imlook4d

Imlook4d is a software tool for visualization of medical images (2D), volumes (3D) and time-dependent volumes (4D). Imlook4d is written in Matlab, which means that it has to be installed into the Matlab path. Only the basic Matlab application is required, that is, the Matlab imaging toolbox is not needed.

Imlook4d started as a viewer for 4-dimensional viewer for medical PET, CT and MRI images. For more than a decade it has evolved to include tools typically not available in image viewers. The most important feature is the easy method to extend functionality, by adding a single Matlab file into a folder (resulting in it becoming an integrated menu in imlook4d).

Features

The program is developed in Matlab and thus works on all operating system platforms supporting the Matlab application (Windows, Mac OS, Linux).

Some features of imlook4d:

  • Full 4D viewer
  • PET pharmaco-kinetic modelling (9 models, both on ROIs and creating parameter images)
  • VOI analysis, using brush tool (easier than polygons), thresholded brushing, flood fill etc. Load and Save VOI definitions
  • DICOM, Nifti, Analyze, ECAT (very fast compared to Matlab routines), and reads binary, interfile and some other formats
  • Export/Import to Matlab workspace, allowing data manipulation in workspace and export back to imlook4d
  • Drop-in SCRIPTS (written in Matlab) makes it easy to add Matlab code to imlook4d menus
  • Some 70 useful scripts for Matrix and ROI processing
  • Interactive help, click on GUI elements to open detailed help window
  • Integrated with SPM (align, co-register, fit to atlas, …)
  • Integrated with ImageJ (move data back and forth between imlook4d and ImageJ). Direct export to ImageJ and import back from ImageJ is supported, thus giving access to all tools available within ImageJ
  • Requires Matlab (without additional toolboxes).
  • Later releases of Imlook4d can be updated using Update in the imlook4d HELP menu.
  • SPM and ImageJ plugin: imlook4d can also integrate with features from external software packages. This is not the basic use case. In case these features are of interest, additional software would have to be downloaded: For instance, experimental image registration using SPM (additional download) . SPM folder would also need to be included in the Matlab path.
  • Imlook4d has a built in volume-of-interest editor, with a brush tool for quick interactive ROI delineation, and via scripts, different ways of thresholding ROIs from parts of the image.  Time activity data is saved to a tab-delimited text file.
  • The principal-component (PC) based Hotelling filter is an integrated part of the program, which allows for interactive noise reduction without loss of quantitation.  A typical work flow for a dynamic data set is to turn on the filter for ROI delineation, and then there is the choice of turning it off for export of time-activity data.  Also the PC images can be used to draw ROIs on, which under some circumstances gives enhanced contrast.
  • Calculation of parametric pharmacokinetic modelling images can be performed interactively, calculated slice by slice as the user scrolls through the volume.  Reference models for Patlak, Logan and Averaged Simple Flow Model applied on 15O-water are implemented, and it is relatively easy to implement other kinetic models.  Similarly, scripts have been developed for regional Patlak and Logan models on ROI data.
Matlab graphical user interface (GUI) of imlook4d application

Reference Links

Main Website, Github Page, Github Code Repository

Download page (after optional registration)

Getting Started Guide (including installation guide and basic operations)

Complex ROI delineation

Scripting Tutorial (~70 scripts in categories such as ROI, Matrix, Header info etc.)

Reference Publications: DiVA Abstract (full text pdf), 2D Hotelling Filter Method, Averaged Simple Flow Model Method

Example of publications citing imlook4d tool: Paper 1, Paper 2, Paper 3, Paper 4

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