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TEMIMPS Software:
Also see Tools Page
Software developed by TEMIMPS member institutions. Available for download.



Drop Shape Analysis for Detergent Concentration (MatLab) (Download Instuctions)
Xtrace Drop Program (Python) (Download Instructions)

The detergent concentration is critical for optimizing the 2D crystallization conditions. It can be measured to satisfactory accuracy using one of two programs available, one of which runs under matlab and the other requires wxPython.

SPARX
(Download Instructions)
(Documentation)
SPARX Helical Processing Routines (Documentation)
Our main area of interest is high-resolution cryo-EM and the development of efficient and largely automatic tools for single particle analysis and three-dimensional reconstruction. Due to a very low Signal-To-Noise Ratio of EM data, there is a necessity to collect and merge large numbers (in excess of 100,000) of individual particle images. We develop, in collaboration with other groups, a single particle software package SPARX (Hohn, et al). SPARX is provided free of charge as a service to the scientific community and its main features include:
1. New generation of 2D and 3D alignment protocols.
2. Ab initio structure determination programs.
3. Resampling methods for investigation of structural heterogeneity (3D variance).
4. Advanced code for multivariate statistical analysis (PCA, Varimax),
5. New generation of interpolation methods relaxing the need for oversampling the data.
6. Wiki-based interactive documentation
7. Extensive C++ library of general and EM-specific image operations with Python bindings, thus accessible to Python programmer.
8. All structure determination applications written as user transparent Python scripts
9. All major scripts parallelized for clusters of workstations using MPI.
More information can be found in: Hohn et al. SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 157(1):47-55.



EM Imaging Processing GUI - EMIP (Download Instructions)

EMIP is a Graphical User Interface written in wxPython that collects information from the user and runs existing programs from a variety of different software packages. Program output and error messages are printed on the console. If a particular program does not exist, is not in your path, is incorrectly configured, or is a version that takes different parameters, the program will fail and probably produce some kind of error message. EMIP requires python (tested on v.2.3, 2.4, 2.5) and wxPython (tested on 2.6 and 2.8), which in turn has its own dependencies (see wxpython). Although EMIP runs on any system with python and wxpython installed (linux, windows, mac), the availability of necessary image processing programs is limited (so stick to linux).




IPLT
(Documentation)
(Download)

The Image Processing Library & Toolbox (IPLT) is image processing software for electron microscopy specializing in 2D electron crystallography. It is based on several modular class libraries written in C++ with Python extensibility. It has built in functionality with several algorithms including CTF correction, lattice fit, peak search and a 9 parameter Gaussian peak fit. The software allows processing of electron micrographs as well as diffraction patterns and merging them into a 3D data set. Novel templates make it easy to add further functionality. A smooth unbending algorithm and scoring functions to identify coherent crystal patches for subsequent single-particle calculations will be implemented. More information can be found in: Philippsen et al. (2007) Collaborative EM image processing with the IPLT image processing library and toolbox. J Struct Biol 157(1):28-37 and Philippsen et al. (2003) Iplt-image processing library and toolkit for the electron microscopy community. J Struct Biol 144(1-2):4-12

IPLT may be downloaded from the website: (Download) Binaries for major platforms as well as GPL Licensed source code is available. There is also a Wiki. Please contact Andreas Engel email at Case Western Reserve University for installation guidance.



AnimatedTEM

ANIMATED-TEM is a software toolbox aimed at the ANalysis of IMages for Automatic Targeting and Extraction of Data in Transmission Electron Microscopy. Combined with a microscope software, it can select targets on-line to realize the automatic examination of 2D-crystal samples, working at several magnifications without human intervention. More information can be found in: Coudray et al. (2010) Automated screening of 2D crystallization trials using transmission electron microscopy: A high-throughput tool-chain for sample preparation and microscopic analysis. J Struct Biol. 173:365-74.








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