User Guide –
The following software are available on BMIT computers for data analysis by users:
It is an open-source software and the primary software that BMIT uses for fast reconstruction of CT data. In-house graphic user interface (GUI) has been developed for use by BMIT users. Currently the reconstruction is performed on BMIT servers which cannot be accessed from outside the CLS.
Bruker microCT formerly known as SkyScan develops and produces wide range of high-end microtomography instruments for life science, material research and in-vivo preclinical studies. Software for CT reconstruction (NRECON) and 3D visualization (CTvox) are available for free download. micro-CT software downloads Note: account needed for access.
GSECARS Tomography Processing Software (Mark Rivers)
The links below contain useful IDL (and not only IDL) code for processing of parallel beam CT data. It is an FFT based reconstruction algorithm that provides valuable alternative to the convoluted backprojection algorithms. The GRIDREC algorithm is highly optimized for regular CPU architectures (does not require specialized high performance graphic cards) and runs 20-40 times faster than the common backprojection algorithm.
PITRE and HPITRE
PITRE (Phase-sensitive x-ray Image processing and Tomography REconstruction) is a freeware developed by INFN Trieste in order to facilitate and standardize the simulation and elaboration of X-ray phase contrast images. It can be used for phase retrieval, extraction of apparent absorption, refraction and ultra-small-angle scattering images for analyzer-based X-ray phase-contrast imaging/tomography (DEI-CT), tomography reconstruction, employing filter back-projection and GRIDREC algorithms, and images format conversion. A batch processing manager called PITRE_BM, can execute a series of tasks ("jobs"), which is created via PITRE, without manual intervention. H-PITRE is a fast tomography reconstruct program by using parallel computing abilities of NVIDIA GPU (graphics processing unit) card.
RecView is a program for microtomographic reconstruction and image processing. It consists of about 14,000 lines of custom source codes in C++ and CUDA C and x86/x64 machine languages. RecView is designed for processing tomographic data obtained at the BL20B2, BL20XU, and BL47XU beamlines of the synchrotron radiation facility SPring-8. Supports both NVIDIA and ATI cards and is oriented towards older type video cards. Looks quite amazing with NVIDIA GeForce GTX470 card.
The software works using only the CPU if the graphics card is not of the supported types.
MCTrace is a program for microtomographic skeletonized model building and refinement with a graphical user interface. It consists of over 50,000 lines of custom source code in C++.
Avizo is a licenced program that can be used for 3D visualization and quantitative data analysis.
ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.
Image processing and analysis in Java. ImageJ provides a framework for working with images. Macros and plugins are used to extend the basic functions and to create image processing functions.
Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.