Computer visualization of three-dimensional image data using IMOD.

@article{Kremer1996ComputerVO,
  title={Computer visualization of three-dimensional image data using IMOD.},
  author={J R Kremer and David N. Mastronarde and J Richard McIntosh},
  journal={Journal of structural biology},
  year={1996},
  volume={116 1},
  pages={
          71-6
        }
}
We have developed a computer software package, IMOD, as a tool for analyzing and viewing three-dimensional biological image data. IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions. The software allows image data to be visualized by several different methods. Models of the image data can be visualized by volume or contour surface rendering and can yield quantitative information. 
Volumetric feature extraction and visualization of tomographic molecular imaging.
Volumetric Filtering , Feature Extraction , and Visualization of Volumetric Tomographic Molecular Imaging
TLDR
An interactive volumetric exploration tool (Volume Rover), which encapsulates implementations of the above filtering, and curve/surface feature extraction algorithms, and additionally uses multi-resolution interactive geometry and volume rendering, for the visualization.
A segmentation method for 3D visualization of neurons imaged with a confocal laser scanning microscope
TLDR
A segmentation method is described for objects recorded with serial section images that can be applied to any high contrast serial slice data set that is well aligned and registered, and applied to the visual neurons of the housefly, Musca domestica.
Image analysis and interactive visualization techniques for electron microscopy tomograms
TLDR
Results indicate that histogram and gradient based measures are useful in producing automatic and coherent visualizations in digital image analysis and three-dimensional visualization techniques for use with transmission electron microscopy (TEM) image data and in particular electron tomography, which provides 3-D reconstructions of the nano-structures.
Optimization method for isodensity surface models obtained with electron microscope tomography data
TLDR
An automatic method is presented for obtaining isodensity surface models that correspond most closely to the steepest contrast boundary at the edge of each component within the volume.
Segmentation method for three-dimensional visualization of microscopic objects imaged with a confocal laser scanning microscope
TLDR
A template-based semiautomatic segmentation method to aid in the segmentation process and 3-D reconstruction of microscopic objects recorded with a confocal laser scanning microscope (CLSM), based on the creation of a user-defined object template.
3D Image Processing for Structural Analysis of Macromolecules Using Cryo-Electron Tomography
TLDR
In this dissertation novel image processing methods are presented and assessed and the introduced processing framework provides a solid basis for users to process massive datasets rapidly and accurately.
Electron tomography of large, multicomponent biological structures.
TLDR
The application of this technique to the reconstruction of large, complex structures such as mitochondria is described in conjunction with several tools for segmentation, measurement, classification, and visualization.
Segmentation of Features in Electron Tomographic Reconstructions
TLDR
This chapter describes computational approaches designed to extract the most accurate information possible from biological electron tomograms.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 20 REFERENCES
The reconstruction of a three-dimensional structure from projections and its application to electron microscopy
A transmission electron micrograph is essentially a projection of the specimen in the direction of view. In order to reconstruct a three-dimensional image of the specimen, it is necessary to be able
A new method for image segmentation
Alignment of tomographic projections using an incomplete set of fiducial markers.
The reconstruction of three-dimensional structure from projections and its application to electron microscopy II. Direct methods
  • P. Gilbert
  • Mathematics
    Proceedings of the Royal Society of London. Series B. Biological Sciences
  • 1972
TLDR
This direct method is shown to be equivalent to the Fourier method and also to certain methods of reconstruction developed for the solution of analogous problems in other fields, and to be very suitable for reconstructing the density of objects with rotational or helical symmetry.
Surface definition for branching, contour-defined objects
TLDR
This report extends minimum flow algorithms to handle contour defined objects which are highly branched and have holes to handle three-dimensional CAT scanner data, topographical map data and object representation for knowledge guided vision systems.
HVEM tomography of the trans-Golgi network: structural insights and identification of a lace-like vesicle coat
TLDR
observing the 3-D structure of trans-Golgi cisternae and trans- Golgi networks in NRK cells led to the following predictions: (a) sorting of molecules must occur prior to the formation of TGN tubules; (b) vesicle formation takes place almost synchronously along a given T GN tubule; and (c) lace-like coats form an exocytic vesicles.
Three-dimensional ultrastructural analysis of the Saccharomyces cerevisiae mitotic spindle
TLDR
The three dimensional organization of microtubules in mitotic spindles of the yeast Saccharomyces cerevisiae has been determined by computer- aided reconstruction from electron micrographs of serially cross- sectioned spindes, and interpretation of these reconstructed spindle offers some insights into the mechanisms of mitosis in this yeast.
Interpolar spindle microtubules in PTK cells
TLDR
Spindle microtubules in PtK1 cells, fixed at stages from metaphase to telophase, have been reconstructed using serial sections, electron microscopy, and computer image processing to study the class ofMTs that form an interdigitating system connecting the two spindle poles and their relationship to the spindle MTs that attach to kinetochores.
...
1
2
...