Software for Biological Microscopy



Icosahedral Virus Reconstruction Software available from NCMI
Program packages used in for the determination of icosahedral structures and the processing of cryo-electron micrographs.

IMAGIC
An integrated commercial image processing package for 2-D Crystals, Single Molecules, Morphology and 3-D processing and reconstruction.

ICE
ICE (Interactive Crystallographic Environment) is an interactive X-Windows program for processing images of two-dimensional arrays. I.C.E. allows the user to run Fourier transforms and apply CTF corrections.I.C.E. includes as subprocesses the programs Spectra and Boxmrc. Boxmrc is the utility that enables the user to display and select the of the image that will be used. Spectra empowers the user to refine the lattice of the Fourier transform.

QVIEW
The QVIEW image-processing software package provides a graphical user interface for user-friendly interactive and rapid selection of particles from digital electron micrographs. This package was developed to facilitate the selection of elliptical, hydrophobic, and aggregating particles, which present complications for other particle selection packages.

PTOOL
PTOOL is a suite of tools which provide a comprehensive package for the selection of particle images from electron cryo-microscopy images. PTOOL is designed using an X window system based graphical user interface where each tool is provided as a flowchart.

PHOELIX & SUPRIM
PHOELIX is an image processing package for helical macromolecular complexes. SUPRIM is a flexible modular software package for the processing of electron micrographs.

Micrograph Data Processing Program (MDPP)
MDPP is a fully-featured general purpose image processing package originally written to support research in structural biology requiring electron microscopy and image processing. It has focused on the analysis of images using Fourier techniques, particularly periodic images, but has extensive tools for other processing options (e.g. DNA sequencing, point-counting, image quantitation and display). Three-dimensional reconstruction methods are supported, including iterative deconvolution schemes for light micrographs.

SPIDER
SPIDER: (System for Processing Image Data from Electron microscopy and Related fields) is a large image processing system for electron microscopy. The emphasis of this package is on averaging of single particle macromolecule specimens, multivariate statistical classification, and 3D reconstruction although it contains modules for processing 2-D crystals, helices and tomography data.

XMIPP
XMIPP is a specialized suite of image processing programs primarily aimed at obtaining the three-dimensional reconstruction of biological specimens from large sets of projection images obtained by transmission electron microscopy.

EDP
EDP is a tool designed to facilitate and processing of electron diffraction patterns.
See also AUTO

STRUL
STRUL (supposedly an acronym for STRUctural alignment tooL) is a program or ultimately a programming environment in which to align (orient) projections through an unknown 3D structure to each other so that the 3D structure can be recovered.

EMAN
EMAN is a complete software package for reconstructing 3d models from a set of randomly oriented projections. This is primarily aimed at the electron cryomicroscopy/single particle analysis community, but many of the utilities and (for programmers) objects can be applied to other image processing problems.





Electron Tomography Codes for Parallel Computing
The application of the combination of the R-weighted and iterative methods to large reconstructions is computationally intensive. In order to expedite processing we have implemented the R-weighted, ART and SIRT reconstruction algorithms on the 400-node Intel Paragon, and more recently, on the 256-processor Cray T3E parallel supercomputer at SDSC. The iterative techniques potentially produce improved reconstructions by facilitating the incorporation of sources of information, in addition to the image data, which constrain the nature of the specimen under reconstruction. These algorithms require even more computational time because they are typically performed after an initial R-weighted computation and multiple iterations to achieve optimum results. This parallel implementation called PTOMO was partially supported by the NCRR funded National Biological Computing Resource (NBCR) at SDSC.

Fido
An interactive fiducial marking tool that can track fiducial marks from image to image.

Xdend
Interactive program for resectioning and deriving measurements from contoured structures.

Xvoxtrace
Interactive contouring tool for defining surfaces within tomographic volumes.

Analyze
A comprehensive and interactive package for multidimensional image visualization, processing, and analysis.

IMOD
IMOD is a set of image processing, modeling and display programs used for 3D reconstruction of EM serial sections, tomographic sections and optical sections developed by The Boulder Laboratory for 3-Dimensional Fine Structure.

