the single dependencies list in pyproject.toml (and to environment.yml). There are deliberately no per-tool extras — one install gets everything.
4. Add a docs page at docs/<your_tool>.md and link it from the table above.
5. Add tests under tests/<your_tool>/.

Acknowledgments

These tools read, write, or interoperate with files from the cryo-ET ecosystem, and build on established open-source software. Please cite the relevant upstream projects when you use the corresponding part of this toolshed (see CITATION.cff for structured references).

Interoperates with / builds on:

• Warp / WarpTools — xml-reconstruct reimplements ts_reconstruct, and several tools read Warp XML / .tomostar / .settings (Tegunov & Cramer, Nat. Methods 2019).
• IMOD / etomo — skipped-views reads etomo taSolution.log; write-ebt builds a batchruntomo .ebt project (Kremer, Mastronarde & McIntosh, J. Struct. Biol. 1996).
• novaCTF — 3D-CTF correction in the tomography pipeline (Turoňová et al., J. Struct. Biol. 2017).
• AreTomo — marker-free tilt-series alignment, an alignment source reflected in the metadata (Zheng et al., 2022).
• RELION — the star-file format target for the helical / oriented-particle tools (RELION 4.x).
• IsoNet — add-defocus fills IsoNet star files.

Built on these Python libraries: mrcfile, starfile, NumPy, SciPy, scikit-image, pandas, Click, NetworkX, connected-components-3d, Matplotlib, Pillow, and lxml.

License

MIT — see LICENSE.