Tools

The Tool suite

The purpose of the tool suite is to provide open source data processing and analysis tool to evaluate imaging data. We focus in particular on the application of neutron imaging, but the nature of the data processing is mostly more general. This makes it possible to use the tool for other modalities too, feel free to explore the application to other modalities.

The tools introduced on this page can be downloaded in the downloads section.

MuhRec

This is a CT reconstruction tool with a GUI to help the user tuning the parameters needed for a successful volume reconstruction from a set of projection data. Guides are added to supprt the user to tune the reconstruction parameters.

Features

  • Aims at reconstructing quantifiable attenuation coefficients.
  • Preprocessing: As collection of filter modules can be to reduce spots and ring artefacts.
  • Reconstruction techniques: Parallel beam filtered back projection, Feldkamp cone beam reconstruction.
  • Supports different acquisition schemes: Sequence, Golden Ratio, list file.
  • Modular processing: MuhRec is built on a modular architecture allowing to select different preprocessing and backprojection algorithms. For advanced users it is also possible to add your own algorithms to the module library.

Technical details

  • Runs in GUI as well as CLI mode. The latter is ideal for scripting of multiple data recosntruction.
  • Supports different file formats, no conversion needed. Input formats: FITS, TIFF, NEXUS. Output TIFF: 8,16bit integer, single precision floating point.
  • Runs on most computers with a 64-bit operating system (laptops included)

Planned features: Support for iterative reconstruction techniques.

KipTool

A general purpose processing tool with the main task to process 3D imaging data. Currently, the most used feature is denoising of volume data using an ROF filter in the inveres scale space framework. New features are processing series of image files (renaming, collation of multiple images into one, volume merge, generic file conversion for reverse engineering of data files).

KIPTool work with a chain of processing modules in a similar manner as the preprocessing modules in muhrec

NGI tool

nGITool is a specific tool for the reduction of phase stepping series acquired using a grating interferometer. The output of the reduction is a series of the image triplet Transmission, Differential Phase Contrast, and Dark field. The tool can flexibly be configured to handle different acquisition schemes with multiple observations e.g. a CT scan can be defined as turning first then phase step or reverse.

Also nGITool is built on a module based architecture, this makes it possible to change the estimation method that finds the parameters from the acquired phase stepping scans.