pytom

PyTom is an open-source Python software package for electron tomography data analysis and 3D reconstruction. It provides tools for processing tilt-series acquired in cryo-electron tomography and related modalities, with a focus on reproducible workflows and scripting.

It includes data input and output facilities for tilt-series, functionality for aligning images, and reconstruction capabilities to convert 2D projections into 3D volumes. The software offers visualization tools for inspecting volumes and supports scripting for automated pipelines. Its modular design allows users to extend PyTom with additional processing modules and to integrate it with other tools in the electron microscopy software ecosystem.

PyTom emphasizes accessibility for researchers, offering a high-level API while exposing lower-level routines for advanced users. It is designed to be platform-agnostic and relies on standard scientific libraries such as NumPy and SciPy, and may interface with external tools used in electron microscopy data processing. The project promotes reproducibility by enabling scriptable analysis pipelines.

Developed by researchers in the electron microscopy community, PyTom is hosted on public code repositories and has seen multiple releases. It is used in academic settings to support cryo-electron tomography studies, as well as in education and method development.