All the Edinburgh Imaging software tools

Anonymization of DICOM images: DICOM Confidential software tool 

• An open source JAVA DICOM de-identification toolkit
• Authors: Dr Jano van Hemert, Dr Dominic Job, & David Rodriguez

Brain imaging of normal subjects (BRAINS) software tool

• Age-specific MR atlases from young adults to the very elderly (v1.0)
• Authors: Dr DA Dickie, Dr D Job, Dr M Valdés-Hernández, Prof JM Wardlaw

Digital human brain atlases software tool

• Collection in Edinburgh Datashare
• Authors: Michael R. Jackson, Dr Maria Valdés-Hernández

Dynamic contrast enhanced magnetic resonance (DCE-MR) software tool

• Patlak modelling of subtle BBB leakage
• Authors - Dr Michael Thrippleton

Electro-encephalography (EEG) statistical analysis software tool 

• LIMO EEG toolbox: for statistical analysis of EEG data across the whole dataspace (EEGLAB compatible)
• Authors: Nicolas Chauveau, Dr Cyril Pernet, Guillaume Rousselet

Functional MR (fMRI): adaptive thresholding software tools

• MATLAB scripts
• Authors: Dr Cyril Pernet, Chris Filo Gorgolewski

Mapping T1 software tool

• Inversion-recovery spin-echo technique
• Authors - Dr Michael Thrippleton

Mapping T1 (volumetric) software tool

• DESPOT1-HIFI or variable flip angle
• Authors - Dr Michael Thrippleton

Mapping T2/T2* software tool

• Authors - Dr Michael Thrippleton

Reference segmentations software tool

• Collection Derived data from ADNI
• Authors: Leonora Fatimah Agan, Dr Maria Valdés-Hernández, Dr Cyril Pernet, Stuart Reid

Robust correlation software tools 

• The Robust Correlation Toolbox is a free collection of MATLAB functions allowing:
  • Visualization of data in univariate & bivariate space
  • Checking assumptions of normality & homoscedasticity
  • Computation of  Pearson's & Spearman's coefficients, percentage bend & skipped correlations with bootstrapped confidence intervals
• Author: Dr Cyril Pernet

Segmentation of brain tissues & lesions software tool

• A multispectral method for segmentation of brain tissues & lesions, developed for the BRIC1936 study
• Authors: Dr Maria Valdés-Hernández, Michael Jackson & Dr Dominic Job  

Segmentation of microbleeds & mineral deposits software tool

Download the Edinburgh Imaging microbleed & mineralization segmentation tool which uses Analyze 11.0 (482.92 KB PDF)

• Authors: Dr Maria Valdés-Hernández 

Segmentation of mineral deposits in MR brain volumes software tool 

• Author: Dr Andreas Glatz

Tissue irregularity map software tool 

• Authors: Dr Maria Valdés-Hernández, Taku Komura & Febrian M. Rachmadi

Vascular assessment & measurement platform for images of the retina (VAMPIRE) – analysis software

• Semi-automatic software to measure fundus images (fundus camera, SLO & Optos ultra-widefield SLO) are also available.
• For further info, please contact:

• Dr Tom MacGillivray

  Senior Research Fellow & Image Analysis Core Laboratory Manager

  • Centre for Clinical Brain Sciences
  • Clinical Research Imaging Centre
  • Wellcome Trust Clinical Research Facility

  Contact details

  • Work: +44 (0)131 242 7756
  • Email: T.J.MacGillivray@ed.ac.uk
  Web: Profile on the University of Edinburgh
  Web: Profile on Edinburgh Research Explorer
  Web: Vampire Retinal Software
  Web: Clinical Research Imaging Centre Image Analysis