3dmod

3dmod is an interactive three-dimensional model viewer and editor that is part of the IMOD software package used in electron tomography and related imaging workflows. It provides a graphical interface for visualizing, editing, and annotating three-dimensional models that represent segmented structures within tomographic volumes.

Its tools support common segmentation tasks, including adding, moving, and deleting points; drawing and editing contours on image slices; converting contours into surface meshes; and smoothing or refining geometry. Users can switch between display modes such as points, wireframes, and shaded surfaces, and can overlay models on raw tilt-series images or reconstructed volumes. The program also offers measurement capabilities and labeling for documentation and analysis.

3dmod reads and writes IMOD model data, with models stored in IMOD's native .mod format and related files describing points, lines, contours, and surfaces. It can import data from other IMOD components and integrate into workflows that include image alignment, reconstruction, and segmentation. The tool is designed to work within the IMOD ecosystem and to support reproducible analyses.

Availability and platform support: 3dmod is distributed with IMOD and runs on major Unix-like systems and macOS. It is open-source software, maintained by the IMOD project and used by researchers in electron tomography, cryo-EM, and related fields. While powerful for specialized modeling tasks in EM workflows, 3dmod is not a general-purpose 3D modeling tool and is targeted at scientific segmentation and annotation within reconstructed volumes.