Software Resources


ImageJ

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. http://imagej.net

Fiji

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. http://fiji.sc/Fiji

CT reconstruction and visualization

NRECON, CTvox

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.

X-TRACT

An image analysis and processing application with functionality targeting researchers working in imaging science and technology fields, especially in optical, electron and X-ray microscopy and astronomy. A subscription is required to get the program. http://xrsi.cmit.csiro.au/Services/AppInfo/X-TRACT.aspx

GSECARS Tomography processing software (Mark Rivers)

The links below contain useful IDL (and not only IDL) code for processing of parallel beam CT data. What I find interesting is the GRIDREC reconstruction algorithm. 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 software.

PITRE (Phase-sensitive x-ray Image processing and Tomography REconstruction) is a software developed by INFN Trieste n order to facilitate and standardize the simulation and elaboration of X-ray phase contrast images. The acronym PITRE in Italian is pronounced /'pi.tre/; the pronunciation is the same of “P3”, which is then chosen as a logo for the PITRE program. A batch processing manager for PITRE, called PITRE_BM, can execute a series of tasks ("jobs"), which is created via PITRE, without manual intervention.

H-PITRE (High-performance software for Phase-sensitive x-ray Image processing and Tomography REconstruction) is a fast tomography reconstruction program which uses the parallel computing abilities of NVIDIA GPU (Graphics Processing Unit).

RecView

A program for microtomographic reconstruction and image processing.
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.https://github.com/mizutanilab/RecView/

MCTrace

MCTrace is a program for microtomographic model building and refinement with a graphical user interface. It consists of over 50,000 lines of custom source code in C++.  https://github.com/mizutanilab/MCTrace/

 ParaView

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. www.paraview.org