 IMOD http://bio3d.colorado.edu/imod/ 
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 IMOD is a set of image processing, modeling and display programs
used for tomographic reconstruction and for 3D reconstruction of EM serial
sections and
optical sections.
The package contains tools for assembling and aligning data within multiple
types and sizes of image stacks, viewing 3-D data from any orientation,
and modeling and display of the image files.
It includes a complete graphical user interface for generating tomograms,
combining tomograms from tilt series taken around two axes, and stacking
tomograms
from serial sections.
OS support: Linux, Windows, Mac OS X
Image format support: MRC, TIFF Cost: Free
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FEI Explore3D http://www.fei.com/
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Explore3D is a professional image acqustition, processing and display
software by FEI Company.
The package is a commercial product and should be the way to go if you
need to get fast results.
OS support: Windows Image format support: MRC
Cost: Unknown
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Protomo www.electrontomography.org/
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Protomo is a suite of programs and shell scripts primarily developed
for electron tomography.
It offers routines for preprocessing micrographs, CTF-correction of images
of untilted andtilted specimens, marker-free alignment of tilt series,
and 3D
reconstruction, besides some general image processing functionality.
OS support: Linux
Image format support: Most formats Cost: Free
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TOM wwwex.biochem.mpg.de/tom/
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The Tomography Toolbox is a collection of functions that extend
the capability of the MATLAB® (+ Image Procesing Toolbox) numeric
computing environment.
The toolbox supports a wide range of functions for tomography.
OS support: Linux, Microsoft Windows Image
format support: EM,MRC,Spider Cost: Free
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UCSF
Tomography
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UCSF Tomography is an integrated software suite that provides full
automation from tomographic data collection to real-time reconstruction
as well as
automated acquisition of random conical data sets.
This software was implemented based upon a novel approach in which the
compustage tilting is modeled as geometric rotation.
The spatial movement of the sample as a result of stage tilting can be
predicted based upon previously collected tomographic images.
Therefore, there is no need to collect tracking and focusing images during
the entire tomographic data collection.
A significant dose saving can thus be achieved and is critical in collecting
cryo tilt series.
Real-time reconstruction is achieved by calculating a weighted back-projection
on a small Linux cluster (five dual-processor computer nodes) concurrently
with the UCSF tomography data collection running on the microscopefs
computer, and using the fiducial-marker free alignment data generated during
the data
collection process.
The real-time reconstructed 3D volume provides users with immediate feedback
to fully asses all aspects of the experiment ranging from sample choice,
ice
thickness, experimental parameters to the quality of specimen preparation.
An on-site scheme was developed for random conical data collection where
tracking and focusing are performed at the same location as the final conical
tilt images.
Lower magnifications combined with short exposure are used to substantially
reduce dose and to allow larger tilt steps.
The system also includes a feature for montaging untilted images to ensure
that all of the particles in the tilted image may be used in the reconstruction.
OS support: Windows 2000, XP Image format support: MRC
Cost: Free for academic use
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EM3D em3d.stanford.edu/index.html
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EM3D is a software application designed to analyze and visualize
electron microscope (EM) tomography data.
It is especially for cellular and molecular biologists. From a tilt series
of 2D electron micrographs taken at many tilt angles with respect to the
electron beam,
this program can then perform autoalign and quickly render those data
into a lucid 3D model, which allows you to perform object rotating for
viewing.
In addition,
EM3D also provides analysis tools for quantify structural information
from the models, including their moments, proximity relationships, and
spatial reliability.
And all of these functions can be executed with a very intuited graphic
user interface. EM3D is available free-of-charge for most computer operation
systems,
inculding MacOS X for PowerPC or Intel, UNIX, Linux, and Windows. EM3D
is being developed in the laboratory of Dr. U. J. McMahan,
Professor of Neurobiology and of Structural Biology at Stanford University
School of Medicine.
OS support: Windows XP, Linux, MacOS X Image format
support: Unknown Cost: Free for academic use
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