STERECON
STERECON (STEREo CONtour Reconstruction System for Microscopy Data) is a facility for making contour-based 3-D reconstructions from microscope images. It is useful for: HVEM/IVEM single and serial thick sections, CTEM serial sections, serial histology sections, SEM, stereopairs, confocal LM z-series volumes, tomographic volumes and stereo macrophotographs.

SEM Align
Align is a Windows program for aligning grayscale images. Version 1.10a accepts only 8-bit per pixel Windows Bitmap (.bmp) images as input and produces only 8-bit per pixel Windows Bitmap grayscale output. The output is suitable for use with IGL Trace for making 3D measurements and reconstructions.



Communication Packages

ACE
A general purpose, high-level, event-driven, Asynchronous Communications Environment (ACE) for the transmission of large data and arbitrary user defined structures in a heterogeneous environment.



Image Handling & Analysis Tools

Btrack
Aids in the analysis of data collected from time lapse experiments especially with fluorescent indicator dyes. Btrack can accommodate changes in the postions of imaged cells/tissue regions, and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field.

DCU
A library of routines designed to provide application programmers an easy-to-use set of tools to implement and utilize common software data structures, interfaces to System V IPC calls, and free space management.

EMTOOL
Emtool is a program for display and manipulation of electron micrographs. It's primary advantage over other programs is that it is much more interactive and easier to use. It specializes in 2d image manipulation.

EM2EM
Program to convert images from/to formats used in the "electron microscopical (3DEM) community"

NIH Image
NIH Image is a public domain image processing and analysis program for the Macintosh. Image can acquire, display, edit, enhance, analyze and animate images. Among its functions, Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles.



Visualization Software

Amira
3D visualization and modelling system. It allows you to visualize scientific data sets from various application areas, e.g. medicine, biology, chemistry, physics, or engineering. 3D objects can be represented as grids suitable for numerical simulations, notably as triangular surface and volumetric tetrahedral grids.

Ducky
A motion scripting language for the rendering of animations (see Hessler et al, 1996).

Synu
A collection of programs for manipulation and visual presentation (see Hessler et al, 1992).

AVS
A flexible, modular, commercial package for analyzing and viewing data.

VMD molecular visualization
A free molecular visualization program designed for interactive image display. This software is capable of animation, manipulation and analysis of proteins, nucleic acids, lipid membranes and other biological molecules.




Software for X-Ray Crystallographic Structure Analysis: Fitting and Docking

XTALVIEW
XTALVIEW is a package for X-ray crystal structure solution from the point at which data is collected through the fitting of a molecular model into an electron density map. XtalView runs on ordinary workstations and does not require 3-D hardware.

O
O is a package for X-ray crystal structure determination for proteins. O is the successor to FRODO.

CCP4
The CCP4 Program Suite is an integrated set of programs for protein crystallography developed in a close collaboration between crystallographers under an initiative by the UK Biotechnology and Biological Sciences Research Council (formerly the SERC). Applications include data processing; various scaling programs; Patterson search and refinement; isomorphous and molecular replacement; structure refinement; phase improvement (density modification); presentation of results.

MolScript
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.

MolView
MolView is a Macintosh application that can read several types of coordinate files and display ribbon, CPK, stick, ball & stick, and surface figures.

Ribbons
The Ribbons software interactively displays molecular models, analyzes crystallographic results, and creates publication quality images.

Situs
A program package for the docking of protein crystal structures to low-resolution maps from electron microscopy.

Cornell Theory Center
Protein modeling software tools

WebMol
WebMol is a program for on-line viewing of macromolecular structures in the Protein Data Bank. It includes many options for analyzing structures.



Remote Instrumentation

CMDA
Provides remote acquisition, analysis, and visualization of data from our Intermediate High Voltage Electron Microscope.

webScope
webScope.TEM is a system for controlling and acquiring images from a transmission electron microscope (TEM) over a distributed network.

MMC/Materials MicroCharacterization Collaboratory
Remote microscopy for material science.