IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data. IMOD has been used across a range of scales from macromolecule structures to organelles to whole cells and can also be used for optical sections. Included in IMOD are tools for image reconstruction, image segmentation, 3D mesh modeling and analysis of 2D and 3D data. IMOD was developed at the . IMOD was first released in 1995, is free to and use for any purpose.
Main Programs
IMOD includes over 180 command line programs and three main GUI programs:
3dmod - IMOD's main GUI used to view and segment images and 3D vector models.
Midas - A program used to align images over the top of each other, typically to apply fine adjustments after automatic cross-correlation.
eTomo - A program used to reconstruct 3D volumes by joining smaller volumes and/or guiding the user through the process of tomographic reconstruction of single and dual axis tilt series. During this process eTomo make many program calls and often launches 3dmod and Midas to allow users to make fine adjustments.
Image Format: The main image format supported by IMOD is MRC file format, which typically have a ".st", ".mrc" or ".rec" extensions and represent various types of "image stacks" which together might represent a tilt series or 3D volume. IMOD will also open TIF files and includes a set of programs to convert between image formats including common microscopy formats like ".raw" and ".dm4". Vector Format: IMOD saves and opens vector data in the form of contour and meshes in an , typically with a ".mod" or ".fid" extension. These IMOD model files are typically over-laid over the top of an image file and can be used to annotate and segment regions of interest. Models can consists of one or more objects, where each object can contain closed, open or scattered point "contours" which are used to generate a 3D mesh.
Main Features
Reconstruction:
* Reconstruction of single and combined dual axis tilt-series using tomographic reconstruction techniques.
* Automatic tracking and registration of fiducial particles to improve tilt-series alignment.
* Ability to parallel process expensive tilt-series reconstruction across multiple machines.
* Combining of montaged datasets.
* Ability to align and then warp images using cross-correlation and the Midas GUI for manual alignment.
* Ability to align and join multiple volumes such as serial sections.
* Rapidly generates contours into meshes for final movies and analysis
* Allows several different meshing options for tubes and arbitrary meshes
* Surface smoothing and generation of low res meshes for faster rendering
Analysis
* Analysis of model files for basic quantitative information such as: volume, number of surfaces, volume, surface area plus the diameter of spheres, and length of open contours.
* Analysis of image density and generation of histograms.
* A series of programs specifically for microtubule analysis.
* Spatial analysis to determine the distribution and proximity of different surfaces.
